Starting phenix.real_space_refine on Sat Jul 4 19:52:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9p6b_71303/07_2026/9p6b_71303.cif Found real_map, /net/cci-nas-00/data/ceres_data/9p6b_71303/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9p6b_71303/07_2026/9p6b_71303.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9p6b_71303/07_2026/9p6b_71303.map" model { file = "/net/cci-nas-00/data/ceres_data/9p6b_71303/07_2026/9p6b_71303.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9p6b_71303/07_2026/9p6b_71303.cif" } 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-dev-6108/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, 488 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'8IJ': 1, 'POV': 8, 'TRD': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain breaks: 1 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, 436 Ad-hoc single atom residues: {' NA': 1} Unusual residues: {'8IJ': 1, 'POV': 7, 'TRD': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain breaks: 1 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: 4.18, per 1000 atoms: 0.18 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.57 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: 3.53 Time building geometry restraints manager: 2.70 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.720 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.740 ------------------------------------------------------------------------------- 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 : 0.788 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: 0.5318 time to fit residues: 283.9833 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 : 0.779 ------------------------------------------------------------------------------- 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 = 0.4744 r_free = 0.4744 target = 0.259573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.214648 restraints weight = 22149.166| |-----------------------------------------------------------------------------| r_work (start): 0.4334 rms_B_bonded: 1.42 r_work: 0.4036 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23084 Z= 0.166 Angle : 0.695 7.538 30844 Z= 0.354 Chirality : 0.042 0.176 3308 Planarity : 0.005 0.038 3676 Dihedral : 24.358 166.116 4528 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.47 % Allowed : 9.60 % Favored : 89.93 % Rotamer: Outliers : 2.07 % Allowed : 9.82 % Favored : 88.12 % 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: -2.55 (0.15), residues: 2552 helix: -1.08 (0.12), residues: 1500 sheet: -1.21 (0.60), residues: 84 loop : -2.62 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 772 TYR 0.014 0.002 TYR C 632 PHE 0.015 0.002 PHE C 430 TRP 0.028 0.002 TRP D 698 HIS 0.004 0.001 HIS C 290 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (23084) covalent geometry : angle 0.69538 / 0.35 (30844) hydrogen bonds : bond 0.04545 / 2.98 ( 1076) hydrogen bonds : angle 4.73761 / 3.27 ( 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 381 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 334 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 TYR cc_start: 0.6369 (m-80) cc_final: 0.6155 (m-80) REVERT: A 363 CYS cc_start: 0.7753 (m) cc_final: 0.7501 (m) REVERT: A 379 HIS cc_start: 0.7709 (p-80) cc_final: 0.7262 (p-80) REVERT: A 398 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7765 (tm-30) REVERT: A 503 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5749 (tmm) REVERT: B 208 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7718 (mm) REVERT: B 363 CYS cc_start: 0.7525 (m) cc_final: 0.7192 (m) REVERT: B 398 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7710 (tm-30) REVERT: B 570 GLU cc_start: 0.8731 (tt0) cc_final: 0.8346 (tt0) REVERT: B 749 ASN cc_start: 0.7557 (t0) cc_final: 0.6863 (m110) REVERT: C 215 MET cc_start: 0.6628 (tpt) cc_final: 0.6409 (tpp) REVERT: C 247 TYR cc_start: 0.7613 (t80) cc_final: 0.7034 (t80) REVERT: C 379 HIS cc_start: 0.7948 (p-80) cc_final: 0.7435 (p90) REVERT: C 398 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7777 (tm-30) REVERT: C 503 MET cc_start: 0.6030 (OUTLIER) cc_final: 0.5445 (tmm) REVERT: C 570 GLU cc_start: 0.8749 (tt0) cc_final: 0.8451 (tt0) REVERT: D 215 MET cc_start: 0.5650 (tpp) cc_final: 0.5427 (tpp) REVERT: D 286 ASN cc_start: 0.7629 (m-40) cc_final: 0.7046 (m-40) REVERT: D 398 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7666 (tm-30) REVERT: D 570 GLU cc_start: 0.8651 (tt0) cc_final: 0.8386 (tt0) REVERT: D 692 GLN cc_start: 0.7364 (mm-40) cc_final: 0.7156 (tp-100) REVERT: D 717 MET cc_start: 0.4801 (tpt) cc_final: 0.4388 (ptm) outliers start: 47 outliers final: 7 residues processed: 364 average time/residue: 0.5421 time to fit residues: 229.8818 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 : 0.804 ------------------------------------------------------------------------------- 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: 0.9980 chunk 187 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 177 optimal weight: 5.9990 chunk 132 optimal weight: 20.0000 chunk 91 optimal weight: 0.0060 chunk 212 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.253595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.210660 restraints weight = 