Starting phenix.real_space_refine on Thu Feb 5 04:38:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10fm_75135/02_2026/10fm_75135.cif Found real_map, /net/cci-nas-00/data/ceres_data/10fm_75135/02_2026/10fm_75135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10fm_75135/02_2026/10fm_75135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10fm_75135/02_2026/10fm_75135.map" model { file = "/net/cci-nas-00/data/ceres_data/10fm_75135/02_2026/10fm_75135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10fm_75135/02_2026/10fm_75135.cif" } resolution = 3.03 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9398 2.51 5 N 2600 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14864 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3713 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 17, 'TRANS': 477} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3717 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 17, 'TRANS': 477} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "C" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3717 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 17, 'TRANS': 477} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3717 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 17, 'TRANS': 477} Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 55 Time building chain proxies: 3.51, per 1000 atoms: 0.24 Number of scatterers: 14864 At special positions: 0 Unit cell: (111.518, 106.634, 101.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2794 8.00 N 2600 7.00 C 9398 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: 1.34 Conformation dependent library (CDL) restraints added in 687.6 milliseconds 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3616 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 12 sheets defined 46.3% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 14 removed outlier: 3.617A pdb=" N ALA A 13 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 60 removed outlier: 3.851A pdb=" N LYS A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN A 58 " --> pdb=" O GLU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 81 removed outlier: 3.885A pdb=" N LEU A 70 " --> pdb=" O LYS A 66 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A 71 " --> pdb=" O ARG A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 94 Processing helix chain 'A' and resid 96 through 117 Processing helix chain 'A' and resid 155 through 168 Processing helix chain 'A' and resid 180 through 198 removed outlier: 3.689A pdb=" N SER A 184 " --> pdb=" O ILE A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.946A pdb=" N SER A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 267 through 281 Proline residue: A 273 - end of helix Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.710A pdb=" N GLN A 313 " --> pdb=" O ASN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 347 Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.279A pdb=" N ALA A 381 " --> pdb=" O MET A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 419 through 427 removed outlier: 3.740A pdb=" N ALA A 423 " --> pdb=" O ASN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.927A pdb=" N PHE A 452 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'B' and resid 10 through 14 removed outlier: 3.618A pdb=" N ALA B 13 " --> pdb=" O GLY B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 3.851A pdb=" N LYS B 57 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 81 removed outlier: 3.884A pdb=" N LEU B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 94 Processing helix chain 'B' and resid 96 through 117 Processing helix chain 'B' and resid 155 through 168 Processing helix chain 'B' and resid 180 through 198 removed outlier: 3.689A pdb=" N SER B 184 " --> pdb=" O ILE B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.945A pdb=" N SER B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'B' and resid 267 through 281 Proline residue: B 273 - end of helix Processing helix chain 'B' and resid 282 through 285 Processing helix chain 'B' and resid 299 through 313 removed outlier: 3.710A pdb=" N GLN B 313 " --> pdb=" O ASN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 347 Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.279A pdb=" N ALA B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 419 through 427 removed outlier: 3.740A pdb=" N ALA B 423 " --> pdb=" O ASN B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.928A pdb=" N PHE B 452 " --> pdb=" O GLY B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 464 Processing helix chain 'B' and resid 467 through 471 Processing helix chain 'C' and resid 10 through 14 removed outlier: 3.618A pdb=" N ALA C 13 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 60 removed outlier: 3.850A pdb=" N LYS C 57 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLN C 58 " --> pdb=" O GLU C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 81 removed outlier: 3.885A pdb=" N LEU C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 94 Processing helix chain 'C' and resid 96 through 117 Processing helix chain 'C' and resid 155 through 168 Processing helix chain 'C' and resid 180 through 198 removed outlier: 3.689A pdb=" N SER C 184 " --> pdb=" O ILE C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.945A pdb=" N SER