Starting phenix.real_space_refine on Fri Aug 7 17:51:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6b_71303/08_2026/9p6b_71303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6b_71303/08_2026/9p6b_71303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9p6b_71303/08_2026/9p6b_71303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6b_71303/08_2026/9p6b_71303.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9p6b_71303/08_2026/9p6b_71303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6b_71303/08_2026/9p6b_71303.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 S 136 5.16 5 Na 2 4.78 5 C 15020 2.51 5 N 3416 2.21 5 O 4152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22762 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5179 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 625} Chain breaks: 1 Chain: "B" Number of atoms: 5179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5179 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 625} Chain breaks: 1 Chain: "C" Number of atoms: 5179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5179 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 625} Chain breaks: 1 Chain: "D" Number of atoms: 5179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 642, 5179 Classifications: {'peptide': 642} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 625} Chain breaks: 1 Chain: "A" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 489 Unusual residues: {' NA': 1, '8IJ': 1, 'POV': 8, 'TRD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 540 Unusual residues: {'8IJ': 1, 'POV': 9, 'TRD': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 488 Unusual residues: {'8IJ': 1, 'POV': 8, 'TRD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "D" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 437 Unusual residues: {' NA': 1, '8IJ': 1, 'POV': 7, 'TRD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Time building chain proxies: 5.16, per 1000 atoms: 0.23 Number of scatterers: 22762 At special positions: 0 Unit cell: (133.985, 133.985, 114.935, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 36 15.00 Na 2 11.00 O 4152 8.00 N 3416 7.00 C 15020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.02 Conformation dependent library (CDL) restraints added in 848.9 milliseconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4856 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 4 sheets defined 62.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 115 through 124 removed outlier: 4.300A pdb=" N PHE A 119 " --> pdb=" O ARG A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 139 removed outlier: 3.802A pdb=" N SER A 132 " --> pdb=" O GLN A 128 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 157 through 165 removed outlier: 3.683A pdb=" N MET A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 3.559A pdb=" N ALA A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 removed outlier: 3.707A pdb=" N VAL A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 3.776A pdb=" N ILE A 208 " --> pdb=" O THR A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 224 removed outlier: 3.594A pdb=" N ASN A 224 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 258 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 299 through 320 removed outlier: 3.926A pdb=" N ALA A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 336 through 344 Processing helix chain 'A' and resid 346 through 355 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 418 through 430 Processing helix chain 'A' and resid 430 through 455 removed outlier: 3.645A pdb=" N PHE A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 498 removed outlier: 3.660A pdb=" N ARG A 474 " --> pdb=" O GLY A 470 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 475 " --> pdb=" O ASP A 471 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY A 485 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 509 removed outlier: 3.543A pdb=" N PHE A 507 " --> pdb=" O MET A 503 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 509 " --> pdb=" O THR A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 531 removed outlier: 3.672A pdb=" N LEU A 515 " --> pdb=" O TYR A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 551 removed outlier: 3.852A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.559A pdb=" N THR A 556 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY A 558 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'A' and resid 575 through 599 removed outlier: 3.635A pdb=" N VAL A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 598 " --> pdb=" O ALA A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 674 through 713 removed outlier: 3.536A pdb=" N ALA A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN A 692 " --> pdb=" O ASN A 688 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU A 693 " --> pdb=" O LYS A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 766 removed outlier: 3.550A pdb=" N GLY A 765 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 128 through 139 removed outlier: 3.803A pdb=" N SER B 132 " --> pdb=" O GLN B 128 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS B 139 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.682A pdb=" N MET B 163 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 184 removed outlier: 3.559A pdb=" N ALA B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 192 removed outlier: 3.708A pdb=" N VAL B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 212 removed outlier: 3.774A pdb=" N ILE B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 224 removed outlier: 3.595A pdb=" N ASN B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 299 through 320 removed outlier: 3.926A pdb=" N ALA B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 346 through 355 Processing helix chain 'B' and resid 360 through 364 Processing helix chain 'B' and resid 395 through 402 Processing helix chain 'B' and resid 418 through 430 Processing helix chain 'B' and resid 430 through 455 removed outlier: 3.646A pdb=" N PHE B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 498 removed outlier: 3.661A pdb=" N ARG B 474 " --> pdb=" O GLY B 470 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 475 " --> pdb=" O ASP B 471 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 509 removed outlier: 3.544A pdb=" N PHE B 507 " --> pdb=" O MET B 503 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 531 removed outlier: 3.670A pdb=" N LEU B 515 " --> pdb=" O TYR B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 551 removed outlier: 3.852A pdb=" N PHE B 543 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 558 removed outlier: 3.559A pdb=" N THR B 556 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 558 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 575 Processing helix chain 'B' and resid 575 through 599 removed outlier: 3.634A pdb=" N VAL B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 639 Processing helix chain 'B' and resid 656 through 671 Processing