22411.699| |-----------------------------------------------------------------------------| r_work (start): 0.4303 rms_B_bonded: 1.97 r_work: 0.3890 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.113 23084 Z= 0.148 Angle : 0.617 7.227 30844 Z= 0.316 Chirality : 0.040 0.194 3308 Planarity : 0.004 0.047 3676 Dihedral : 22.902 166.069 4528 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.66 % Favored : 90.87 % Rotamer: Outliers : 2.60 % Allowed : 12.46 % Favored : 84.95 % 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: 0.08 (0.13), residues: 1508 sheet: -0.71 (0.61), residues: 84 loop : -2.07 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 744 TYR 0.017 0.002 TYR D 352 PHE 0.016 0.002 PHE A 522 TRP 0.017 0.002 TRP A 698 HIS 0.005 0.001 HIS B 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (23084) covalent geometry : angle 0.61664 / 0.32 (30844) hydrogen bonds : bond 0.04075 / 2.67 ( 1076) hydrogen bonds : angle 4.28053 / 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 343 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 284 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8238 (mtm) cc_final: 0.7933 (mtp) REVERT: A 398 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7916 (tm-30) REVERT: A 714 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6212 (mp) REVERT: A 717 MET cc_start: 0.4264 (mmm) cc_final: 0.1458 (ptp) REVERT: A 718 ARG cc_start: 0.3260 (OUTLIER) cc_final: 0.3039 (ppt170) REVERT: B 363 CYS cc_start: 0.7666 (m) cc_final: 0.7394 (m) REVERT: B 398 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7878 (tm-30) REVERT: B 509 ASP cc_start: 0.7100 (p0) cc_final: 0.6565 (p0) REVERT: B 652 GLU cc_start: 0.7930 (mp0) cc_final: 0.7674 (mm-30) REVERT: B 714 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.6132 (mp) REVERT: B 717 MET cc_start: 0.4264 (mmm) cc_final: 0.1604 (ptm) REVERT: C 315 MET cc_start: 0.8160 (mtm) cc_final: 0.7896 (mtp) REVERT: C 398 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7944 (tm-30) REVERT: C 503 MET cc_start: 0.6190 (OUTLIER) cc_final: 0.5569 (tmm) REVERT: C 652 GLU cc_start: 0.8048 (mp0) cc_final: 0.7700 (mm-30) REVERT: C 714 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6148 (mp) REVERT: C 718 ARG cc_start: 0.3200 (OUTLIER) cc_final: 0.2907 (ppt170) REVERT: D 335 MET cc_start: 0.7825 (mmt) cc_final: 0.7622 (mmt) REVERT: D 363 CYS cc_start: 0.7370 (m) cc_final: 0.7091 (m) REVERT: D 398 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7833 (tm-30) REVERT: D 509 ASP cc_start: 0.7257 (p0) cc_final: 0.6930 (p0) REVERT: D 714 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.6028 (mp) REVERT: D 717 MET cc_start: 0.4876 (tpt) cc_final: 0.4166 (pp-130) REVERT: D 747 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7174 (mt-10) REVERT: D 774 LEU cc_start: 0.2627 (OUTLIER) cc_final: 0.1882 (pt) outliers start: 59 outliers final: 13 residues processed: 322 average time/residue: 0.5836 time to fit residues: 216.9768 Evaluate side-chains 271 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 250 time to evaluate : 0.808 ------------------------------------------------------------------------------- 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 714 LEU 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 C residue 714 LEU Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 651 THR Chi-restraints excluded: chain D residue 714 LEU Chi-restraints excluded: chain D residue 746 ASP Chi-restraints excluded: chain D residue 774 LEU 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: 0.6980 chunk 80 optimal weight: 30.0000 chunk 241 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 84 optimal weight: 0.0050 chunk 21 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 203 GLN B 261 GLN B 365 HIS B 766 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 GLN D 365 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.254692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.210479 restraints weight = 22082.615| |-----------------------------------------------------------------------------| r_work (start): 0.4294 rms_B_bonded: 1.90 r_work: 0.3911 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23084 Z= 0.115 Angle : 0.557 10.194 30844 Z= 0.289 Chirality : 0.039 0.214 3308 Planarity : 0.004 0.031 3676 Dihedral : 22.093 157.368 4528 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.99 % Favored : 91.54 % Rotamer: Outliers : 1.89 % Allowed : 14.66 % Favored : 83.45 % 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: -0.27 (0.17), residues: 2552 helix: 0.87 (0.13), residues: 1500 sheet: -0.54 (0.62), 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 0.012 0.001 TYR D 352 PHE 0.011 0.001 PHE A 639 TRP 0.016 0.001 TRP B 698 HIS 0.007 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (23084) covalent geometry : angle 0.55728 / 0.29 (30844) hydrogen bonds : bond 0.03446 / 2.26 ( 1076) hydrogen bonds : angle 4.00071 / 2.76 ( 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 327 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 284 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8187 (mtm) cc_final: 0.7895 (mtp) REVERT: A 398 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7938 (tm-30) REVERT: A 714 LEU cc_start: 0.6493 (OUTLIER) cc_final: 0.6171 (mp) REVERT: A 718 ARG cc_start: 0.3116 (OUTLIER) cc_final: 0.2652 (ptm160) REVERT: B 315 MET cc_start: 0.7932 (mtm) cc_final: 0.7695 (mtp) REVERT: B 363 CYS cc_start: 0.7725 (m) cc_final: 0.7449 (m) REVERT: B 398 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7902 (tm-30) REVERT: B 410 ARG cc_start: 0.7425 (ttp80) cc_final: 0.7057 (ttt180) REVERT: B 466 MET cc_start: 0.6840 (mpp) cc_final: 0.6371 (mtm) REVERT: B 509 ASP cc_start: 0.7074 (p0) cc_final: 0.6503 (p0) REVERT: B 636 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7945 (tp) REVERT: B 714 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6108 (mp) REVERT: B 762 GLU cc_start: 0.5775 (mt-10) cc_final: 0.5416 (tm-30) REVERT: C 315 MET cc_start: 0.8052 (mtm) cc_final: 0.7804 (mtp) REVERT: C 503 MET cc_start: 0.6309 (OUTLIER) cc_final: 0.5694 (tmm) REVERT: C 714 LEU cc_start: 0.6363 (OUTLIER) cc_final: 0.6043 (mp) REVERT: C 718 ARG cc_start: 0.3092 (OUTLIER) cc_final: 0.2642 (ptm160) REVERT: D 261 GLN cc_start: 0.6710 (OUTLIER) cc_final: 0.5418 (mp-120) REVERT: D 363 CYS cc_start: 0.7434 (m) cc_final: 0.7172 (m) REVERT: D 398 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7896 (tm-30) REVERT: D 509 ASP cc_start: 0.7256 (p0) cc_final: 0.6851 (p0) REVERT: D 717 MET cc_start: 0.4587 (tpt) cc_final: 0.3896 (pp-130) REVERT: D 747 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7153 (mt-10) outliers start: 43 outliers final: 6 residues processed: 309 average time/residue: 0.5996 time to fit residues: 213.4206 Evaluate side-chains 269 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 GLU Chi-restraints excluded: chain A residue 651 THR Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 636 LEU Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 636 LEU Chi-restraints excluded: chain C residue 714 LEU Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain D residue 261 GLN Chi-restraints excluded: chain D residue 357 GLU 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: 10.0000 chunk 122 optimal weight: 7.9990 chunk 198 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 193 optimal weight: 40.0000 chunk 78 optimal weight: 6.9990 chunk 35 optimal weight: 8.9990 chunk 219 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 GLN 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 D 302 ASN D 692 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.245549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.200417 restraints weight = 21823.508| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 1.74 r_work: 0.3812 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.4218 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= 0.360 Angle : 0.817 10.583 30844 Z= 0.400 Chirality : 0.051 0.231 3308 Planarity : 0.005 0.038 3676 Dihedral : 23.573 168.526 4528 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.13 % Favored : 90.83 % Rotamer: Outliers : 3.96 % Allowed : 13.25 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -1.04 (0.16), residues: 2552 helix: 0.03 (0.13), residues: 1528 sheet: -0.86 (0.48), residues: 120 loop : -1.83 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 356 TYR 0.026 0.003 TYR A 584 PHE 0.025 0.003 PHE B 522 TRP 0.020 0.003 TRP C 698 HIS 0.007 0.002 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00851 / 0.36 (23084) covalent geometry : angle 0.81705 / 0.40 (30844) hydrogen bonds : bond 0.04978 / 3.29 ( 1076) hydrogen bonds : angle 4.64723 / 3.21 ( 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 367 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 277 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 ASN cc_start: 0.6311 (t0) cc_final: 0.6096 (t0) REVERT: A 315 MET cc_start: 0.8344 (mtm) cc_final: 0.8053 (mtp) REVERT: A 466 MET cc_start: 0.6891 (mpp) cc_final: 0.6512 (mtm) REVERT: A 503 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5802 (tmm) REVERT: A 652 GLU cc_start: 0.8085 (mp0) cc_final: 0.7605 (mm-30) REVERT: A 711 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7459 (mtpt) REVERT: A 717 MET cc_start: 0.3890 (OUTLIER) cc_final: 0.1598 (ptm) REVERT: A 718 ARG cc_start: 0.3487 (OUTLIER) cc_final: 0.2612 (ptm160) REVERT: B 281 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7405 (mmt90) REVERT: B 363 CYS cc_start: 0.7973 (m) cc_final: 0.7713 (m) REVERT: B 410 ARG cc_start: 0.7697 (ttp80) cc_final: 0.7445 (ttt180) REVERT: B 466 MET cc_start: 0.6739 (mpp) cc_final: 0.6480 (mtm) REVERT: B 509 ASP cc_start: 0.7553 (p0) cc_final: 0.7185 (p0) REVERT: B 714 LEU cc_start: 0.6650 (OUTLIER) cc_final: 0.6314 (mm) REVERT: B 717 MET cc_start: 0.4252 (mmm) cc_final: 0.2229 (pp-130) REVERT: C 211 GLU cc_start: 0.7080 (tm-30) cc_final: 0.6008 (tt0) REVERT: C 315 MET cc_start: 0.8311 (mtm) cc_final: 0.8031 (mtp) REVERT: C 503 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.5879 (tmm) REVERT: C 692 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7426 (tp-100) REVERT: C 711 LYS cc_start: 0.7918 (mtpp) cc_final: 0.7669 (mptm) REVERT: C 714 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6292 (mm) REVERT: C 718 ARG cc_start: 0.3419 (OUTLIER) cc_final: 0.2478 (ptm160) REVERT: C 766 ASN cc_start: 0.6692 (t0) cc_final: 0.6118 (t0) REVERT: D 363 CYS cc_start: 0.7913 (m) cc_final: 