C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 245 Processing helix chain 'C' and resid 267 through 281 Proline residue: C 273 - end of helix Processing helix chain 'C' and resid 282 through 285 Processing helix chain 'C' and resid 299 through 313 removed outlier: 3.710A pdb=" N GLN C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 347 Processing helix chain 'C' and resid 377 through 382 removed outlier: 4.279A pdb=" N ALA C 381 " --> pdb=" O MET C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 419 through 427 removed outlier: 3.740A pdb=" N ALA C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.928A pdb=" N PHE C 452 " --> pdb=" O GLY C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 464 Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'D' and resid 10 through 14 removed outlier: 3.618A pdb=" N ALA D 13 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 60 removed outlier: 3.850A pdb=" N LYS D 57 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN D 58 " --> pdb=" O GLU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 81 removed outlier: 3.885A pdb=" N LEU D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 71 " --> pdb=" O ARG D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 94 Processing helix chain 'D' and resid 96 through 117 Processing helix chain 'D' and resid 155 through 168 Processing helix chain 'D' and resid 180 through 198 removed outlier: 3.689A pdb=" N SER D 184 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.946A pdb=" N SER D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 245 Processing helix chain 'D' and resid 267 through 281 Proline residue: D 273 - end of helix Processing helix chain 'D' and resid 282 through 285 Processing helix chain 'D' and resid 299 through 313 removed outlier: 3.710A pdb=" N GLN D 313 " --> pdb=" O ASN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 347 Processing helix chain 'D' and resid 377 through 382 removed outlier: 4.279A pdb=" N ALA D 381 " --> pdb=" O MET D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 419 through 427 removed outlier: 3.740A pdb=" N ALA D 423 " --> pdb=" O ASN D 419 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 removed outlier: 3.928A pdb=" N PHE D 452 " --> pdb=" O GLY D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 464 Processing helix chain 'D' and resid 467 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 22 through 26 removed outlier: 3.522A pdb=" N THR A 25 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 35 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 128 removed outlier: 8.054A pdb=" N ALA C 437 " --> pdb=" O ARG A 475 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR A 477 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N VAL C 439 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N THR A 479 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER C 413 " --> pdb=" O ASN C 438 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA C 259 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE C 416 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE C 261 " --> pdb=" O PHE C 416 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N THR C 260 " --> pdb=" O PHE C 294 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS C 296 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE C 262 " --> pdb=" O HIS C 296 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE C 370 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 206 removed outlier: 6.570A pdb=" N VAL A 144 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY A 231 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.668A pdb=" N ILE A 370 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR A 260 " --> pdb=" O PHE A 294 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N HIS A 296 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N ILE A 262 " --> pdb=" O HIS A 296 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA A 259 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE A 416 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE A 261 " --> pdb=" O PHE A 416 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 413 " --> pdb=" O ASN A 438 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 479 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 26 removed outlier: 3.522A pdb=" N THR B 25 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA B 35 " --> pdb=" O THR B 25 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 124 through 128 removed outlier: 8.128A pdb=" N ALA D 437 " --> pdb=" O ARG B 475 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR B 477 " --> pdb=" O ALA D 437 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL D 439 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N THR B 479 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N SER D 413 " --> pdb=" O ASN D 438 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 259 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N PHE D 416 " --> pdb=" O ALA D 259 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE D 261 " --> pdb=" O PHE D 416 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR D 260 " --> pdb=" O PHE D 294 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS D 296 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE D 262 " --> pdb=" O HIS D 296 