helix chain 'B' and resid 674 through 713 removed outlier: 3.537A pdb=" N ALA B 691 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN B 692 " --> pdb=" O ASN B 688 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU B 693 " --> pdb=" O LYS B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 766 removed outlier: 3.550A pdb=" N GLY B 765 " --> pdb=" O GLU B 762 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 124 Processing helix chain 'C' and resid 128 through 139 removed outlier: 3.803A pdb=" N SER C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS C 139 " --> pdb=" O LEU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 149 Processing helix chain 'C' and resid 157 through 165 removed outlier: 3.683A pdb=" N MET C 163 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 184 removed outlier: 3.557A pdb=" N ALA C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 192 removed outlier: 3.706A pdb=" N VAL C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 212 removed outlier: 3.776A pdb=" N ILE C 208 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 224 removed outlier: 3.595A pdb=" N ASN C 224 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 238 Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 299 through 320 removed outlier: 3.926A pdb=" N ALA C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 336 through 344 Processing helix chain 'C' and resid 346 through 355 Processing helix chain 'C' and resid 360 through 364 Processing helix chain 'C' and resid 395 through 402 Processing helix chain 'C' and resid 418 through 430 Processing helix chain 'C' and resid 430 through 455 removed outlier: 3.647A pdb=" N PHE C 437 " --> pdb=" O ARG C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 498 removed outlier: 3.661A pdb=" N ARG C 474 " --> pdb=" O GLY C 470 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL C 475 " --> pdb=" O ASP C 471 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 484 " --> pdb=" O LEU C 480 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 485 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 509 removed outlier: 3.543A pdb=" N PHE C 507 " --> pdb=" O MET C 503 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP C 509 " --> pdb=" O THR C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 531 removed outlier: 3.671A pdb=" N LEU C 515 " --> pdb=" O TYR C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 551 removed outlier: 3.852A pdb=" N PHE C 543 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 558 removed outlier: 3.559A pdb=" N THR C 556 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY C 558 " --> pdb=" O TYR C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 575 Processing helix chain 'C' and resid 575 through 599 removed outlier: 3.634A pdb=" N VAL C 583 " --> pdb=" O ARG C 579 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU C 598 " --> pdb=" O ALA C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 639 Processing helix chain 'C' and resid 656 through 671 Processing helix chain 'C' and resid 674 through 713 removed outlier: 3.537A pdb=" N ALA C 691 " --> pdb=" O VAL C 687 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN C 692 " --> pdb=" O ASN C 688 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLU C 693 " --> pdb=" O LYS C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 766 removed outlier: 3.550A pdb=" N GLY C 765 " --> pdb=" O GLU C 762 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 Processing helix chain 'D' and resid 128 through 139 removed outlier: 3.803A pdb=" N SER D 132 " --> pdb=" O GLN D 128 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 149 Processing helix chain 'D' and resid 157 through 165 removed outlier: 3.683A pdb=" N MET D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 184 removed outlier: 3.557A pdb=" N ALA D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.707A pdb=" N VAL D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 212 removed outlier: 3.774A pdb=" N ILE D 208 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 removed outlier: 3.595A pdb=" N ASN D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 238 Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 261 through 270 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 299 through 320 removed outlier: 3.927A pdb=" N ALA D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 336 through 344 Processing helix chain 'D' and resid 346 through 355 Processing helix chain 'D' and resid 360 through 364 Processing helix chain 'D' and resid 395 through 402 Processing helix chain 'D' and resid 418 through 430 Processing helix chain 'D' and resid 430 through 455 removed outlier: 3.646A pdb=" N PHE D 437 " --> pdb=" O ARG D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 498 removed outlier: 3.660A pdb=" N ARG D 474 " --> pdb=" O GLY D 470 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D 475 " --> pdb=" O ASP D 471 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY D 484 " --> pdb=" O LEU D 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY D 485 " --> pdb=" O SER D 481 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY D 492 " --> pdb=" O PHE D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 509 removed outlier: 3.544A pdb=" N PHE D 507 " --> pdb=" O MET D 503 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 531 removed outlier: 3.670A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 551 removed outlier: 3.852A pdb=" N PHE D 543 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 558 removed outlier: 3.560A pdb=" N THR D 556 " --> pdb=" O LEU D 553 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY D 558 " --> pdb=" O TYR D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 575 Processing helix chain 'D' and resid 575 through 599 removed outlier: 3.635A pdb=" N VAL D 583 " --> pdb=" O ARG D 579 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU D 598 " --> pdb=" O ALA D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 639 Processing helix chain 'D' and resid 656 through 671 Processing helix chain 'D' and resid 674 through 713 removed outlier: 3.537A pdb=" N ALA D 691 " --> pdb=" O VAL D 687 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N GLN D 692 " --> pdb=" O ASN D 688 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU D 693 " --> pdb=" O LYS D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 766 removed outlier: 3.550A pdb=" N GLY D 765 " --> pdb=" O GLU D 762 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 369 through 373 removed outlier: 6.620A pdb=" N SER A 380 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP A 738 " --> pdb=" O VAL A 729 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 369 through 373 removed outlier: 6.618A pdb=" N SER B 380 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP B 738 " --> pdb=" O VAL B 729 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 369 through 373 removed outlier: 6.620A pdb=" N SER C 380 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP C 738 " --> pdb=" O VAL C 729 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 369 through 373 removed outlier: 6.619A pdb=" N SER D 380 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ASP D 738 " --> pdb=" O VAL D 729 " (cutoff:3.500A) 1076 hydrogen bonds defined for protein. 