0.7680 (m) REVERT: D 509 ASP cc_start: 0.7516 (p0) cc_final: 0.7159 (p0) REVERT: D 631 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8133 (tp) REVERT: D 711 LYS cc_start: 0.8067 (mmmt) cc_final: 0.7576 (mmmt) REVERT: D 717 MET cc_start: 0.4753 (tpt) cc_final: 0.3993 (pp-130) REVERT: D 749 ASN cc_start: 0.8035 (t0) cc_final: 0.7714 (t0) REVERT: D 762 GLU cc_start: 0.6483 (pp20) cc_final: 0.6123 (mt-10) outliers start: 90 outliers final: 26 residues processed: 334 average time/residue: 0.6059 time to fit residues: 234.2724 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 : 0.852 ------------------------------------------------------------------------------- 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 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 281 ARG Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 446 MET 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 668 VAL 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 446 MET 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 714 LEU Chi-restraints excluded: chain C residue 718 ARG 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 631 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 213 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 182 optimal weight: 1.9990 chunk 204 optimal weight: 0.0050 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 30.0000 chunk 155 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 B 261 GLN C 261 GLN C 692 GLN D 261 GLN D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4639 r_free = 0.4639 target = 0.247029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.201338 restraints weight = 22134.286| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.72 r_work: 0.3871 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23084 Z= 0.132 Angle : 0.582 7.206 30844 Z= 0.300 Chirality : 0.039 0.266 3308 Planarity : 0.004 0.039 3676 Dihedral : 22.145 165.817 4528 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.42 % Allowed : 15.76 % Favored : 81.82 % 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: -0.22 (0.17), residues: 2552 helix: 0.81 (0.13), residues: 1520 sheet: -0.73 (0.54), residues: 96 loop : -1.66 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 499 TYR 0.014 0.001 TYR D 352 PHE 0.013 0.001 PHE A 639 TRP 0.018 0.002 TRP D 698 HIS 0.005 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (23084) covalent geometry : angle 0.58178 / 0.30 (30844) hydrogen bonds : bond 0.03618 / 2.38 ( 1076) hydrogen bonds : angle 4.14257 / 2.86 ( 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 327 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 272 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.8177 (mtm) cc_final: 0.7937 (mtp) REVERT: A 466 MET cc_start: 0.6934 (mpp) cc_final: 0.6585 (mtt) REVERT: A 503 MET cc_start: 0.6403 (OUTLIER) cc_final: 0.5870 (tmm) REVERT: A 652 GLU cc_start: 0.7915 (mp0) cc_final: 0.7550 (mm-30) REVERT: A 718 ARG cc_start: 0.3294 (OUTLIER) cc_final: 0.2310 (ptm160) REVERT: A 749 ASN cc_start: 0.8004 (t0) cc_final: 0.7414 (t0) REVERT: B 211 GLU cc_start: 0.6903 (tm-30) cc_final: 0.6665 (tm-30) REVERT: B 214 ASN cc_start: 0.6043 (t0) cc_final: 0.5822 (t0) REVERT: B 315 MET cc_start: 0.8031 (mtp) cc_final: 0.7803 (mtp) REVERT: B 363 CYS cc_start: 0.7776 (m) cc_final: 0.7476 (m) REVERT: B 372 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7484 (tt0) REVERT: B 398 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: B 466 MET cc_start: 0.6820 (mpp) cc_final: 0.6559 (mtm) REVERT: B 491 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6901 (mmt90) REVERT: B 509 ASP cc_start: 0.7059 (p0) cc_final: 0.6647 (p0) REVERT: B 714 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6220 (mp) REVERT: B 717 MET cc_start: 0.4079 (mmm) cc_final: 0.2194 (pp-130) REVERT: B 747 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C 163 MET cc_start: 0.5835 (OUTLIER) cc_final: 0.5086 (mtm) REVERT: C 211 GLU cc_start: 0.6967 (tm-30) cc_final: 0.5876 (tt0) REVERT: C 315 MET cc_start: 0.8148 (mtm) cc_final: 0.7896 (mtp) REVERT: C 503 MET cc_start: 0.6418 (OUTLIER) cc_final: 0.5833 (tmm) REVERT: C 718 ARG cc_start: 0.3172 (OUTLIER) cc_final: 0.2318 (ptm160) REVERT: C 747 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 214 ASN cc_start: 0.5724 (t0) cc_final: 0.5385 (t0) REVERT: D 363 CYS cc_start: 0.7668 (m) cc_final: 0.7361 (m) REVERT: D 509 ASP cc_start: 0.7144 (p0) cc_final: 0.6770 (p0) REVERT: D 711 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7493 (mmmt) REVERT: D 717 MET cc_start: 0.4474 (tpt) cc_final: 0.3830 (pp-130) REVERT: D 749 ASN cc_start: 0.8006 (t0) cc_final: 0.7664 (t0) REVERT: D 762 GLU cc_start: 0.6341 (pp20) cc_final: 0.5981 (mt-10) outliers start: 55 outliers final: 13 residues processed: 300 average time/residue: 0.6040 time to fit residues: 209.6509 Evaluate side-chains 278 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 257 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR 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 717 MET Chi-restraints excluded: chain A residue 718 ARG 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 651 THR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 163 MET Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 