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 370 " --> pdb=" O LEU D 353 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 205 through 206 removed outlier: 6.571A pdb=" N VAL B 144 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 231 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.667A pdb=" N ILE B 370 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N THR B 260 " --> pdb=" O PHE B 294 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N HIS B 296 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N ILE B 262 " --> pdb=" O HIS B 296 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 259 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE B 416 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE B 261 " --> pdb=" O PHE B 416 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER B 413 " --> pdb=" O ASN B 438 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR D 479 " --> pdb=" O ALA B 437 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 26 removed outlier: 3.521A pdb=" N THR C 25 " --> pdb=" O ALA C 35 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA C 35 " --> pdb=" O THR C 25 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 205 through 206 removed outlier: 6.570A pdb=" N VAL C 144 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY C 231 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.522A pdb=" N THR D 25 " --> pdb=" O ALA D 35 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA D 35 " --> pdb=" O THR D 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 206 removed outlier: 6.571A pdb=" N VAL D 144 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 231 " --> pdb=" O GLU D 253 " (cutoff:3.500A) 750 hydrogen bonds defined for protein. 2106 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: 2.77 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5004 1.34 - 1.46: 2997 1.46 - 1.58: 7007 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 15128 Sorted by residual: bond pdb=" CA THR A 282 " pdb=" CB THR A 282 " ideal model delta sigma weight residual 1.529 1.544 -0.015 1.62e-02 3.81e+03 8.24e-01 bond pdb=" CA THR D 282 " pdb=" CB THR D 282 " ideal model delta sigma weight residual 1.529 1.544 -0.015 1.62e-02 3.81e+03 8.24e-01 bond pdb=" CA THR B 282 " pdb=" CB THR B 282 " ideal model delta sigma weight residual 1.529 1.544 -0.015 1.62e-02 3.81e+03 8.24e-01 bond pdb=" CA THR C 282 " pdb=" CB THR C 282 " ideal model delta sigma weight residual 1.529 1.543 -0.014 1.62e-02 3.81e+03 7.99e-01 bond pdb=" CA THR A 282 " pdb=" C THR A 282 " ideal model delta sigma weight residual 1.526 1.537 -0.011 1.29e-02 6.01e+03 7.71e-01 ... (remaining 15123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 20271 1.28 - 2.56: 187 2.56 - 3.84: 53 3.84 - 5.12: 8 5.12 - 6.40: 12 Bond angle restraints: 20531 Sorted by residual: angle pdb=" OG1 THR D 282 " pdb=" CB THR D 282 " pdb=" CG2 THR D 282 " ideal model delta sigma weight residual 109.30 103.78 5.52 2.00e+00 2.50e-01 7.61e+00 angle pdb=" OG1 THR A 282 " pdb=" CB THR A 282 " pdb=" CG2 THR A 282 " ideal model delta sigma weight residual 109.30 103.82 5.48 2.00e+00 2.50e-01 7.52e+00 angle pdb=" OG1 THR C 282 " pdb=" CB THR C 282 " pdb=" CG2 THR C 282 " ideal model delta sigma weight residual 109.30 103.83 5.47 2.00e+00 2.50e-01 7.49e+00 angle pdb=" OG1 THR B 282 " pdb=" CB THR B 282 " pdb=" CG2 THR B 282 " ideal model delta sigma weight residual 109.30 103.84 5.46 2.00e+00 2.50e-01 7.46e+00 angle pdb=" CA LEU D 320 " pdb=" CB LEU D 320 " pdb=" CG LEU D 320 " ideal model delta sigma weight residual 116.30 122.70 -6.40 3.50e+00 8.16e-02 3.34e+00 ... (remaining 20526 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 7904 16.93 - 33.85: 811 33.85 - 50.78: 265 50.78 - 67.70: 45 67.70 - 84.63: 12 Dihedral angle restraints: 9037 sinusoidal: 3401 harmonic: 5636 Sorted by residual: dihedral pdb=" CB GLU B 372 " pdb=" CG GLU B 372 " pdb=" CD GLU B 372 " pdb=" OE1 GLU B 372 " ideal model delta sinusoidal sigma weight residual 0.00 -84.63 84.63 1 3.00e+01 1.11e-03 9.67e+00 dihedral pdb=" CB GLU C 372 " pdb=" CG GLU C 372 " pdb=" CD GLU C 372 " pdb=" OE1 GLU C 372 " ideal model delta sinusoidal sigma weight residual 0.00 -84.63 84.63 1 3.00e+01 1.11e-03 9.67e+00 dihedral pdb=" CB GLU D 372 " pdb=" CG GLU D 372 " pdb=" CD GLU D 372 " pdb=" OE1 GLU D 372 " ideal model delta sinusoidal sigma weight residual 0.00 -84.62 84.62 1 3.00e+01 1.11e-03 9.67e+00 ... (remaining 9034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1416 0.026 - 0.052: 574 0.052 - 0.078: 217 0.078 - 0.104: 85 0.104 - 0.130: 80 Chirality restraints: 2372 Sorted by residual: chirality pdb=" CB THR D 282 " pdb=" CA THR D 282 " pdb=" OG1 THR D 282 " pdb=" CG2 THR D 282 " both_signs ideal model delta sigma weight residual False 2.55 2.68 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CB THR A 282 " pdb=" CA THR A 282 " pdb=" OG1 THR A 282 " pdb=" CG2 THR A 282 " both_signs ideal model delta sigma weight residual False 2.55 2.68 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CB THR B 282 " pdb=" CA THR B 282 " pdb=" OG1 THR B 282 " pdb=" CG2 THR B 282 " both_signs ideal model delta sigma weight residual False 2.55 2.68 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 2369 not shown) Planarity restraints: 2675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 75 