3108 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: 3.84 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3627 1.32 - 1.45: 5880 1.45 - 1.57: 13281 1.57 - 1.70: 72 1.70 - 1.82: 224 Bond restraints: 23084 Sorted by residual: bond pdb=" O12 POV D1204 " pdb=" P POV D1204 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" O12 POV D1202 " pdb=" P POV D1202 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.96e+00 bond pdb=" O12 POV C1204 " pdb=" P POV C1204 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.92e+00 bond pdb=" O12 POV A1201 " pdb=" P POV A1201 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.88e+00 bond pdb=" O12 POV B1205 " pdb=" P POV B1205 " ideal model delta sigma weight residual 1.657 1.594 0.063 2.00e-02 2.50e+03 9.86e+00 ... (remaining 23079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 29809 2.71 - 5.42: 937 5.42 - 8.13: 78 8.13 - 10.85: 8 10.85 - 13.56: 12 Bond angle restraints: 30844 Sorted by residual: angle pdb=" CA LEU C 675 " pdb=" CB LEU C 675 " pdb=" CG LEU C 675 " ideal model delta sigma weight residual 116.30 129.86 -13.56 3.50e+00 8.16e-02 1.50e+01 angle pdb=" CA LEU A 675 " pdb=" CB LEU A 675 " pdb=" CG LEU A 675 " ideal model delta sigma weight residual 116.30 129.83 -13.53 3.50e+00 8.16e-02 1.49e+01 angle pdb=" CA LEU B 675 " pdb=" CB LEU B 675 " pdb=" CG LEU B 675 " ideal model delta sigma weight residual 116.30 129.80 -13.50 3.50e+00 8.16e-02 1.49e+01 angle pdb=" CA LEU D 675 " pdb=" CB LEU D 675 " pdb=" CG LEU D 675 " ideal model delta sigma weight residual 116.30 129.79 -13.49 3.50e+00 8.16e-02 1.49e+01 angle pdb=" CA ARG D 718 " pdb=" CB ARG D 718 " pdb=" CG ARG D 718 " ideal model delta sigma weight residual 114.10 121.63 -7.53 2.00e+00 2.50e-01 1.42e+01 ... (remaining 30839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 13701 35.74 - 71.48: 411 71.48 - 107.22: 141 107.22 - 142.97: 35 142.97 - 178.71: 20 Dihedral angle restraints: 14308 sinusoidal: 6768 harmonic: 7540 Sorted by residual: dihedral pdb=" CA SER A 777 " pdb=" C SER A 777 " pdb=" N LEU A 778 " pdb=" CA LEU A 778 " ideal model delta harmonic sigma weight residual 180.00 -133.92 -46.08 0 5.00e+00 4.00e-02 8.49e+01 dihedral pdb=" CA SER D 777 " pdb=" C SER D 777 " pdb=" N LEU D 778 " pdb=" CA LEU D 778 " ideal model delta harmonic sigma weight residual -180.00 -133.95 -46.05 0 5.00e+00 4.00e-02 8.48e+01 dihedral pdb=" CA SER C 777 " pdb=" C SER C 777 " pdb=" N LEU C 778 " pdb=" CA LEU C 778 " ideal model delta harmonic sigma weight residual -180.00 -133.96 -46.04 0 5.00e+00 4.00e-02 8.48e+01 ... (remaining 14305 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2657 0.061 - 0.123: 562 0.123 - 0.184: 60 0.184 - 0.246: 22 0.246 - 0.307: 7 Chirality restraints: 3308 Sorted by residual: chirality pdb=" C2 POV D1207 " pdb=" C1 POV D1207 " pdb=" C3 POV D1207 " pdb=" O21 POV D1207 " both_signs ideal model delta sigma weight residual False 2.43 2.12 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C2 POV C1208 " pdb=" C1 POV C1208 " pdb=" C3 POV C1208 " pdb=" O21 POV C1208 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C2 POV A1206 " pdb=" C1 POV A1206 " pdb=" C3 POV A1206 " pdb=" O21 POV A1206 " both_signs ideal model delta sigma weight residual False 2.43 2.13 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3305 not shown) Planarity restraints: 3676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 774 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.02e+00 pdb=" C LEU A 774 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU A 774 " 0.013 2.00e-02 2.50e+03 pdb=" N SER A 775 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 774 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C LEU D 774 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU D 774 " 0.013 2.00e-02 2.50e+03 pdb=" N SER D 775 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 774 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEU C 774 " 0.034 2.00e-02 2.50e+03 pdb=" O LEU C 774 " -0.013 2.00e-02 2.50e+03 pdb=" N SER C 775 " -0.012 2.00e-02 2.50e+03 ... (remaining 3673 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 321 2.54 - 3.13: 18236 3.13 - 3.72: 35348 3.72 - 4.31: 55944 4.31 - 4.90: 88753 Nonbonded interactions: 198602 Sorted by model distance: nonbonded pdb=" O GLY A 765 " pdb=" OH TYR B 200 " model vdw 1.949 3.040 nonbonded pdb=" O GLY C 765 " pdb=" OH TYR D 200 " model vdw 1.975 3.040 nonbonded pdb=" OE1 GLU B 637 " pdb=" O HOH B1301 " model vdw 2.039 3.040 nonbonded pdb=" OE1 GLU C 637 " pdb=" O HOH C1301 " model vdw 2.040 3.040 nonbonded pdb=" OE1 GLU A 637 " pdb=" O HOH A1301 " model vdw 2.041 3.040 ... (remaining 198597 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 'A' and (resid 115 through 1201 or resid 1208 through 1209)) selection = (chain 'B' and (resid 115 through 1201 or resid 1208 through 1209)) selection = (chain 'C' and (resid 115 through 1201 or resid 1208 through 1209)) selection = (chain 'D' and (resid 115 through 1201 or resid 1208 through 1209)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.780 Find NCS groups from input model: 0.600 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:8.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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 : 0.009 0.079 23084 Z= 0.403 Angle : 1.099 13.557 30844 Z= 0.566 Chirality : 0.054 0.307 3308 Planarity : 0.004 0.033 3676 Dihedral : 20.711 178.707 9452 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.89 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.56 (0.13), residues: 2552 helix: -3.04 (0.10), residues: 1400 sheet: -2.00 (0.45), residues: 112 loop : -2.93 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 368 TYR 0.020 0.003 TYR D 537 PHE 0.026 0.003 PHE C 305 TRP 0.023 0.004 TRP C 698 HIS 0.015 0.003 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00909 / 0.40 (23084) covalent geometry : angle 1.09898 / 0.57 (30844) hydrogen bonds : bond 0.26624 / 17.48 ( 1076) hydrogen bonds : angle 9.71227 / 6.73 ( 3108) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LYS cc_start: 0.7506 (tptt) cc_final: 0.7302 (tptt) REVERT: A 363 CYS cc_start: 0.7600 (m) cc_final: 0.7201 (m) REVERT: A 379 HIS cc_start: 0.7509 (p90) cc_final: 0.6814 (p-80) REVERT: A 570 GLU cc_start: 0.8206 (tt0) cc_final: 0.8000 (tt0) REVERT: A 711 LYS cc_start: 0.7770 (mtpp) cc_final: 0.7239 (mtpt) REVERT: A 747 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7057 (mt-10) REVERT: A 749 ASN cc_start: 0.7973 (t160) cc_final: 0.7666 (t0) REVERT: B 327 GLU cc_start: 0.6026 (mt-10) cc_final: 0.5790 (tm-30) REVERT: B 482 VAL cc_start: 0.8418 (t) cc_final: 0.8145 (m) REVERT: B 570 GLU cc_start: 0.8098 (tt0) cc_final: 0.7472 (tm-30) REVERT: B 736 LYS cc_start: 0.7654 (mttm) cc_final: 0.7355 (mmtm) REVERT: B 747 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6728 (mt-10) REVERT: B 749 ASN cc_start: 0.7462 (t160) cc_final: 0.6612 (m110) REVERT: C 161 LYS cc_start: 0.7643 (tptt) cc_final: 0.7334 (tptt) REVERT: C 247 TYR cc_start: 0.6905 (t80) cc_final: 0.6502 (t80) REVERT: C 363 CYS cc_start: 0.7313 (m) cc_final: 0.7003 (m) REVERT: C 379 HIS cc_start: 0.7907 (p90) cc_final: 0.7278 (p90) REVERT: C 398 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6869 (mt-10) REVERT: C 570 GLU cc_start: 0.8161 (tt0) cc_final: 0.7653 (tm-30) REVERT: C 711 LYS cc_start: 0.7803 (mtpp) cc_final: 0.7388 (mtpt) REVERT: C 747 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7123 (mt-10) REVERT: C 749 ASN cc_start: 0.8024 (t160) cc_final: 0.7664 (t0) REVERT: D 352 TYR cc_start: 0.6232 (t80) cc_final: 0.5278 (t80) REVERT: D 370 PHE cc_start: 0.7966 (m-80) cc_final: 0.7705 (m-80) REVERT: D 398 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6688 (mm-30) REVERT: D 570 GLU cc_start: 0.7970 (tt0) cc_final: 0.7421 (tm-30) REVERT: D 642 THR cc_start: 0.6013 (t) cc_final: 0.5599 (t) REVERT: D 717 MET cc_start: 0.4388 (tpt) cc_final: 0.4076 (mmm) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.5249 time to fit residues: 279.8440 Evaluate side-chains 279 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.0370 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.0570 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 71 optimal weight: 8.9990 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 ASN A 298 ASN A 379 HIS A 438 ASN A 749 ASN B 165 ASN B 203 GLN B 261 GLN B 298 ASN ** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN B 749 ASN B 766 ASN C 165 ASN C 203 GLN C 229 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 379 HIS C 438 ASN C 749 ASN D 165 ASN D 214 ASN D 261 GLN D 298 ASN D 365 HIS D 379 HIS D 438 ASN D 653 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4746 r_free = 0.4746 target = 0.259842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.214814 restraints weight = 22134.876| |-----------------------------------------------------------------------------| r_work (start): 0.4335 rms_B_bonded: 1.44 r_work: 0.4038 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23084 Z= 0.151 Angle : 0.700 7.518 30844 Z= 0.356 Chirality : 0.042 0.181 3308 Planarity : 0.005 0.040 3676 Dihedral : 24.319 165.825 4528 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.60 % Favored : 89.93 % Rotamer: Outliers : 2.20 % Allowed : 9.86 % Favored : 87.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.47 (0.15), residues: 2552 helix: -1.00 (0.12), residues: 1500 sheet: -1.16 (0.60), residues: 84 loop : -2.61 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 772 TYR 0.016 0.002 TYR A 352 PHE 0.014 0.002 PHE D 473 TRP 0.028 0.002 TRP D 698 HIS 0.004 0.001 HIS B 365 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (23084) covalent geometry : angle 0.69994 / 0.36 (30844) hydrogen bonds : bond 0.04199 / 2.75 ( 1076) hydrogen bonds : angle 4.66146 / 3.22 ( 3108) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 336 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 363 CYS cc_start: 0.7742 (m) cc_final: 0.7509 (m) REVERT: A 379 HIS cc_start: 0.7717 (p-80) cc_final: 0.7281 (p-80) REVERT: A 398 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7769 (tm-30) REVERT: A 503 MET cc_start: 0.6302 (OUTLIER) cc_final: 0.5793 (tmm) REVERT: B 208 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (mm) REVERT: B 363 CYS cc_start: 0.7519 (m) cc_final: 0.7202 (m) REVERT: B 398 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7718 (tm-30) REVERT: B 570 GLU cc_start: 0.8728 (tt0) cc_final: 0.8320 (tt0) REVERT: B 749 ASN cc_start: 0.7562 (t0) cc_final: 0.6870 (m110) REVERT: C 215 MET cc_start: 0.6597 (tpt) cc_final: 0.6329 (tpp) REVERT: C 247 TYR cc_start: 0.7620 (t80) cc_final: 0.7026 (t80) REVERT: C 379 HIS cc_start: 0.7945 (p-80) cc_final: 0.7727 (p90) REVERT: C 398 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7797 (tm-30) REVERT: C 503 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5424 (tmm) REVERT: C 570 GLU cc_start: 0.8745 (tt0) cc_final: 0.8429 (tt0) REVERT: D 286 ASN cc_start: 0.7623 (m-40) cc_final: 0.7051 (m-40) REVERT: D 363 CYS cc_start: 0.7071 (m) cc_final: 0.6769 (m) REVERT: D 375 TYR cc_start: 0.8289 (t80) cc_final: 0.8001 (t80) REVERT: D 379 HIS cc_start: 0.7627 (p-80) cc_final: 0.7426 (p-80) REVERT: D 398 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7681 (tm-30) REVERT: D 570 GLU cc_start: 0.8661 (tt0) cc_final: 0.8402 (tt0) REVERT: D 692 GLN cc_start: 0.7344 (mm-40) cc_final: 0.7144 (tp-100) REVERT: D 717 MET cc_start: 0.4775 (tpt) cc_final: 0.4376 (ptm) outliers start: 50 outliers final: 7 residues processed: 369 average time/residue: 0.5176 time to fit residues: 222.2243 Evaluate side-chains 282 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 272 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 112 optimal weight: 0.0470 chunk 187 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 91 optimal weight: 0.0020 chunk 212 optimal weight: 0.0670 chunk 110 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.0228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 203 GLN B 261 GLN B 365 HIS C 261 GLN C 365 HIS D 203 GLN D 261 GLN D 365 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.254586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.210437 restraints weight = 22381.609| |-----------------------------------------------------------------------------| r_work (start): 0.4296 rms_B_bonded: 1.87 r_work: 0.3914 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 23084 Z= 0.144 Angle : 0.608 6.778 30844 Z= 0.312 Chirality : 0.040 0.166 3308 Planarity : 0.004 0.038 3676 Dihedral : 22.906 164.822 4528 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.58 % Favored : 90.95 % Rotamer: Outliers : 2.46 % Allowed : 12.46 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2552 helix: 0.10 (0.13), residues: 1504 sheet: -0.57 (0.63), residues: 84 loop : -2.14 (0.20), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 744 TYR 0.016 0.002 TYR D 352 PHE 0.014 0.001 PHE D 522 TRP 0.016 0.001 TRP C 698 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (23084) covalent geometry : angle 0.60807 / 0.31 (30844) hydrogen bonds : bond 0.04075 / 2.67 ( 1076) hydrogen bonds : angle 4.28025 / 2.95 ( 3108) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 279 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8276 (mtm) cc_final: 0.7973 (mtp) REVERT: A 363 CYS cc_start: 0.7875 (m) cc_final: 0.7675 (m) REVERT: A 692 GLN cc_start: 0.7566 (tp40) cc_final: 0.7343 (mm-40) REVERT: A 718 ARG cc_start: 0.3198 (OUTLIER) cc_final: 0.2938 (ppt170) REVERT: B 211 GLU cc_start: 0.6558 (tm-30) cc_final: 0.6318 (tm-30) REVERT: B 363 CYS cc_start: 0.7642 (m) cc_final: 0.7385 (m) REVERT: B 398 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7872 (tm-30) REVERT: B 509 ASP cc_start: 0.7060 (p0) cc_final: 0.6560 (p0) REVERT: B 714 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.6054 (mp) REVERT: B 717 MET cc_start: 0.4248 (mmm) cc_final: 0.1627 (ptm) REVERT: C 503 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5496 (tmm) REVERT: C 652 GLU cc_start: 0.7934 (mp0) cc_final: 0.7647 (mm-30) REVERT: D 335 MET cc_start: 0.7833 (mmt) cc_final: 0.7604 (mmt) REVERT: D 363 CYS cc_start: 0.7274 (m) cc_final: 0.7019 (m) REVERT: D 372 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: D 379 HIS cc_start: 0.7772 (p-80) cc_final: 0.7539 (p-80) REVERT: D 398 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7810 (tm-30) REVERT: D 509 ASP cc_start: 0.7215 (p0) cc_final: 0.6895 (p0) REVERT: D 717 MET cc_start: 0.4873 (tpt) cc_final: 0.4164 (pp-130) outliers start: 56 outliers final: 13 residues processed: 313 average time/residue: 0.5680 time to fit residues: 205.6230 Evaluate side-chains 267 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 250 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 372 GLU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 746 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 104 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 241 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 233 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN B 365 HIS B 692 GLN B 766 ASN C 261 GLN C 692 GLN D 261 GLN D 365 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.249129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.203669 restraints weight = 22062.394| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 1.76 r_work: 0.3839 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23084 Z= 0.158 Angle : 0.613 7.833 30844 Z= 0.314 Chirality : 0.041 0.214 3308 Planarity : 0.004 0.042 3676 Dihedral : 22.598 166.155 4528 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 8.42 % Favored : 91.14 % Rotamer: Outliers : 2.38 % Allowed : 13.86 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2552 helix: 0.57 (0.13), residues: 1500 sheet: -0.56 (0.61), residues: 84 loop : -1.85 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 364 TYR 0.013 0.002 TYR A 584 PHE 0.017 0.002 PHE A 439 TRP 0.015 0.002 TRP D 698 HIS 0.008 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (23084) covalent geometry : angle 0.61253 / 0.31 (30844) hydrogen bonds : bond 0.03861 / 2.55 ( 1076) hydrogen bonds : angle 4.19172 / 2.89 ( 3108) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 MET cc_start: 0.5390 (OUTLIER) cc_final: 0.4943 (mtm) REVERT: A 315 MET cc_start: 0.8220 (mtm) cc_final: 0.7953 (mtp) REVERT: A 363 CYS cc_start: 0.7874 (m) cc_final: 0.7645 (m) REVERT: A 503 MET cc_start: 0.6431 (OUTLIER) cc_final: 0.5871 (tmm) REVERT: A 718 ARG cc_start: 0.3194 (OUTLIER) cc_final: 0.2658 (ppt170) REVERT: B 363 CYS cc_start: 0.7734 (m) cc_final: 0.7482 (m) REVERT: B 398 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7987 (tm-30) REVERT: B 410 ARG cc_start: 0.7530 (ttp80) cc_final: 0.7184 (ttt180) REVERT: B 466 MET cc_start: 0.6799 (mpp) cc_final: 0.6378 (mtm) REVERT: B 509 ASP cc_start: 0.7223 (p0) cc_final: 0.6704 (p0) REVERT: B 714 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6143 (mp) REVERT: C 315 MET cc_start: 0.8201 (mtm) cc_final: 0.7888 (mtp) REVERT: C 466 MET cc_start: 0.6810 (mpp) cc_final: 0.6394 (mtm) REVERT: C 503 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5770 (tmm) REVERT: C 652 GLU cc_start: 0.8044 (mp0) cc_final: 0.7786 (mm-30) REVERT: D 214 ASN cc_start: 0.5529 (t0) cc_final: 0.5286 (t0) REVERT: D 363 CYS cc_start: 0.7645 (m) cc_final: 0.7402 (m) REVERT: D 398 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7935 (tm-30) REVERT: D 509 ASP cc_start: 0.7323 (p0) cc_final: 0.7015 (p0) REVERT: D 717 MET cc_start: 0.4646 (tpt) cc_final: 0.3918 (pp-130) REVERT: D 749 ASN cc_start: 0.7804 (t0) cc_final: 0.7512 (t0) REVERT: D 762 GLU cc_start: 0.6210 (pp20) cc_final: 0.5805 (pp20) outliers start: 54 outliers final: 18 residues processed: 293 average time/residue: 0.5808 time to fit residues: 195.4349 Evaluate side-chains 275 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 MET Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 74 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 224 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 193 optimal weight: 30.0000 chunk 78 optimal weight: 8.9990 chunk 35 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 183 GLN B 261 GLN B 692 GLN C 261 GLN D 183 GLN D 261 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.246211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.201194 restraints weight = 21768.765| |-----------------------------------------------------------------------------| r_work (start): 0.4232 rms_B_bonded: 1.75 r_work: 0.3810 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 23084 Z= 0.291 Angle : 0.758 9.889 30844 Z= 0.376 Chirality : 0.048 0.225 3308 Planarity : 0.005 0.040 3676 Dihedral : 23.339 165.121 4528 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.79 % Allowed : 13.56 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 2552 helix: 0.16 (0.13), residues: 1528 sheet: -0.96 (0.47), residues: 120 loop : -1.82 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 356 TYR 0.023 0.003 TYR A 584 PHE 0.023 0.003 PHE B 522 TRP 0.018 0.002 TRP D 698 HIS 0.006 0.002 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 (23084) covalent geometry : angle 0.75785 / 0.38 (30844) hydrogen bonds : bond 0.04735 / 3.13 ( 1076) hydrogen bonds : angle 4.56298 / 3.15 ( 3108) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 274 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8351 (mtm) cc_final: 0.8097 (mtp) REVERT: A 466 MET cc_start: 0.6965 (mpp) cc_final: 0.6571 (mtm) REVERT: A 491 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.7120 (mmt90) REVERT: A 503 MET cc_start: 0.6449 (OUTLIER) cc_final: 0.5888 (tmm) REVERT: A 718 ARG cc_start: 0.3416 (OUTLIER) cc_final: 0.2478 (ppt170) REVERT: B 363 CYS cc_start: 0.8040 (m) cc_final: 0.7761 (m) REVERT: B 466 MET cc_start: 0.6775 (mpp) cc_final: 0.6468 (mtm) REVERT: B 509 ASP cc_start: 0.7380 (p0) cc_final: 0.7029 (p0) REVERT: B 717 MET cc_start: 0.4231 (mmm) cc_final: 0.2214 (pp-130) REVERT: B 744 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8071 (ttm110) REVERT: B 747 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7943 (mt-10) REVERT: C 315 MET cc_start: 0.8342 (mtm) cc_final: 0.8060 (mtp) REVERT: C 410 ARG cc_start: 0.7586 (ttp80) cc_final: 0.7386 (ttt180) REVERT: C 466 MET cc_start: 0.6758 (mpp) cc_final: 0.6478 (mtm) REVERT: C 503 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.5873 (tmm) REVERT: C 652 GLU cc_start: 0.8032 (mp0) cc_final: 0.7697 (mm-30) REVERT: C 717 MET cc_start: 0.4102 (mmm) cc_final: 0.2139 (pp-130) REVERT: C 766 ASN cc_start: 0.6605 (t0) cc_final: 0.6053 (t0) REVERT: D 363 CYS cc_start: 0.7933 (m) cc_final: 0.7687 (m) REVERT: D 509 ASP cc_start: 0.7395 (p0) cc_final: 0.7102 (p0) REVERT: D 711 LYS cc_start: 0.8227 (mmmt) cc_final: 0.7837 (mtmt) REVERT: D 717 MET cc_start: 0.4780 (tpt) cc_final: 0.3985 (pp-130) REVERT: D 749 ASN cc_start: 0.8069 (t0) cc_final: 0.7653 (t0) REVERT: D 774 LEU cc_start: 0.3259 (OUTLIER) cc_final: 0.2619 (pt) outliers start: 86 outliers final: 25 residues processed: 332 average time/residue: 0.5321 time to fit residues: 205.1540 Evaluate side-chains 283 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 774 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 213 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 128 optimal weight: 7.9990 chunk 5 optimal weight: 30.0000 chunk 182 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 57 optimal weight: 0.0770 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS A 692 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN C 224 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.246911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.202464 restraints weight = 21953.982| |-----------------------------------------------------------------------------| r_work (start): 0.4241 rms_B_bonded: 1.76 r_work: 0.3838 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 23084 Z= 0.237 Angle : 0.677 7.936 30844 Z= 0.339 Chirality : 0.044 0.260 3308 Planarity : 0.004 0.035 3676 Dihedral : 22.825 167.219 4528 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 3.26 % Allowed : 15.36 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.17), residues: 2552 helix: 0.37 (0.13), residues: 1528 sheet: -0.62 (0.54), residues: 96 loop : -1.81 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 499 TYR 0.018 0.002 TYR A 584 PHE 0.017 0.002 PHE D 639 TRP 0.018 0.002 TRP A 698 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.24 (23084) covalent geometry : angle 0.67705 / 0.34 (30844) hydrogen bonds : bond 0.04273 / 2.83 ( 1076) hydrogen bonds : angle 4.37396 / 3.02 ( 3108) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 262 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8293 (mtm) cc_final: 0.8034 (mtp) REVERT: A 491 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.7095 (mmt90) REVERT: A 503 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.5949 (tmm) REVERT: A 718 ARG cc_start: 0.3325 (OUTLIER) cc_final: 0.2177 (ppt170) REVERT: B 214 ASN cc_start: 0.6415 (t0) cc_final: 0.6137 (t0) REVERT: B 315 MET cc_start: 0.8120 (mtp) cc_final: 0.7906 (mtp) REVERT: B 363 CYS cc_start: 0.7983 (m) cc_final: 0.7686 (m) REVERT: B 372 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: B 398 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: B 466 MET cc_start: 0.6787 (mpp) cc_final: 0.6513 (mtm) REVERT: B 509 ASP cc_start: 0.7348 (p0) cc_final: 0.6970 (p0) REVERT: B 717 MET cc_start: 0.4214 (mmm) cc_final: 0.2079 (pp-130) REVERT: C 315 MET cc_start: 0.8260 (mtm) cc_final: 0.7993 (mtp) REVERT: C 466 MET cc_start: 0.6745 (mpp) cc_final: 0.6501 (mtm) REVERT: C 503 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.5966 (tmm) REVERT: C 717 MET cc_start: 0.4054 (mmm) cc_final: 0.2039 (pp-130) REVERT: C 718 ARG cc_start: 0.2578 (OUTLIER) cc_final: 0.0696 (mtm-85) REVERT: C 747 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7905 (mt-10) REVERT: C 766 ASN cc_start: 0.6691 (t0) cc_final: 0.6193 (t0) REVERT: D 201 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7453 (ttpp) REVERT: D 214 ASN cc_start: 0.6104 (t0) cc_final: 0.5802 (t0) REVERT: D 363 CYS cc_start: 0.7812 (m) cc_final: 0.7555 (m) REVERT: D 509 ASP cc_start: 0.7355 (p0) cc_final: 0.7023 (p0) REVERT: D 692 GLN cc_start: 0.7580 (tp-100) cc_final: 0.7344 (tp-100) REVERT: D 711 LYS cc_start: 0.8222 (mmmt) cc_final: 0.7896 (mmtp) REVERT: D 717 MET cc_start: 0.4795 (tpt) cc_final: 0.3974 (pp-130) REVERT: D 749 ASN cc_start: 0.8100 (t0) cc_final: 0.7654 (t0) outliers start: 74 outliers final: 32 residues processed: 305 average time/residue: 0.6065 time to fit residues: 213.7510 Evaluate side-chains 290 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 357 GLU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain D residue 201 LYS Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 668 VAL Chi-restraints excluded: chain D residue 746 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 187 optimal weight: 8.9990 chunk 40 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 204 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN B 224 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.234125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183697 restraints weight = 22138.650| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.47 r_work: 0.3619 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23084 Z= 0.131 Angle : 0.572 8.014 30844 Z= 0.294 Chirality : 0.039 0.287 3308 Planarity : 0.003 0.032 3676 Dihedral : 21.721 169.396 4528 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 2.64 % Allowed : 16.64 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.17), residues: 2552 helix: 1.03 (0.13), residues: 1496 sheet: -0.60 (0.54), residues: 96 loop : -1.54 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.013 0.001 TYR D 352 PHE 0.012 0.001 PHE D 639 TRP 0.018 0.002 TRP A 698 HIS 0.005 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (23084) covalent geometry : angle 0.57224 / 0.29 (30844) hydrogen bonds : bond 0.03576 / 2.36 ( 1076) hydrogen bonds : angle 4.05887 / 2.81 ( 3108) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6635 (tm-30) cc_final: 0.6424 (tm-30) REVERT: A 315 MET cc_start: 0.8012 (mtm) cc_final: 0.7757 (mtp) REVERT: A 491 ARG cc_start: 0.7026 (mmm-85) cc_final: 0.6617 (mmt90) REVERT: A 503 MET cc_start: 0.6491 (OUTLIER) cc_final: 0.5947 (tmm) REVERT: A 718 ARG cc_start: 0.3268 (OUTLIER) cc_final: 0.1818 (ptt90) REVERT: A 747 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7817 (mt-10) REVERT: A 766 ASN cc_start: 0.6719 (t0) cc_final: 0.6099 (t0) REVERT: B 184 THR cc_start: 0.5591 (OUTLIER) cc_final: 0.5227 (t) REVERT: B 214 ASN cc_start: 0.5980 (t0) cc_final: 0.5691 (t0) REVERT: B 315 MET cc_start: 0.7873 (mtp) cc_final: 0.7637 (mtp) REVERT: B 363 CYS cc_start: 0.7720 (m) cc_final: 0.7426 (m) REVERT: B 372 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7306 (tt0) REVERT: B 398 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7492 (tm-30) REVERT: B 509 ASP cc_start: 0.7028 (p0) cc_final: 0.6771 (p0) REVERT: B 717 MET cc_start: 0.4179 (mmm) cc_final: 0.2162 (pp-130) REVERT: B 749 ASN cc_start: 0.8007 (t0) cc_final: 0.7362 (t0) REVERT: C 211 GLU cc_start: 0.6794 (tm-30) cc_final: 0.5701 (tt0) REVERT: C 315 MET cc_start: 0.8067 (mtm) cc_final: 0.7803 (mtp) REVERT: C 503 MET cc_start: 0.6495 (OUTLIER) cc_final: 0.5950 (tmm) REVERT: C 717 MET cc_start: 0.4074 (mmm) cc_final: 0.2330 (pp-130) REVERT: C 718 ARG cc_start: 0.2336 (OUTLIER) cc_final: 0.0615 (mtm-85) REVERT: C 747 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7838 (mp0) REVERT: C 766 ASN cc_start: 0.6651 (t0) cc_final: 0.6100 (t0) REVERT: D 184 THR cc_start: 0.5401 (OUTLIER) cc_final: 0.5089 (t) REVERT: D 214 ASN cc_start: 0.5806 (t0) cc_final: 0.5550 (t0) REVERT: D 359 GLN cc_start: 0.7950 (mm-40) cc_final: 0.7688 (mp10) REVERT: D 363 CYS cc_start: 0.7677 (m) cc_final: 0.7412 (m) REVERT: D 509 ASP cc_start: 0.7039 (p0) cc_final: 0.6763 (p0) REVERT: D 692 GLN cc_start: 0.7426 (tp40) cc_final: 0.7174 (tp-100) REVERT: D 711 LYS cc_start: 0.8027 (mmmt) cc_final: 0.7624 (mtmt) REVERT: D 717 MET cc_start: 0.4736 (tpt) cc_final: 0.4007 (pp-130) REVERT: D 749 ASN cc_start: 0.7942 (t0) cc_final: 0.7444 (t0) outliers start: 60 outliers final: 19 residues processed: 310 average time/residue: 0.5740 time to fit residues: 206.8030 Evaluate side-chains 286 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 260 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 717 MET Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain C residue 746 ASP Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 668 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 93 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 175 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 133 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN D 224 ASN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.233526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.182242 restraints weight = 21871.749| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.36 r_work: 0.3618 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23084 Z= 0.138 Angle : 0.571 7.003 30844 Z= 0.294 Chirality : 0.040 0.312 3308 Planarity : 0.003 0.033 3676 Dihedral : 21.233 173.210 4528 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 2.51 % Allowed : 17.17 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2552 helix: 1.16 (0.13), residues: 1500 sheet: -0.50 (0.54), residues: 96 loop : -1.52 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.013 0.001 TYR A 584 PHE 0.011 0.001 PHE D 639 TRP 0.017 0.001 TRP A 698 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (23084) covalent geometry : angle 0.57083 / 0.29 (30844) hydrogen bonds : bond 0.03662 / 2.42 ( 1076) hydrogen bonds : angle 4.04260 / 2.80 ( 3108) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 268 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 315 MET cc_start: 0.8047 (mtm) cc_final: 0.7810 (mtp) REVERT: A 402 TYR cc_start: 0.8544 (m-10) cc_final: 0.8259 (m-10) REVERT: A 466 MET cc_start: 0.7029 (mpp) cc_final: 0.6551 (mtm) REVERT: A 503 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5898 (tmm) REVERT: A 711 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7551 (mtmt) REVERT: A 717 MET cc_start: 0.3054 (mmm) cc_final: 0.1406 (ttm) REVERT: A 718 ARG cc_start: 0.3207 (OUTLIER) cc_final: 0.1768 (ptt90) REVERT: A 747 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7890 (mp0) REVERT: A 749 ASN cc_start: 0.7866 (t0) cc_final: 0.7296 (t0) REVERT: A 766 ASN cc_start: 0.6762 (t0) cc_final: 0.6136 (t0) REVERT: B 184 THR cc_start: 0.5524 (OUTLIER) cc_final: 0.5154 (t) REVERT: B 214 ASN cc_start: 0.6011 (t0) cc_final: 0.5733 (t0) REVERT: B 363 CYS cc_start: 0.7732 (m) cc_final: 0.7455 (m) REVERT: B 372 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: B 398 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7546 (tm-30) REVERT: B 466 MET cc_start: 0.7010 (mpp) cc_final: 0.6480 (mtm) REVERT: B 496 PHE cc_start: 0.6935 (t80) cc_final: 0.6258 (m-80) REVERT: B 509 ASP cc_start: 0.7074 (p0) cc_final: 0.6844 (p0) REVERT: B 717 MET cc_start: 0.4213 (mmm) cc_final: 0.2372 (pp-130) REVERT: C 211 GLU cc_start: 0.6733 (tm-30) cc_final: 0.5626 (tt0) REVERT: C 315 MET cc_start: 0.8073 (mtm) cc_final: 0.7833 (mtp) REVERT: C 503 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5852 (tmm) REVERT: C 717 MET cc_start: 0.3640 (mmm) cc_final: 0.2172 (pp-130) REVERT: C 747 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7793 (mp0) REVERT: C 766 ASN cc_start: 0.6647 (t0) cc_final: 0.6138 (t0) REVERT: D 184 THR cc_start: 0.5332 (OUTLIER) cc_final: 0.5007 (t) REVERT: D 214 ASN cc_start: 0.5893 (t0) cc_final: 0.5628 (t0) REVERT: D 359 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7738 (mp10) REVERT: D 363 CYS cc_start: 0.7692 (m) cc_final: 0.7417 (m) REVERT: D 496 PHE cc_start: 0.6957 (t80) cc_final: 0.6288 (m-80) REVERT: D 711 LYS cc_start: 0.8079 (mmmt) cc_final: 0.7697 (mtmt) REVERT: D 717 MET cc_start: 0.4741 (tpt) cc_final: 0.3915 (pp-130) REVERT: D 749 ASN cc_start: 0.7946 (t0) cc_final: 0.7469 (t0) outliers start: 57 outliers final: 29 residues processed: 303 average time/residue: 0.5414 time to fit residues: 192.9120 Evaluate side-chains 298 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 263 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 471 ASP Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 668 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 180 optimal weight: 0.7980 chunk 150 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 247 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 217 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.234572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.184207 restraints weight = 22002.753| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.34 r_work: 0.3645 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23084 Z= 0.131 Angle : 0.556 6.736 30844 Z= 0.288 Chirality : 0.040 0.315 3308 Planarity : 0.003 0.032 3676 Dihedral : 20.626 178.280 4528 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.68 % Allowed : 17.39 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.17), residues: 2552 helix: 1.29 (0.13), residues: 1500 sheet: -0.46 (0.54), residues: 96 loop : -1.45 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.019 0.001 TYR D 445 PHE 0.011 0.001 PHE D 639 TRP 0.016 0.001 TRP A 698 HIS 0.007 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (23084) covalent geometry : angle 0.55641 / 0.29 (30844) hydrogen bonds : bond 0.03543 / 2.34 ( 1076) hydrogen bonds : angle 3.98288 / 2.76 ( 3108) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 275 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6783 (tm-30) cc_final: 0.5704 (tt0) REVERT: A 315 MET cc_start: 0.8030 (mtm) cc_final: 0.7806 (mtp) REVERT: A 402 TYR cc_start: 0.8516 (m-10) cc_final: 0.8281 (m-10) REVERT: A 466 MET cc_start: 0.7035 (mpp) cc_final: 0.6563 (mtm) REVERT: A 503 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5835 (tmm) REVERT: A 711 LYS cc_start: 0.8110 (mmtp) cc_final: 0.7593 (mtmt) REVERT: A 717 MET cc_start: 0.2909 (mmm) cc_final: 0.1537 (ttp) REVERT: A 718 ARG cc_start: 0.3065 (OUTLIER) cc_final: 0.0859 (tmm-80) REVERT: B 184 THR cc_start: 0.5406 (OUTLIER) cc_final: 0.4989 (t) REVERT: B 214 ASN cc_start: 0.6006 (t0) cc_final: 0.5722 (t0) REVERT: B 363 CYS cc_start: 0.7752 (m) cc_final: 0.7468 (m) REVERT: B 398 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7566 (tm-30) REVERT: B 466 MET cc_start: 0.7013 (mpp) cc_final: 0.6546 (mtm) REVERT: B 496 PHE cc_start: 0.6849 (t80) cc_final: 0.6118 (m-80) REVERT: B 509 ASP cc_start: 0.6979 (p0) cc_final: 0.6764 (p0) REVERT: B 717 MET cc_start: 0.3797 (mmm) cc_final: 0.2418 (pp-130) REVERT: C 211 GLU cc_start: 0.6746 (tm-30) cc_final: 0.5633 (tt0) REVERT: C 315 MET