279 SER 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 718 ARG Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 305 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 187 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 chunk 166 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 204 optimal weight: 0.0980 chunk 13 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 224 ASN ** C 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN D 261 GLN D 692 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.246172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.201070 restraints weight = 22041.879| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 1.81 r_work: 0.3840 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4586 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= 0.144 Angle : 0.578 6.779 30844 Z= 0.296 Chirality : 0.040 0.295 3308 Planarity : 0.004 0.032 3676 Dihedral : 21.581 167.753 4528 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 2.82 % Allowed : 15.62 % Favored : 81.56 % 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: 0.13 (0.17), residues: 2552 helix: 1.12 (0.14), residues: 1496 sheet: -0.51 (0.54), residues: 96 loop : -1.51 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 499 TYR 0.013 0.002 TYR A 584 PHE 0.017 0.001 PHE D 370 TRP 0.015 0.001 TRP B 698 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (23084) covalent geometry : angle 0.57816 / 0.30 (30844) hydrogen bonds : bond 0.03667 / 2.42 ( 1076) hydrogen bonds : angle 4.07936 / 2.82 ( 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 331 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 267 time to evaluate : 0.759 Fit side-chains REVERT: A 214 ASN cc_start: 0.6060 (OUTLIER) cc_final: 0.5813 (t0) REVERT: A 315 MET cc_start: 0.8142 (mtm) cc_final: 0.7902 (mtp) REVERT: A 491 ARG cc_start: 0.7215 (mmm-85) cc_final: 0.6916 (mmt90) REVERT: A 503 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5851 (tmm) REVERT: A 652 GLU cc_start: 0.7963 (mp0) cc_final: 0.7651 (mm-30) REVERT: A 717 MET cc_start: 0.3863 (mmm) cc_final: 0.1844 (pp-130) REVERT: A 718 ARG cc_start: 0.3254 (OUTLIER) cc_final: 0.2365 (mtm-85) REVERT: A 749 ASN cc_start: 0.8075 (t0) cc_final: 0.7505 (t0) REVERT: B 184 THR cc_start: 0.5445 (OUTLIER) cc_final: 0.5107 (t) REVERT: B 363 CYS cc_start: 0.7791 (m) cc_final: 0.7521 (m) REVERT: B 372 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7524 (tt0) REVERT: B 398 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: B 466 MET cc_start: 0.6917 (mpp) cc_final: 0.6602 (mtm) REVERT: B 509 ASP cc_start: 0.7184 (p0) cc_final: 0.6806 (p0) REVERT: B 714 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.6201 (mp) REVERT: B 717 MET cc_start: 0.4088 (mmm) cc_final: 0.2315 (pp-130) REVERT: B 747 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 749 ASN cc_start: 0.8313 (t0) cc_final: 0.8092 (t0) REVERT: C 211 GLU cc_start: 0.6892 (tm-30) cc_final: 0.5720 (tt0) REVERT: C 315 MET cc_start: 0.8120 (mtm) cc_final: 0.7892 (mtp) REVERT: C 475 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7564 (p) REVERT: C 491 ARG cc_start: 0.7248 (mmm-85) cc_final: 0.6977 (mmt90) REVERT: C 503 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5856 (tmm) REVERT: C 717 MET cc_start: 0.3833 (mmm) cc_final: 0.1835 (pp-130) REVERT: C 718 ARG cc_start: 0.3314 (OUTLIER) cc_final: 0.2486 (mtm-85) REVERT: C 747 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7823 (mt-10) REVERT: D 184 THR cc_start: 0.5335 (OUTLIER) cc_final: 0.5007 (t) REVERT: D 214 ASN cc_start: 0.5803 (t0) cc_final: 0.5522 (t0) REVERT: D 363 CYS cc_start: 0.7669 (m) cc_final: 0.7390 (m) REVERT: D 475 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7476 (p) REVERT: D 509 ASP cc_start: 0.7265 (p0) cc_final: 0.7011 (p0) REVERT: D 711 LYS cc_start: 0.8054 (mmmt) cc_final: 0.7741 (mmtp) REVERT: D 717 MET cc_start: 0.4540 (tpt) cc_final: 0.3870 (pp-130) REVERT: D 749 ASN cc_start: 0.8032 (t0) cc_final: 0.7686 (t0) outliers start: 64 outliers final: 19 residues processed: 300 average time/residue: 0.5455 time to fit residues: 190.7694 Evaluate side-chains 289 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 279 SER 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 718 ARG Chi-restraints excluded: chain A residue 746 ASP Chi-restraints excluded: chain B residue 184 THR 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 372 GLU Chi-restraints excluded: chain B residue 398 GLU Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 746 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL 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 D residue 184 THR 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 475 VAL Chi-restraints excluded: chain D residue 651 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 93 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 173 optimal weight: 0.9990 chunk 175 optimal weight: 0.5980 chunk 184 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 7 optimal weight: 30.0000 overall best weight: 1.0586 ------------------------------------------------------------------------------- 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** D 224 ASN D 261 GLN D 692 