Starting phenix.real_space_refine on Fri Sep 11 17:46:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.cif" model { file = "/net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3q_10094/09_2026/6s3q_10094.map" } resolution = 3.34 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 69 5.16 5 C 6816 2.51 5 N 1563 2.21 5 O 1827 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3241 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3241 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "C" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3241 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 417} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {'7O9': 1, 'PC1': 5, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {'7O9': 1, 'PC1': 5, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 189 Unusual residues: {'7O9': 1, 'PC1': 5, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 175 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PC1:plan-2': 2, 'PC1:plan-1': 1} Unresolved non-hydrogen planarities: 11 Time building chain proxies: 2.55, per 1000 atoms: 0.25 Number of scatterers: 10290 At special positions: 0 Unit cell: (116.202, 117.288, 89.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 6 15.00 F 9 9.00 O 1827 8.00 N 1563 7.00 C 6816 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: 0.83 Conformation dependent library (CDL) restraints added in 344.4 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 76.3% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 11 through 18 Processing helix chain 'A' and resid 19 through 40 Processing helix chain 'A' and resid 54 through 66 removed outlier: 3.828A pdb=" N LYS A 64 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 4.091A pdb=" N MET A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 117 removed outlier: 4.002A pdb=" N VAL A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 148 removed outlier: 4.028A pdb=" N ALA A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 229 Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.948A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 4.073A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 297 Processing helix chain 'A' and resid 300 through 310 Processing helix chain 'A' and resid 312 through 318 removed outlier: 3.603A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.569A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 359 " --> pdb=" O THR A 355 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.630A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 removed outlier: 3.558A pdb=" N ALA A 371 " --> pdb=" O MET A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 403 removed outlier: 3.547A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 425 removed outlier: 3.618A pdb=" N LEU A 423 " --> pdb=" O MET A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.878A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 433 through 441 removed outlier: 4.387A pdb=" N VAL A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 466 removed outlier: 3.855A pdb=" N THR A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A 463 " --> pdb=" O THR A 459 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 464 " --> pdb=" O GLY A 460 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A 465 " --> pdb=" O ILE A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 476 removed outlier: 3.893A pdb=" N GLU A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 18 Processing helix chain 'B' and resid 19 through 40 Processing helix chain 'B' and resid 54 through 66 removed outlier: 3.828A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 86 removed outlier: 4.092A pdb=" N MET B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 117 removed outlier: 4.002A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 148 removed outlier: 4.028A pdb=" N ALA B 141 " --> pdb=" O SER B 137 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 229 Processing helix chain 'B' and resid 233 through 270 removed outlier: 3.948A pdb=" N VAL B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Proline residue: B 259 - end of helix removed outlier: 4.072A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 297 Processing helix chain 'B' and resid 300 through 310 Processing helix chain 'B' and resid 312 through 318 removed outlier: 3.603A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.569A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.631A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.558A