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" CG ASP C 75 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP C 75 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP C 75 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 75 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" CG ASP A 75 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASP A 75 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP A 75 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 75 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.52e+00 pdb=" CG ASP B 75 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP B 75 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 75 " -0.010 2.00e-02 2.50e+03 ... (remaining 2672 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 10124 3.09 - 3.54: 15588 3.54 - 4.00: 23002 4.00 - 4.45: 29031 4.45 - 4.90: 44469 Nonbonded interactions: 122214 Sorted by model distance: nonbonded pdb=" N THR C 43 " pdb=" OG1 THR C 43 " model vdw 2.639 2.496 nonbonded pdb=" N THR A 43 " pdb=" OG1 THR A 43 " model vdw 2.639 2.496 nonbonded pdb=" N THR B 43 " pdb=" OG1 THR B 43 " model vdw 2.639 2.496 nonbonded pdb=" N THR D 43 " pdb=" OG1 THR D 43 " model vdw 2.639 2.496 nonbonded pdb=" O GLY C 465 " pdb=" OG SER C 466 " model vdw 2.648 3.040 ... (remaining 122209 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' selection = (chain 'B' and (resid 2 through 304 or (resid 305 and (name N or name CA or name \ C or name O or name CB )) or resid 306 through 496)) selection = (chain 'C' and (resid 2 through 304 or (resid 305 and (name N or name CA or name \ C or name O or name CB )) or resid 306 through 496)) selection = (chain 'D' and (resid 2 through 304 or (resid 305 and (name N or name CA or name \ C or name O or name CB )) or resid 306 through 496)) } 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.020 Find NCS groups from input model: 0.260 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 : 0.002 0.019 15128 Z= 0.084 Angle : 0.404 6.399 20531 Z= 0.218 Chirality : 0.040 0.130 2372 Planarity : 0.003 0.029 2675 Dihedral : 15.573 84.629 5421 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.51 % Allowed : 19.49 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.20), residues: 1972 helix: 2.55 (0.19), residues: 776 sheet: 1.21 (0.29), residues: 352 loop : -0.03 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 38 TYR 0.007 0.001 TYR A 311 PHE 0.006 0.001 PHE D 394 TRP 0.014 0.001 TRP B 158 HIS 0.003 0.000 HIS C 457 Details of bonding type rmsd covalent geometry : bond 0.00155 (15128) covalent geometry : angle 0.40352 (20531) hydrogen bonds : bond 0.15845 ( 750) hydrogen bonds : angle 5.64224 ( 2106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 229 time to evaluate : 0.578 Fit side-chains REVERT: A 38 ARG cc_start: 0.6927 (ttt90) cc_final: 0.6416 (tpp-160) REVERT: A 307 MET cc_start: 0.7327 (mmm) cc_final: 0.7125 (mmm) REVERT: A 337 ASN cc_start: 0.7841 (t0) cc_final: 0.7391 (t0) REVERT: A 382 GLU cc_start: 0.7682 (tt0) cc_final: 0.7253 (tt0) REVERT: A 407 VAL cc_start: 0.8870 (t) cc_final: 0.8640 (m) REVERT: B 38 ARG cc_start: 0.6885 (ttt90) cc_final: 0.6311 (tpp-160) REVERT: B 307 MET cc_start: 0.7420 (mmm) cc_final: 0.7180 (mmm) REVERT: B 337 ASN cc_start: 0.7860 (t0) cc_final: 0.7410 (t0) REVERT: B 382 GLU cc_start: 0.7681 (tt0) cc_final: 0.7355 (tt0) REVERT: B 383 GLU cc_start: 0.6733 (pt0) cc_final: 0.6200 (mt-10) REVERT: B 407 VAL cc_start: 0.8822 (t) cc_final: 0.8581 (m) REVERT: C 38 ARG cc_start: 0.6951 (ttt90) cc_final: 0.6389 (ttm-80) REVERT: C 45 MET cc_start: 0.7026 (tpp) cc_final: 0.6800 (ttm) REVERT: C 337 ASN cc_start: 0.7922 (t0) cc_final: 0.7479 (t0) REVERT: C 382 GLU cc_start: 0.7658 (tt0) cc_final: 0.7335 (tt0) REVERT: C 407 VAL cc_start: 0.8838 (t) cc_final: 0.8612 (m) REVERT: D 38 ARG cc_start: 0.6928 (ttt90) cc_final: 0.6319 (tpp-160) REVERT: D 307 MET cc_start: 0.7255 (mmm) cc_final: 0.7028 (mmm) REVERT: D 337 ASN cc_start: 0.7914 (t0) cc_final: 0.7470 (t0) REVERT: D 382 GLU cc_start: 0.7719 (tt0) cc_final: 0.7353 (tt0) outliers start: 8 outliers final: 7 residues processed: 234 average time/residue: 0.1236 time to fit residues: 43.7861 Evaluate side-chains 215 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 208 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 THR Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 486 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.0870 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 131 HIS A 258 ASN B 131 HIS B 242 GLN B 258 ASN C 189 ASN C 242 GLN C 258 ASN C 322 GLN D 131 HIS D 242 GLN D 258 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.159691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142833 restraints weight = 16241.237| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.60 r_work: 0.3484 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15128 Z= 0.169 Angle : 0.478 6.237 20531 Z= 0.255 Chirality : 0.043 0.138 2372 Planarity : 0.004 0.031 2675 Dihedral : 3.975 18.752 2101 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.51 % Allowed : 18.46 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.19), residues: 1972 helix: 2.13 (0.19), residues: 788 sheet: 0.53 (0.26), residues: 404 loop : -0.11 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 38 TYR 0.009 0.001 TYR B 311 