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.235270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.185083 restraints weight = 21842.581| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.38 r_work: 0.3635 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23084 Z= 0.126 Angle : 0.553 6.161 30844 Z= 0.286 Chirality : 0.039 0.304 3308 Planarity : 0.003 0.038 3676 Dihedral : 21.031 169.240 4528 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 2.68 % Allowed : 16.55 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 1.30 (0.14), residues: 1496 sheet: -0.51 (0.54), residues: 96 loop : -1.45 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.011 0.001 TYR A 584 PHE 0.011 0.001 PHE D 639 TRP 0.015 0.001 TRP D 698 HIS 0.005 0.001 HIS D 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (23084) covalent geometry : angle 0.55342 / 0.29 (30844) hydrogen bonds : bond 0.03505 / 2.31 ( 1076) hydrogen bonds : angle 4.00904 / 2.77 ( 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 332 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 271 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7949 (mtm) cc_final: 0.7716 (mtp) REVERT: A 466 MET cc_start: 0.6961 (mpp) cc_final: 0.6479 (mtm) REVERT: A 491 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6532 (mmt90) REVERT: A 503 MET cc_start: 0.6409 (OUTLIER) cc_final: 0.5863 (tmm) REVERT: A 652 GLU cc_start: 0.7713 (mp0) cc_final: 0.7164 (mm-30) REVERT: A 718 ARG cc_start: 0.3292 (OUTLIER) cc_final: 0.1265 (mtm-85) REVERT: B 184 THR cc_start: 0.5569 (OUTLIER) cc_final: 0.5160 (t) REVERT: B 214 ASN cc_start: 0.5464 (t0) cc_final: 0.5217 (t0) REVERT: B 363 CYS cc_start: 0.7681 (m) cc_final: 0.7385 (m) REVERT: B 372 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: B 398 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7601 (tm-30) REVERT: B 466 MET cc_start: 0.6830 (mpp) cc_final: 0.6460 (mtm) REVERT: B 491 ARG cc_start: 0.6919 (mmm-85) cc_final: 0.6488 (mmt90) REVERT: B 496 PHE cc_start: 0.6951 (t80) cc_final: 0.6217 (m-80) REVERT: B 509 ASP cc_start: 0.6954 (p0) cc_final: 0.6667 (p0) REVERT: B 714 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6255 (mp) REVERT: B 717 MET cc_start: 0.4123 (mmm) cc_final: 0.2330 (pp-130) REVERT: B 747 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7508 (mt-10) REVERT: C 211 GLU cc_start: 0.6695 (tm-30) cc_final: 0.5626 (tt0) REVERT: C 315 MET cc_start: 0.7949 (mtm) cc_final: 0.7728 (mtp) REVERT: C 475 VAL cc_start: 0.7571 (OUTLIER) cc_final: 0.7346 (p) REVERT: C 491 ARG cc_start: 0.6965 (mmm-85) cc_final: 0.6598 (mmt90) REVERT: C 503 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5805 (tmm) REVERT: C 718 ARG cc_start: 0.3175 (OUTLIER) cc_final: 0.1212 (mtm-85) REVERT: C 747 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 749 ASN cc_start: 0.7863 (t0) cc_final: 0.7156 (t0) REVERT: D 184 THR cc_start: 0.5393 (OUTLIER) cc_final: 0.5062 (t) REVERT: D 214 ASN cc_start: 0.5574 (t0) cc_final: 0.5271 (t0) REVERT: D 363 CYS cc_start: 0.7579 (m) cc_final: 0.7291 (m) REVERT: D 475 VAL cc_start: 0.7499 (OUTLIER) cc_final: 0.7255 (p) REVERT: D 496 PHE cc_start: 0.6918 (t80) cc_final: 0.6283 (m-80) REVERT: D 509 ASP cc_start: 0.7038 (p0) cc_final: 0.6725 (p0) REVERT: D 711 LYS cc_start: 0.7953 (mmmt) cc_final: 0.7517 (mmtp) REVERT: D 717 MET cc_start: 0.4601 (tpt) cc_final: 0.3928 (pp-130) REVERT: D 749 ASN cc_start: 0.7840 (t0) cc_final: 0.7411 (t0) outliers start: 61 outliers final: 25 residues processed: 306 average time/residue: 0.5096 time to fit residues: 183.3759 Evaluate side-chains 298 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 262 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 279 SER 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 184 THR 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 451 MET Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 503 MET Chi-restraints excluded: chain C residue 651 THR Chi-restraints excluded: chain C residue 718 ARG Chi-restraints excluded: chain D residue 184 THR 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 471 ASP Chi-restraints excluded: chain D residue 475 VAL 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: 2.9990 chunk 150 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 166 optimal weight: 9.9990 chunk 247 optimal weight: 0.8980 chunk 118 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 7.9990 chunk 250 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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 D 692 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.234184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183310 restraints weight = 22008.792| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 2.38 r_work: 0.3630 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23084 Z= 0.147 Angle : 0.571 6.087 30844 Z= 0.294 Chirality : 0.040 0.317 3308 Planarity : 0.003 0.033 3676 Dihedral : 20.780 169.193 4528 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.77 % Allowed : 16.81 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.35 (0.17), residues: 2552 helix: 1.30 (0.14), residues: 1496 sheet: -0.46 (0.53), residues: 96 loop : -1.44 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 499 TYR 0.026 0.002 TYR D 472 PHE 0.018 0.001 PHE