pdb=" N ALA B 371 " --> pdb=" O MET B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 403 removed outlier: 3.547A pdb=" N ILE B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 425 removed outlier: 3.618A pdb=" N LEU B 423 " --> pdb=" O MET B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.876A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 433 through 441 removed outlier: 4.386A pdb=" N VAL B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP B 441 " --> pdb=" O ILE B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 466 removed outlier: 3.854A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU B 465 " --> pdb=" O ILE B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 3.894A pdb=" N GLU B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 18 Processing helix chain 'C' and resid 19 through 40 Processing helix chain 'C' and resid 54 through 66 removed outlier: 3.828A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 4.092A pdb=" N MET C 75 " --> pdb=" O ILE C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 117 removed outlier: 4.002A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 148 removed outlier: 4.028A pdb=" N ALA C 141 " --> pdb=" O SER C 137 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 229 Processing helix chain 'C' and resid 233 through 270 removed outlier: 3.948A pdb=" N VAL C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 250 " --> pdb=" O ALA C 246 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 4.072A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 297 Processing helix chain 'C' and resid 300 through 310 Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.603A pdb=" N PHE C 316 " --> pdb=" O ASN C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 330 Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.568A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.630A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.557A pdb=" N ALA C 371 " --> pdb=" O MET C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 403 removed outlier: 3.548A pdb=" N ILE C 395 " --> pdb=" O ILE C 391 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N THR C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 425 removed outlier: 3.618A pdb=" N LEU C 423 " --> pdb=" O MET C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.877A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 441 removed outlier: 4.388A pdb=" N VAL C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TRP C 441 " --> pdb=" O ILE C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 443 through 466 removed outlier: 3.854A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU C 465 " --> pdb=" O ILE C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 476 removed outlier: 3.893A pdb=" N GLU C 471 " --> pdb=" O LYS C 467 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 168 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 168 Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 168 651 hydrogen bonds defined for protein. 1944 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: 1.42 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1656 1.32 - 1.44: 2361 1.44 - 1.56: 6273 1.56 - 1.68: 15 1.68 - 1.80: 123 Bond restraints: 10428 Sorted by residual: bond pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 1.205 1.341 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C21 PC1 C 506 " pdb=" O22 PC1 C 506 " ideal model delta sigma weight residual 1.205 1.341 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" C21 PC1 A 605 " pdb=" O22 PC1 A 605 " ideal model delta sigma weight residual 1.205 1.341 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C21 PC1 A 605 " pdb=" O21 PC1 A 605 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.00e-02 2.50e+03 4.25e+01 bond pdb=" C21 PC1 B 506 " pdb=" O21 PC1 B 506 " ideal model delta sigma weight residual 1.331 1.201 0.130 2.00e-02 2.50e+03 4.22e+01 ... (remaining 10423 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 13674 2.83 - 5.66: 360 5.66 - 8.49: 48 8.49 - 11.32: 0 11.32 - 14.15: 6 Bond angle restraints: 14088 Sorted by residual: angle pdb=" C22 PC1 A 605 " pdb=" C21 PC1 A 605 " pdb=" O22 PC1 A 605 " ideal model delta sigma weight residual 125.37 111.22 14.15 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C22 PC1 B 506 " pdb=" C21 PC1 B 506 " pdb=" O22 