PHE 0.009 0.002 PHE B 452 TRP 0.013 0.001 TRP D 158 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00408 (15128) covalent geometry : angle 0.47838 (20531) hydrogen bonds : bond 0.04420 ( 750) hydrogen bonds : angle 4.53930 ( 2106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 0.559 Fit side-chains REVERT: A 38 ARG cc_start: 0.7082 (ttt90) cc_final: 0.6585 (tpp-160) REVERT: A 263 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.8102 (m-30) REVERT: A 382 GLU cc_start: 0.7611 (tt0) cc_final: 0.7142 (tt0) REVERT: A 407 VAL cc_start: 0.9013 (t) cc_final: 0.8750 (m) REVERT: B 382 GLU cc_start: 0.7524 (tt0) cc_final: 0.7207 (tt0) REVERT: C 380 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7883 (m) REVERT: C 382 GLU cc_start: 0.7541 (tt0) cc_final: 0.7201 (tt0) REVERT: D 380 VAL cc_start: 0.8346 (OUTLIER) cc_final: 0.7918 (m) outliers start: 39 outliers final: 29 residues processed: 232 average time/residue: 0.1160 time to fit residues: 40.5223 Evaluate side-chains 218 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 258 ASN Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 258 ASN Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 258 ASN Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 10 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 158 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 129 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 ASN A 242 GLN B 131 HIS C 131 HIS D 131 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.158131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.140735 restraints weight = 16403.037| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.64 r_work: 0.3347 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15128 Z= 0.133 Angle : 0.441 5.675 20531 Z= 0.237 Chirality : 0.042 0.130 2372 Planarity : 0.004 0.032 2675 Dihedral : 3.801 16.415 2088 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.70 % Allowed : 18.78 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 1972 helix: 2.13 (0.19), residues: 788 sheet: 0.54 (0.25), residues: 404 loop : -0.20 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 38 TYR 0.008 0.001 TYR D 311 PHE 0.008 0.001 PHE D 394 TRP 0.015 0.001 TRP D 158 HIS 0.003 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00314 (15128) covalent geometry : angle 0.44123 (20531) hydrogen bonds : bond 0.03956 ( 750) hydrogen bonds : angle 4.30728 ( 2106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 189 time to evaluate : 0.614 Fit side-chains REVERT: A 38 ARG cc_start: 0.7140 (ttt90) cc_final: 0.6560 (tpp-160) REVERT: A 382 GLU cc_start: 0.7544 (tt0) cc_final: 0.7159 (tt0) REVERT: A 407 VAL cc_start: 0.8991 (t) cc_final: 0.8726 (m) REVERT: B 38 ARG cc_start: 0.7131 (ttt90) cc_final: 0.6541 (tpp-160) REVERT: B 382 GLU cc_start: 0.7522 (tt0) cc_final: 0.7166 (tt0) REVERT: C 38 ARG cc_start: 0.7139 (ttt90) cc_final: 0.6562 (ttm-80) REVERT: C 380 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.7829 (m) REVERT: D 263 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8050 (m-30) outliers start: 42 outliers final: 30 residues processed: 219 average time/residue: 0.1193 time to fit residues: 39.8018 Evaluate side-chains 217 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 429 SER Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 380 VAL Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 430 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 194 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 79 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 HIS D 131 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.142755 restraints weight = 16342.269| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 1.61 r_work: 0.3448 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15128 Z= 0.129 Angle : 0.433 5.468 20531 Z= 0.232 Chirality : 0.042 0.129 2372 Planarity : 0.004 0.032 2675 Dihedral : 3.798 16.765 2088 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.77 % Allowed : 17.62 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.19), residues: 1972 helix: 2.17 (0.19), residues: 788 sheet: 0.53 (0.25), residues: 404 loop : -0.23 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.008 0.001 TYR B 311 PHE 0.009 0.001 PHE C 394 TRP 0.015 0.001 TRP D 158 HIS 0.003 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00304 (15128) covalent geometry : angle 0.43326 (20531) hydrogen bonds : bond 0.03802 ( 750) hydrogen bonds : angle 4.18487 ( 2106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.564 Fit side-chains REVERT: A 38 ARG cc_start: 0.7093 (ttt90) cc_final: 0.6552 (tpp-160) REVERT: B 38 ARG cc_start: 0.7077 (ttt90) cc_final: 0.6514 (tpp-160) REVERT: B 382 GLU cc_start: 0.7483 (tt0) cc_final: 0.6777 (tt0) REVERT: C 38 ARG cc_start: 0.7062 (ttt90) cc_final: 0.6524 (ttm-80) REVERT: D 120 MET cc_start: 0.8253 (mtp) cc_final: 0.7974 (mtt) REVERT: D 380 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.7809 (m) outliers start: 43 outliers final: 35 residues processed: 236 average time/residue: 0.1178 time to fit residues: 42.2156 Evaluate side-chains 221 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain A residue 429 SER Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 38 optimal weight: 0.0980 chunk 16 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 0.1980 chunk 152 optimal