D 370 TRP 0.014 0.001 TRP D 698 HIS 0.005 0.001 HIS A 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (23084) covalent geometry : angle 0.57137 / 0.29 (30844) hydrogen bonds : bond 0.03654 / 2.41 ( 1076) hydrogen bonds : angle 4.04089 / 2.80 ( 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 333 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 270 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: A 214 ASN cc_start: 0.5936 (OUTLIER) cc_final: 0.5654 (p0) REVERT: A 315 MET cc_start: 0.8022 (mtm) cc_final: 0.7793 (mtp) REVERT: A 466 MET cc_start: 0.6968 (mpp) cc_final: 0.6530 (mtm) REVERT: A 491 ARG cc_start: 0.7042 (mmm-85) cc_final: 0.6642 (mmt90) REVERT: A 503 MET cc_start: 0.6360 (OUTLIER) cc_final: 0.5804 (tmm) REVERT: A 652 GLU cc_start: 0.7774 (mp0) cc_final: 0.7342 (mm-30) REVERT: A 717 MET cc_start: 0.3194 (mmm) cc_final: 0.1889 (pp-130) REVERT: A 718 ARG cc_start: 0.3012 (OUTLIER) cc_final: 0.2272 (tmm-80) REVERT: A 766 ASN cc_start: 0.6792 (t0) cc_final: 0.6153 (t0) REVERT: B 184 THR cc_start: 0.5316 (OUTLIER) cc_final: 0.4915 (t) REVERT: B 211 GLU cc_start: 0.6770 (tm-30) cc_final: 0.5822 (tm-30) REVERT: B 214 ASN cc_start: 0.5485 (t0) cc_final: 0.5219 (t0) REVERT: B 363 CYS cc_start: 0.7754 (m) cc_final: 0.7456 (m) REVERT: B 398 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7826 (tm-30) REVERT: B 466 MET cc_start: 0.6833 (mpp) cc_final: 0.6506 (mtm) REVERT: B 491 ARG cc_start: 0.7037 (mmm-85) cc_final: 0.6635 (mmt90) REVERT: B 496 PHE cc_start: 0.6869 (t80) cc_final: 0.6170 (m-80) REVERT: B 509 ASP cc_start: 0.7091 (p0) cc_final: 0.6842 (p0) REVERT: B 717 MET cc_start: 0.4259 (mmm) cc_final: 0.2443 (pp-130) REVERT: B 747 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7565 (mt-10) REVERT: B 749 ASN cc_start: 0.8293 (t0) cc_final: 0.7999 (t0) REVERT: C 211 GLU cc_start: 0.6833 (tm-30) cc_final: 0.5738 (tt0) REVERT: C 315 MET cc_start: 0.8043 (mtm) cc_final: 0.7817 (mtp) REVERT: C 475 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7402 (p) REVERT: C 491 ARG cc_start: 0.7050 (mmm-85) cc_final: 0.6716 (mmt90) REVERT: C 503 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5834 (tmm) REVERT: C 717 MET cc_start: 0.3121 (mmm) cc_final: 0.1859 (pp-130) REVERT: C 718 ARG cc_start: 0.2930 (OUTLIER) cc_final: 0.2240 (tmm-80) REVERT: C 747 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7789 (mp0) REVERT: C 749 ASN cc_start: 0.7951 (t0) cc_final: 0.7289 (t0) REVERT: C 766 ASN cc_start: 0.6700 (t0) cc_final: 0.6179 (t0) REVERT: D 184 THR cc_start: 0.5149 (OUTLIER) cc_final: 0.4835 (t) REVERT: D 214 ASN cc_start: 0.5828 (t0) cc_final: 0.5538 (t0) REVERT: D 359 GLN cc_start: 0.7958 (mm-40) cc_final: 0.7734 (mp10) REVERT: D 363 CYS cc_start: 0.7673 (m) cc_final: 0.7410 (m) REVERT: D 402 TYR cc_start: 0.8534 (m-10) cc_final: 0.8277 (m-10) REVERT: D 496 PHE cc_start: 0.6912 (t80) cc_final: 0.6262 (m-80) REVERT: D 509 ASP cc_start: 0.7157 (p0) cc_final: 0.6940 (p0) REVERT: D 711 LYS cc_start: 0.8003 (mmmt) cc_final: 0.7575 (mtmt) REVERT: D 717 MET cc_start: 0.4491 (tpt) cc_final: 0.3840 (pp-130) REVERT: D 749 ASN cc_start: 0.7904 (t0) cc_final: 0.7466 (t0) outliers start: 63 outliers final: 30 residues processed: 304 average time/residue: 0.5269 time to fit residues: 187.8125 Evaluate side-chains 298 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 259 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN 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 357 GLU Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 503 MET Chi-restraints excluded: chain A residue 651 THR 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 279 SER Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 357 GLU Chi-restraints excluded: chain B residue 398 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 279 SER Chi-restraints excluded: chain C residue 305 PHE Chi-restraints excluded: chain C residue 475 VAL 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 D residue 184 THR Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain D residue 261 GLN 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 62 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 159 optimal weight: 0.8980 chunk 99 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 225 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 D 692 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.235027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.185398 restraints weight = 21939.480| |-----------------------------------------------------------------------------| r_work (start): 0.4026 rms_B_bonded: 2.32 r_work: 0.3641 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23084 Z= 0.126 Angle : 0.557 6.015 30844 Z= 0.289 Chirality : 0.040 0.323 3308 Planarity : 0.003 0.035 3676 Dihedral : 20.528 169.377 4528 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.11 % Allowed : 17.56 % Favored : 80.33 % 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: 0.45 (0.17), residues: 2552 helix: 1.40 (0.14), residues: 1496 sheet: -0.45 (0.54), residues: 96 loop : -1.42 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 744 TYR 0.016 0.001 TYR D 445 PHE 0.011 0.001 PHE D 639 TRP 0.015 0.001 TRP D 698 HIS 0.004 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (23084) covalent