PC1 B 506 " ideal model delta sigma weight residual 125.37 111.23 14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C22 PC1 C 506 " pdb=" C21 PC1 C 506 " pdb=" O22 PC1 C 506 " ideal model delta sigma weight residual 125.37 111.24 14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C22 PC1 B 506 " pdb=" C21 PC1 B 506 " pdb=" O21 PC1 B 506 " ideal model delta sigma weight residual 111.12 124.87 -13.75 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C22 PC1 C 506 " pdb=" C21 PC1 C 506 " pdb=" O21 PC1 C 506 " ideal model delta sigma weight residual 111.12 124.83 -13.71 3.00e+00 1.11e-01 2.09e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5601 17.59 - 35.17: 507 35.17 - 52.76: 78 52.76 - 70.35: 15 70.35 - 87.94: 6 Dihedral angle restraints: 6207 sinusoidal: 2502 harmonic: 3705 Sorted by residual: dihedral pdb=" CA ILE B 391 " pdb=" C ILE B 391 " pdb=" N GLY B 392 " pdb=" CA GLY B 392 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLU B 48 " pdb=" C GLU B 48 " pdb=" N LYS B 49 " pdb=" CA LYS B 49 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA GLU C 48 " pdb=" C GLU C 48 " pdb=" N LYS C 49 " pdb=" CA LYS C 49 " ideal model delta harmonic sigma weight residual 180.00 162.99 17.01 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1161 0.054 - 0.107: 440 0.107 - 0.161: 123 0.161 - 0.214: 16 0.214 - 0.268: 6 Chirality restraints: 1746 Sorted by residual: chirality pdb=" C1 7O9 B 502 " pdb=" C 7O9 B 502 " pdb=" C2 7O9 B 502 " pdb=" N1 7O9 B 502 " both_signs ideal model delta sigma weight residual False 2.37 2.64 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 7O9 C 502 " pdb=" C 7O9 C 502 " pdb=" C2 7O9 C 502 " pdb=" N1 7O9 C 502 " both_signs ideal model delta sigma weight residual False 2.37 2.64 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C1 7O9 A 601 " pdb=" C 7O9 A 601 " pdb=" C2 7O9 A 601 " pdb=" N1 7O9 A 601 " both_signs ideal model delta sigma weight residual False 2.37 2.64 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 1743 not shown) Planarity restraints: 1677 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 275 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.00e+00 pdb=" CG ASP B 275 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP B 275 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP B 275 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 275 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.96e+00 pdb=" CG ASP A 275 " -0.039 2.00e-02 2.50e+03 pdb=" OD1 ASP A 275 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP A 275 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 275 " 0.011 2.00e-02 2.50e+03 2.21e-02 4.86e+00 pdb=" CG ASP C 275 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP C 275 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP C 275 " 0.013 2.00e-02 2.50e+03 ... (remaining 1674 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 3679 2.89 - 3.39: 9647 3.39 - 3.89: 15933 3.89 - 4.40: 18403 4.40 - 4.90: 32524 Nonbonded interactions: 80186 Sorted by model distance: nonbonded pdb=" NH1 ARG C 447 " pdb=" O2 7O9 C 502 " model vdw 2.383 3.120 nonbonded pdb=" NH1 ARG B 447 " pdb=" O2 7O9 B 502 " model vdw 2.383 3.120 nonbonded pdb=" NH1 ARG A 447 " pdb=" O2 7O9 A 601 " model vdw 2.384 3.120 nonbonded pdb=" O THR B 138 " pdb=" OG1 THR B 138 " model vdw 2.395 3.040 nonbonded pdb=" O THR A 138 " pdb=" OG1 THR A 138 " model vdw 2.395 3.040 ... (remaining 80181 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 476 or (resid 604 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name O21 or name O22)) or resid 605 or (resid 607 an \ d (name C1 or name C2 or name C3 or name C31 or name C32 or name C33 or name C34 \ or name C35 or name C36 or name C37 or name C38 or name C39 or name C3A or name \ C3B or name C3C or name O21 or name O31 or name O32)))) selection = (chain 'B' and (resid 10 through 476 or (resid 504 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name O21 or name O22)) or (resid 505 and (name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C2A or name C2B or name C2C or name C2D or name O21 or na \ me O22)) or resid 507)) selection = (chain 'C' and (resid 10 through 476 or (resid 504 and (name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C29 \ or name C2A or name C2B or name O21 or name O22)) or (resid 505 and (name C21 o \ r name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C \ 28 or name C29 or name C2A or name