weight: 6.9990 chunk 81 optimal weight: 0.0870 chunk 117 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 133 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 overall best weight: 0.4560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 HIS B 220 ASN B 495 ASN C 131 HIS C 457 HIS C 495 ASN D 131 HIS D 258 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.164383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.146114 restraints weight = 16371.657| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 1.84 r_work: 0.3488 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 15128 Z= 0.082 Angle : 0.398 7.669 20531 Z= 0.211 Chirality : 0.040 0.127 2372 Planarity : 0.003 0.032 2675 Dihedral : 3.530 15.820 2088 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.67 % Allowed : 18.97 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 1972 helix: 2.46 (0.19), residues: 788 sheet: 0.61 (0.25), residues: 404 loop : -0.11 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.009 0.001 TYR B 311 PHE 0.007 0.001 PHE D 394 TRP 0.017 0.001 TRP D 158 HIS 0.002 0.000 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00170 (15128) covalent geometry : angle 0.39839 (20531) hydrogen bonds : bond 0.02995 ( 750) hydrogen bonds : angle 3.89579 ( 2106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.695 Fit side-chains REVERT: A 24 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: A 38 ARG cc_start: 0.6926 (ttt90) cc_final: 0.6442 (ttm-80) REVERT: A 382 GLU cc_start: 0.7323 (tt0) cc_final: 0.6682 (tt0) REVERT: B 24 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7217 (mp0) REVERT: B 38 ARG cc_start: 0.6950 (ttt90) cc_final: 0.6439 (ttm-80) REVERT: B 382 GLU cc_start: 0.7291 (tt0) cc_final: 0.6516 (tt0) REVERT: C 38 ARG cc_start: 0.6933 (ttt90) cc_final: 0.6424 (ttm-80) REVERT: C 135 MET cc_start: 0.8166 (mtt) cc_final: 0.7777 (mtt) REVERT: C 295 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7643 (mt) REVERT: C 324 ASN cc_start: 0.7735 (m-40) cc_final: 0.7459 (m-40) REVERT: C 382 GLU cc_start: 0.7309 (tt0) cc_final: 0.6548 (tt0) REVERT: D 38 ARG cc_start: 0.6975 (ttt90) cc_final: 0.6411 (ttm-80) REVERT: D 120 MET cc_start: 0.8222 (mtp) cc_final: 0.7922 (mtt) REVERT: D 380 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7743 (m) REVERT: D 382 GLU cc_start: 0.7325 (tt0) cc_final: 0.6535 (tt0) outliers start: 26 outliers final: 18 residues processed: 210 average time/residue: 0.1248 time to fit residues: 39.8381 Evaluate side-chains 205 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 380 VAL Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 186 optimal weight: 0.9990 chunk 44 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 109 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS C 131 HIS C 495 ASN D 131 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.159139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142599 restraints weight = 16319.507| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 1.58 r_work: 0.3450 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15128 Z= 0.138 Angle : 0.445 7.592 20531 Z= 0.236 Chirality : 0.042 0.129 2372 Planarity : 0.003 0.032 2675 Dihedral : 3.779 16.761 2088 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.12 % Allowed : 19.04 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 1972 helix: 2.24 (0.19), residues: 788 sheet: 0.61 (0.25), residues: 404 loop : -0.21 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 134 TYR 0.008 0.001 TYR D 311 PHE 0.008 0.001 PHE A 394 TRP 0.013 0.001 TRP D 158 HIS 0.004 0.001 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00327 (15128) covalent geometry : angle 0.44517 (20531) hydrogen bonds : bond 0.03794 ( 750) hydrogen bonds : angle 4.05181 ( 2106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 182 time to evaluate : 0.603 Fit side-chains REVERT: A 24 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 38 ARG cc_start: 0.7035 (ttt90) cc_final: 0.6548 (ttm-80) REVERT: A 382 GLU cc_start: 0.7509 (tt0) cc_final: 0.6790 (tt0) REVERT: B 24 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7327 (mp0) REVERT: B 38 ARG cc_start: 0.7070 (ttt90) cc_final: 0.6574 (ttm-80) REVERT: B 324 ASN cc_start: 0.7828 (m-40) cc_final: 0.7614 (m-40) REVERT: B 382 GLU cc_start: 0.7499 (tt0) cc_final: 0.6786 (tt0) REVERT: C 38 ARG cc_start: 0.7012 (ttt90) cc_final: 0.6553 (ttm-80) REVERT: C 295 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8060 (mt) REVERT: C 382 GLU cc_start: 0.7534 (tt0) cc_final: 0.6833 (tt0) REVERT: D 38 ARG cc_start: 0.7085 (ttt90) cc_final: 0.6580 (ttm-80) REVERT: D 382 GLU cc_start: 0.7521 (tt0) cc_final: 0.6790 (tt0) outliers start: 33 outliers final: 24 residues processed: 209 average time/residue: 0.1304 time to fit residues: 40.3892 Evaluate side-chains 208 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 195 optimal weight: 0.0980 chunk 126 optimal weight: 0.1980 chunk 89 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 131 HIS C 220 ASN C 495 ASN D 131 HIS D 220 ASN D 324 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.158521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139756 restraints weight = 16307.335| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.89 r_work: 0.3461 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15128 Z= 0.090 Angle : 0.401 7.029 20531 Z= 0.213 Chirality : 0.041 0.127 2372 Planarity : 0.003 0.039 2675 Dihedral : 3.599 16.212 2088 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.74 % Allowed : 19.81 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.19), residues: 1972 helix: 2.43 (0.19), residues: 788 sheet: 0.69 (0.25), residues: 424 loop : -0.17 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.009 0.001 TYR C 311 PHE 0.007 0.001 PHE D 394 TRP 0.017 0.001 TRP D 158 HIS 0.002 0.000 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00193 (15128) covalent geometry : angle 0.40063 (20531) hydrogen bonds : bond 0.03131 ( 750) hydrogen bonds : angle 3.86785 ( 2106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 187 time to evaluate : 0.591 Fit side-chains REVERT: A 24 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 38 ARG cc_start: 0.6997 (ttt90) cc_final: 0.6530 (ttm-80) REVERT: A 120 MET cc_start: 0.8233 (mtp) cc_final: 0.7928 (mtt) REVERT: A 382 GLU cc_start: 0.7368 (tt0) cc_final: 0.6603 (tt0) REVERT: B 24 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: B 38 ARG cc_start: 0.7003 (ttt90) cc_final: 0.6495 (ttm-80) REVERT: B 382 GLU cc_start: 0.7368 (tt0) cc_final: 0.6621 (tt0) REVERT: C 38 ARG cc_start: 0.7024 (ttt90) cc_final: 0.6514 (ttm-80) REVERT: C 120 MET cc_start: 0.8273 (mtp) cc_final: 0.7986 (mtt) REVERT: C 295 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7710 (mt) REVERT: C 382 GLU cc_start: 0.7433 (tt0) cc_final: 0.6692 (tt0) REVERT: D 38 ARG cc_start: 0.7047 (ttt90) cc_final: 0.6510 (ttm-80) REVERT: D 382 GLU cc_start: 0.7414 (tt0) cc_final: 0.6632 (tt0) outliers start: 27 outliers final: 22 residues processed: 208 average time/residue: 0.1213 time to fit residues: 38.4271 Evaluate side-chains 205 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 180 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 188 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 37 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 177 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 HIS C 495 ASN D 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.158176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141647 restraints weight = 16284.540| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.58 r_work: 0.3318 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15128 Z= 0.150 Angle : 0.457 7.447 20531 Z= 0.242 Chirality : 0.042 0.129 2372 Planarity : 0.004 0.036 2675 Dihedral : 3.841 17.137 2088 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.32 % Allowed : 19.55 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 1972 helix: 2.16 (0.19), residues: 792 sheet: 0.58 (0.25), residues: 424 loop : -0.25 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 223 TYR 0.009 0.001 TYR D 311 PHE 0.008 0.001 PHE C 394 TRP 0.012 0.001 TRP A 158 HIS 0.004 0.001 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00362 (15128) covalent geometry : angle 0.45732 (20531) hydrogen bonds : bond 0.03913 ( 750) hydrogen bonds : angle 4.05859 ( 2106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.689 Fit side-chains REVERT: A 24 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: A 38 ARG cc_start: 0.7054 (ttt90) cc_final: 0.6593 (ttm-80) REVERT: A 120 MET cc_start: 0.8257 (mtp) cc_final: 0.7970 (mtt) REVERT: B 24 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: B 38 ARG cc_start: 0.7072 (ttt90) cc_final: 0.6583 (ttm-80) REVERT: B 382 GLU cc_start: 0.7524 (tt0) cc_final: 0.6754 (tt0) REVERT: C 38 ARG cc_start: 0.7047 (ttt90) cc_final: 0.6586 (ttm-80) REVERT: C 120 MET cc_start: 0.8292 (mtp) cc_final: 0.8025 (mtt) REVERT: C 295 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8057 (mt) REVERT: C 382 GLU cc_start: 0.7557 (tt0) cc_final: 0.6808 (tt0) REVERT: D 38 ARG cc_start: 0.7079 (ttt90) cc_final: 0.6564 (ttm-80) REVERT: D 382 GLU cc_start: 0.7533 (tt0) cc_final: 0.6772 (tt0) outliers start: 36 outliers final: 33 residues processed: 212 average time/residue: 0.1265 time to fit residues: 40.1660 Evaluate side-chains 217 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 181 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 40 optimal weight: 0.1980 chunk 175 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 495 ASN D 131 HIS ** D 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.159931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.143575 restraints weight = 16396.895| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.58 r_work: 0.3384 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15128 Z= 0.108 Angle : 0.421 7.022 20531 Z= 0.224 Chirality : 0.041 0.127 2372 Planarity : 0.004 0.038 2675 Dihedral : 3.739 16.852 2088 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.12 % Allowed : 19.87 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1972 helix: 2.28 (0.19), residues: 792 sheet: 0.62 (0.25), residues: 424 loop : -0.24 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 286 TYR 0.010 0.001 TYR C 311 PHE 0.008 0.001 PHE A 394 TRP 0.015 0.001 TRP D 158 HIS 0.004 0.000 HIS D 457 Details of bonding type rmsd covalent geometry : bond 0.00248 (15128) covalent geometry : angle 0.42104 (20531) hydrogen bonds : bond 0.03426 ( 750) hydrogen bonds : angle 3.94040 ( 2106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 183 time to evaluate : 0.704 Fit side-chains