cc_start: 0.8088 (mtm) cc_final: 0.7867 (mtp) REVERT: C 402 TYR cc_start: 0.8578 (m-10) cc_final: 0.8297 (m-10) REVERT: C 471 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7789 (m-30) REVERT: C 503 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5900 (tmm) REVERT: C 711 LYS cc_start: 0.8113 (mmtt) cc_final: 0.7512 (mtmt) REVERT: C 717 MET cc_start: 0.3435 (mmm) cc_final: 0.2584 (pp-130) REVERT: C 749 ASN cc_start: 0.7989 (t0) cc_final: 0.7409 (t0) REVERT: C 766 ASN cc_start: 0.6740 (t0) cc_final: 0.6355 (t0) REVERT: D 184 THR cc_start: 0.5351 (OUTLIER) cc_final: 0.4981 (t) REVERT: D 214 ASN cc_start: 0.5850 (t0) cc_final: 0.5550 (t0) REVERT: D 359 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7725 (mp10) REVERT: D 363 CYS cc_start: 0.7728 (m) cc_final: 0.7469 (m) REVERT: D 496 PHE cc_start: 0.6905 (t80) cc_final: 0.6298 (m-80) REVERT: D 711 LYS cc_start: 0.8068 (mmmt) cc_final: 0.7701 (mtmt) REVERT: D 717 MET cc_start: 0.4781 (tpt) cc_final: 0.4005 (pp-130) REVERT: D 749 ASN cc_start: 0.7929 (t0) cc_final: 0.7497 (t0) outliers start: 61 outliers final: 29 residues processed: 308 average time/residue: 0.4701 time to fit residues: 171.7097 Evaluate side-chains 293 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 258 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 217 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 471 ASP Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 668 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 62 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 151 optimal weight: 0.6980 chunk 159 optimal weight: 0.2980 chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.235386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184326 restraints weight = 21958.933| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.38 r_work: 0.3652 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23084 Z= 0.117 Angle : 0.545 6.489 30844 Z= 0.284 Chirality : 0.039 0.339 3308 Planarity : 0.003 0.043 3676 Dihedral : 20.135 176.644 4528 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 1.98 % Allowed : 18.62 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.17), residues: 2552 helix: 1.45 (0.13), residues: 1500 sheet: -0.48 (0.54), residues: 96 loop : -1.43 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 499 TYR 0.022 0.001 TYR D 472 PHE 0.011 0.001 PHE C 650 TRP 0.016 0.001 TRP A 698 HIS 0.007 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (23084) covalent geometry : angle 0.54493 / 0.28 (30844) hydrogen bonds : bond 0.03434 / 2.27 ( 1076) hydrogen bonds : angle 3.94291 / 2.74 ( 3108) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 275 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 GLU cc_start: 0.6792 (tm-30) cc_final: 0.5684 (tt0) REVERT: A 315 MET cc_start: 0.8017 (mtm) cc_final: 0.7808 (mtp) REVERT: A 466 MET cc_start: 0.7038 (mpp) cc_final: 0.6581 (mtm) REVERT: A 503 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5817 (tmm) REVERT: A 711 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7578 (mtmt) REVERT: A 717 MET cc_start: 0.3034 (mmm) cc_final: 0.2314 (pp-130) REVERT: A 718 ARG cc_start: 0.3095 (OUTLIER) cc_final: 0.1967 (tmm-80) REVERT: B 184 THR cc_start: 0.5315 (OUTLIER) cc_final: 0.4890 (t) REVERT: B 214 ASN cc_start: 0.5960 (t0) cc_final: 0.5696 (t0) REVERT: B 363 CYS cc_start: 0.7777 (m) cc_final: 0.7487 (m) REVERT: B 398 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7661 (tm-30) REVERT: B 466 MET cc_start: 0.6996 (mpp) cc_final: 0.6558 (mtm) REVERT: B 496 PHE cc_start: 0.6848 (t80) cc_final: 0.6137 (m-80) REVERT: B 509 ASP cc_start: 0.7025 (p0) cc_final: 0.6789 (p0) REVERT: B 717 MET cc_start: 0.3607 (mmm) cc_final: 0.2574 (pp-130) REVERT: B 762 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5618 (tm-30) REVERT: C 211 GLU cc_start: 0.6790 (tm-30) cc_final: 0.5685 (tt0) REVERT: C 315 MET cc_start: 0.8095 (mtm) cc_final: 0.7872 (mtp) REVERT: C 402 TYR cc_start: 0.8572 (m-10) cc_final: 0.8264 (m-10) REVERT: C 503 MET cc_start: 0.6487 (OUTLIER) cc_final: 0.5910 (tmm) REVERT: C 711 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7526 (mtmt) REVERT: C 717 MET cc_start: 0.3401 (mmm) cc_final: 0.2670 (pp-130) REVERT: C 766 ASN cc_start: 0.6753 (t0) cc_final: 0.6357 (t0) REVERT: D 184 THR cc_start: 0.5179 (OUTLIER) cc_final: 0.4796 (t) REVERT: D 214 ASN cc_start: 0.5846 (t0) cc_final: 0.5510 (t0) REVERT: D 359 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7776 (mp10) REVERT: D 363 CYS cc_start: 0.7735 (m) cc_final: 0.7476 (m) REVERT: D 496 PHE cc_start: 0.6875 (t80) cc_final: 0.6274 (m-80) REVERT: D 711 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7712 (mtmt) REVERT: D 717 MET cc_start: 0.4713 (tpt) cc_final: 0.3982 (pp-130) REVERT: D 749 ASN cc_start: 0.7931 (t0) cc_final: 0.7502 (t0) outliers start: 45 outliers final: 28 residues processed: 299 average time/residue: 0.4689 time to fit residues: 166.1759 Evaluate side-chains 294 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 305 PHE Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 636 LEU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 668 VAL Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 451 MET Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 762 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 271 ASN Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 451 MET Chi-restraints excluded: chain C residue 479 ILE Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 668 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 98 optimal weight: 10.0000 chunk 234 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 127 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 214 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 241 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 692 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 692 GLN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN ** D 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.234424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.183615 restraints weight = 21969.953| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 2.35 r_work: 0.3633 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 23084 Z= 0.113 Angle : 0.535 6.365 30844 Z= 0.279 Chirality : 0.039 0.343 3308 Planarity : 0.003 0.041 3676 Dihedral : 19.511 175.723 4528 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.20 % Allowed : 18.66 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2552 helix: 1.52 (0.13), residues: 1516 sheet: -0.42 (0.54), residues: 96 loop : -1.53 (0.21), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 182 TYR 0.027 0.001 TYR A 445 PHE 0.011 0.001 PHE C 650 TRP 0.016 0.001 TRP A 698 HIS 0.008 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (23084) covalent geometry : angle 0.53532 / 0.28 (30844) hydrogen bonds : bond 0.03362 / 2.22 ( 1076) hydrogen bonds : angle 3.90157 / 2.72 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7151.88 seconds wall clock time: 122 minutes 54.13 seconds (7374.13 seconds total)