C2B or name C2C or name C2D or name O21 or na \ me O22)) or resid 507)) } 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: 0.460 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.410 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 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 : 0.012 0.136 10428 Z= 0.483 Angle : 1.105 14.154 14088 Z= 0.581 Chirality : 0.061 0.268 1746 Planarity : 0.007 0.050 1677 Dihedral : 13.971 87.937 3813 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer: Outliers : 0.57 % Allowed : 7.16 % Favored : 92.26 % 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: -4.53 (0.16), residues: 1272 helix: -2.83 (0.11), residues: 915 sheet: None (None), residues: 0 loop : -2.90 (0.26), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 310 TYR 0.028 0.003 TYR B 373 PHE 0.025 0.003 PHE A 159 TRP 0.009 0.002 TRP A 19 HIS 0.001 0.001 HIS C 296 Details of bonding type rmsd/Z covalent geometry : bond 0.01178 / 0.48 (10428) covalent geometry : angle 1.10505 / 0.58 (14088) hydrogen bonds : bond 0.15504 / 10.12 ( 651) hydrogen bonds : angle 6.74530 / 4.49 ( 1944) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.268 Fit side-chains REVERT: A 60 MET cc_start: 0.8678 (mmt) cc_final: 0.8206 (mmt) REVERT: A 232 LYS cc_start: 0.8310 (mtmt) cc_final: 0.7970 (mtmt) REVERT: A 255 MET cc_start: 0.8939 (mmt) cc_final: 0.8618 (mmt) REVERT: A 315 ARG cc_start: 0.7824 (mmt90) cc_final: 0.6839 (ttt90) REVERT: B 60 MET cc_start: 0.8727 (mmt) cc_final: 0.8393 (mmt) REVERT: B 315 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7011 (ttt90) REVERT: C 75 MET cc_start: 0.8841 (mmm) cc_final: 0.8477 (mmm) REVERT: C 90 ILE cc_start: 0.8899 (tt) cc_final: 0.8669 (tt) REVERT: C 232 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8076 (mtmt) REVERT: C 255 MET cc_start: 0.9045 (mmt) cc_final: 0.8716 (mmm) REVERT: C 315 ARG cc_start: 0.7789 (mmt90) cc_final: 0.7501 (mmt90) outliers start: 6 outliers final: 0 residues processed: 144 average time/residue: 0.0931 time to fit residues: 19.5180 Evaluate side-chains 112 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 322 GLN A 347 ASN A 366 ASN A 385 ASN A 413 GLN B 322 GLN B 366 ASN B 385 ASN B 413 GLN C 322 GLN C 366 ASN C 385 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.129272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.091356 restraints weight = 11560.592| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.61 r_work: 0.2687 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2548 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10428 Z= 0.130 Angle : 0.561 5.736 14088 Z= 0.295 Chirality : 0.039 0.146 1746 Planarity : 0.004 0.034 1677 Dihedral : 8.413 69.128 1650 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.48 % Allowed : 13.18 % Favored : 86.34 % 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: -1.53 (0.23), residues: 1272 helix: -0.50 (0.17), residues: 930 sheet: -2.34 (0.65), residues: 60 loop : -1.95 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.012 0.001 TYR A 257 PHE 0.019 0.001 PHE A 357 TRP 0.011 0.001 TRP C 441 HIS 0.000 0.000 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (10428) covalent geometry : angle 0.56069 / 0.30 (14088) hydrogen bonds : bond 0.05125 / 3.40 ( 651) hydrogen bonds : angle 4.85498 / 3.22 ( 1944) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 0.355 Fit side-chains REVERT: A 60 MET cc_start: 0.9093 (mmt) cc_final: 0.8769 (mmt) REVERT: A 232 LYS cc_start: 0.8831 (mtmt) cc_final: 0.8381 (mtmt) REVERT: A 315 ARG cc_start: 0.7771 (mmt90) cc_final: 0.6470 (ttt90) REVERT: A 359 LEU cc_start: 0.8757 (mt) cc_final: 0.8542 (mt) REVERT: B 60 MET cc_start: 0.9096 (mmt) cc_final: 0.8867 (mmt) REVERT: B 231 GLU cc_start: 0.8683 (tp30) cc_final: 0.8392 (tp30) REVERT: B 255 MET cc_start: 0.9004 (mmt) cc_final: 0.8423 (mmt) REVERT: B 315 ARG cc_start: 0.7984 (mmt90) cc_final: 0.6769 (ttt90) REVERT: C 90 ILE cc_start: 0.8777 (tt) cc_final: 0.8516 (tt) REVERT: C 231 GLU cc_start: 0.8679 (tp30) cc_final: 0.8278 (tp30) REVERT: C 232 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8517 (mtmt) REVERT: C 255 MET cc_start: 0.8974 (mmt) cc_final: 0.8680 (mmm) REVERT: C 286 MET cc_start: 0.7923 (mtm) cc_final: 0.7639 (mtp) REVERT: C 315 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7527 (mmt90) REVERT: C 449 MET cc_start: 0.8470 (ttp) cc_final: 0.8236 (ttp) outliers start: 5 outliers final: 5 residues processed: 