geometry : angle 0.55741 / 0.29 (30844) hydrogen bonds : bond 0.03537 / 2.33 ( 1076) hydrogen bonds : angle 4.00962 / 2.78 ( 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 313 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 214 ASN cc_start: 0.5890 (OUTLIER) cc_final: 0.5636 (p0) REVERT: A 315 MET cc_start: 0.8033 (mtm) cc_final: 0.7810 (mtp) REVERT: A 466 MET cc_start: 0.7010 (mpp) cc_final: 0.6527 (mtm) REVERT: A 491 ARG cc_start: 0.7078 (mmm-85) cc_final: 0.6685 (mmt90) REVERT: A 503 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5726 (tmm) REVERT: A 652 GLU cc_start: 0.7806 (mp0) cc_final: 0.7355 (mm-30) REVERT: A 717 MET cc_start: 0.3104 (mmm) cc_final: 0.1951 (pp-130) REVERT: A 718 ARG cc_start: 0.2980 (OUTLIER) cc_final: 0.2224 (tmm-80) REVERT: A 766 ASN cc_start: 0.6792 (t0) cc_final: 0.6125 (t0) REVERT: B 184 THR cc_start: 0.5454 (OUTLIER) cc_final: 0.5026 (t) REVERT: B 211 GLU cc_start: 0.6735 (tm-30) cc_final: 0.5755 (tm-30) REVERT: B 363 CYS cc_start: 0.7725 (m) cc_final: 0.7433 (m) REVERT: B 398 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7824 (tm-30) REVERT: B 466 MET cc_start: 0.6876 (mpp) cc_final: 0.6545 (mtm) REVERT: B 491 ARG cc_start: 0.7060 (mmm-85) cc_final: 0.6660 (mmt90) REVERT: B 496 PHE cc_start: 0.6866 (t80) cc_final: 0.6174 (m-80) REVERT: B 509 ASP cc_start: 0.7049 (p0) cc_final: 0.6771 (p0) REVERT: B 714 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6227 (mp) REVERT: B 717 MET cc_start: 0.4195 (mmm) cc_final: 0.2465 (pp-130) REVERT: B 747 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7543 (mt-10) REVERT: B 749 ASN cc_start: 0.8302 (t0) cc_final: 0.8017 (t0) REVERT: B 762 GLU cc_start: 0.6205 (tt0) cc_final: 0.5416 (tm-30) REVERT: C 211 GLU cc_start: 0.6797 (tm-30) cc_final: 0.5727 (tt0) REVERT: C 315 MET cc_start: 0.8048 (mtm) cc_final: 0.7830 (mtp) REVERT: C 475 VAL cc_start: 0.7626 (OUTLIER) cc_final: 0.7396 (p) REVERT: C 491 ARG cc_start: 0.7053 (mmm-85) cc_final: 0.6711 (mmt90) REVERT: C 503 MET cc_start: 0.6500 (OUTLIER) cc_final: 0.5898 (tmm) REVERT: C 717 MET cc_start: 0.3118 (mmm) cc_final: 0.1944 (pp-130) REVERT: C 718 ARG cc_start: 0.2931 (OUTLIER) cc_final: 0.2212 (tmm-80) REVERT: C 747 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7811 (mp0) REVERT: C 749 ASN cc_start: 0.7953 (t0) cc_final: 0.7323 (t0) REVERT: C 766 ASN cc_start: 0.6694 (t0) cc_final: 0.6178 (t0) REVERT: D 184 THR cc_start: 0.5297 (OUTLIER) cc_final: 0.4953 (t) REVERT: D 214 ASN cc_start: 0.5815 (t0) cc_final: 0.5526 (t0) REVERT: D 359 GLN cc_start: 0.7968 (mm-40) cc_final: 0.7740 (mp10) REVERT: D 363 CYS cc_start: 0.7677 (m) cc_final: 0.7410 (m) REVERT: D 402 TYR cc_start: 0.8534 (m-10) cc_final: 0.8273 (m-10) REVERT: D 496 PHE cc_start: 0.6890 (t80) cc_final: 0.6284 (m-80) REVERT: D 509 ASP cc_start: 0.7101 (p0) cc_final: 0.6823 (p0) REVERT: D 711 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7588 (mtmt) REVERT: D 717 MET cc_start: 0.4483 (tpt) cc_final: 0.3805 (pp-130) REVERT: D 749 ASN cc_start: 0.7891 (t0) cc_final: 0.7458 (t0) REVERT: D 766 ASN cc_start: 0.6891 (t0) cc_final: 0.6561 (t0) outliers start: 48 outliers final: 29 residues processed: 294 average time/residue: 0.5471 time to fit residues: 189.0623 Evaluate side-chains 302 residues out of total 2272 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 263 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ASN 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 357 GLU Chi-restraints excluded: chain A residue 503 MET 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 279 SER Chi-restraints excluded: chain B residue 305 PHE Chi-restraints excluded: chain B residue 398 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 B residue 714 LEU 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 475 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 98 optimal weight: 5.9990 chunk 234 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 chunk 214 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 142 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 D 692 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.233588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.183085 restraints weight = 21901.700| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 2.45 r_work: 0.3614 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 23084 Z= 0.153 Angle : 0.581 5.870 30844 Z= 0.299 Chirality : 0.041 0.326 3308 Planarity : 0.003 0.034 3676 Dihedral : 20.248 171.252 4528 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 2.33 % Allowed : 17.61 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.36 (0.17), residues: 2552 helix: 1.32 (0.13), residues: 1496 sheet: -0.41 (0.54), residues: 96 loop : -1.45 (0.21), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 499 TYR 0.019 0.002 TYR C 445 PHE 0.019 0.001 PHE D 370 TRP 0.014 0.002 TRP D 698 HIS 0.006 0.001 HIS C 379 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (23084) covalent geometry : angle 0.58145 / 0.30 (30844) hydrogen bonds : bond 0.03747 / 2.46 ( 1076) hydrogen bonds : angle 4.08229 / 2.83 ( 3108) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7490.11 seconds wall clock time: 128 minutes 50.29 seconds (7730.29 seconds total)