REVERT: A 24 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7341 (mp0) REVERT: A 38 ARG cc_start: 0.7073 (ttt90) cc_final: 0.6646 (ttm-80) REVERT: A 322 GLN cc_start: 0.8410 (mt0) cc_final: 0.8143 (mt0) REVERT: A 382 GLU cc_start: 0.7544 (tt0) cc_final: 0.6810 (tt0) REVERT: B 24 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 38 ARG cc_start: 0.7099 (ttt90) cc_final: 0.6648 (ttm-80) REVERT: B 382 GLU cc_start: 0.7524 (tt0) cc_final: 0.6801 (tt0) REVERT: C 38 ARG cc_start: 0.7085 (ttt90) cc_final: 0.6642 (ttm-80) REVERT: C 120 MET cc_start: 0.8256 (mtp) cc_final: 0.7982 (mtt) REVERT: C 295 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8025 (mt) REVERT: C 382 GLU cc_start: 0.7562 (tt0) cc_final: 0.6846 (tt0) REVERT: D 38 ARG cc_start: 0.7098 (ttt90) cc_final: 0.6615 (ttm-80) REVERT: D 135 MET cc_start: 0.8381 (mtt) cc_final: 0.8073 (mtt) REVERT: D 382 GLU cc_start: 0.7554 (tt0) cc_final: 0.6881 (tt0) outliers start: 33 outliers final: 29 residues processed: 212 average time/residue: 0.1235 time to fit residues: 39.8902 Evaluate side-chains 212 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 136 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 52 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 99 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 ASN C 131 HIS C 495 ASN D 131 HIS D 324 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.159231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.142716 restraints weight = 16343.307| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 1.60 r_work: 0.3427 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15128 Z= 0.121 Angle : 0.433 7.277 20531 Z= 0.230 Chirality : 0.041 0.127 2372 Planarity : 0.004 0.037 2675 Dihedral : 3.795 16.922 2088 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.25 % Allowed : 19.94 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 1972 helix: 2.22 (0.19), residues: 792 sheet: 0.66 (0.25), residues: 424 loop : -0.28 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 134 TYR 0.011 0.001 TYR C 311 PHE 0.009 0.001 PHE A 394 TRP 0.014 0.001 TRP D 158 HIS 0.003 0.000 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00283 (15128) covalent geometry : angle 0.43333 (20531) hydrogen bonds : bond 0.03582 ( 750) hydrogen bonds : angle 3.96755 ( 2106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3944 Ramachandran restraints generated. 1972 Oldfield, 0 Emsley, 1972 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.609 Fit side-chains REVERT: A 24 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: A 38 ARG cc_start: 0.7038 (ttt90) cc_final: 0.6588 (ttm-80) REVERT: A 382 GLU cc_start: 0.7547 (tt0) cc_final: 0.6851 (tt0) REVERT: B 24 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: B 38 ARG cc_start: 0.7060 (ttt90) cc_final: 0.6589 (ttm-80) REVERT: B 382 GLU cc_start: 0.7533 (tt0) cc_final: 0.6831 (tt0) REVERT: C 38 ARG cc_start: 0.7045 (ttt90) cc_final: 0.6584 (ttm-80) REVERT: C 295 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8019 (mt) REVERT: C 382 GLU cc_start: 0.7577 (tt0) cc_final: 0.6894 (tt0) REVERT: D 38 ARG cc_start: 0.7083 (ttt90) cc_final: 0.6594 (ttm-80) REVERT: D 135 MET cc_start: 0.8381 (mtt) cc_final: 0.8100 (mtt) REVERT: D 382 GLU cc_start: 0.7555 (tt0) cc_final: 0.6866 (tt0) outliers start: 35 outliers final: 32 residues processed: 211 average time/residue: 0.1249 time to fit residues: 39.7442 Evaluate side-chains 214 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLU Chi-restraints excluded: chain A residue 90 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 418 ASP Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 90 SER Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 288 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 354 THR Chi-restraints excluded: chain B residue 418 ASP Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 354 THR Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain D residue 418 ASP Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 183 optimal weight: 0.0980 chunk 136 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 133 optimal weight: 0.6980 chunk 165 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 HIS C 495 ASN D 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.162139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.145882 restraints weight = 16327.455| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.58 r_work: 0.3489 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 15128 Z= 0.089 Angle : 0.401 6.661 20531 Z= 0.214 Chirality : 0.041 0.126 2372 Planarity : 0.003 0.033 2675 Dihedral : 3.607 16.029 2088 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.74 % Allowed : 20.19 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.19), residues: 1972 helix: 2.42 (0.19), residues: 792 sheet: 0.76 (0.26), residues: 424 loop : -0.21 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 38 TYR 0.011 0.001 TYR C 311 PHE 0.007 0.001 PHE A 394 TRP 0.017 0.001 TRP D 158 HIS 0.002 0.000 HIS B 457 Details of bonding type rmsd covalent geometry : bond 0.00195 (15128) covalent geometry : angle 0.40139 (20531) hydrogen bonds : bond 0.03067 ( 750) hydrogen bonds : angle 3.81576 ( 2106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.40 seconds wall clock time: 62 minutes 50.24 seconds (3770.24 seconds total)