141 average time/residue: 0.0791 time to fit residues: 17.1466 Evaluate side-chains 120 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 271 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.128864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.089995 restraints weight = 11678.443| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 1.67 r_work: 0.2660 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2520 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 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 : 0.003 0.029 10428 Z= 0.145 Angle : 0.552 5.606 14088 Z= 0.284 Chirality : 0.040 0.154 1746 Planarity : 0.003 0.030 1677 Dihedral : 8.437 67.823 1650 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.05 % Allowed : 14.04 % Favored : 84.91 % 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: -0.49 (0.24), residues: 1272 helix: 0.27 (0.18), residues: 936 sheet: -2.23 (0.66), residues: 60 loop : -1.58 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.010 0.001 TYR C 257 PHE 0.015 0.002 PHE B 159 TRP 0.013 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (10428) covalent geometry : angle 0.55210 / 0.28 (14088) hydrogen bonds : bond 0.04862 / 3.20 ( 651) hydrogen bonds : angle 4.49866 / 2.99 ( 1944) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.334 Fit side-chains REVERT: A 60 MET cc_start: 0.9072 (mmt) cc_final: 0.8839 (mmt) REVERT: A 232 LYS cc_start: 0.8833 (mtmt) cc_final: 0.8470 (mtmt) REVERT: A 255 MET cc_start: 0.8961 (mmt) cc_final: 0.8273 (mmt) REVERT: A 315 ARG cc_start: 0.7806 (mmt90) cc_final: 0.6518 (ttt90) REVERT: B 60 MET cc_start: 0.9012 (mmt) cc_final: 0.8756 (mmt) REVERT: B 231 GLU cc_start: 0.8789 (tp30) cc_final: 0.8473 (tp30) REVERT: B 255 MET cc_start: 0.9027 (mmt) cc_final: 0.8459 (mmt) REVERT: B 315 ARG cc_start: 0.7983 (mmt90) cc_final: 0.6751 (ttt90) REVERT: B 357 PHE cc_start: 0.8120 (t80) cc_final: 0.7828 (t80) REVERT: C 90 ILE cc_start: 0.8730 (tt) cc_final: 0.8416 (tt) REVERT: C 231 GLU cc_start: 0.8726 (tp30) cc_final: 0.8488 (tp30) REVERT: C 232 LYS cc_start: 0.8977 (mtmt) cc_final: 0.8586 (mtmt) REVERT: C 255 MET cc_start: 0.9007 (mmt) cc_final: 0.8725 (mmm) REVERT: C 286 MET cc_start: 0.7898 (mtm) cc_final: 0.7623 (mtp) REVERT: C 315 ARG cc_start: 0.7805 (mmt90) cc_final: 0.7519 (mmt90) REVERT: C 449 MET cc_start: 0.8505 (ttp) cc_final: 0.8243 (tmm) outliers start: 11 outliers final: 10 residues processed: 138 average time/residue: 0.0776 time to fit residues: 16.4929 Evaluate side-chains 133 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 109 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 0.4980 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 95 optimal weight: 1.9990 overall best weight: 1.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.130658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.091698 restraints weight = 11623.590| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 1.67 r_work: 0.2683 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10428 Z= 0.121 Angle : 0.511 5.510 14088 Z= 0.262 Chirality : 0.039 0.133 1746 Planarity : 0.003 0.030 1677 Dihedral : 8.272 65.328 1650 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.72 % Allowed : 15.19 % Favored : 83.09 % 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: 0.18 (0.25), residues: 1272 helix: 0.79 (0.18), residues: 927 sheet: -2.08 (0.67), residues: 60 loop : -1.36 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 310 TYR 0.012 0.001 TYR B 257 PHE 0.012 0.001 PHE B 159 TRP 0.016 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10428) covalent geometry : angle 0.51062 / 0.26 (14088) hydrogen bonds : bond 0.04316 / 2.85 ( 651) hydrogen bonds : angle 4.26666 / 2.84 ( 1944) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.282 Fit side-chains REVERT: A 232 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8485 (mtmt) REVERT: A 255 MET cc_start: 0.8876 (mmt) cc_final: 0.8272 (mmt) REVERT: A 315 ARG cc_start: 0.7845 (mmt90) cc_final: 0.6523 (ttt90) REVERT: B 60 MET cc_start: 0.8932 (mmt) cc_final: 0.8697 (mmt) REVERT: B 231 GLU cc_start: 0.8781 (tp30) cc_final: 0.8528 (tp30) REVERT: B 235 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8227 (tp) REVERT: B 255 MET cc_start: 0.9004 (mmt) cc_final: 0.8482 (mmt) REVERT: B 315 ARG cc_start: 0.7860 (mmt90) cc_final: 0.6659 (ttt90) REVERT: C 90 ILE cc_start: 0.8714 (tt) cc_final: 0.8419 (tt) REVERT: C 231 GLU cc_start: 0.8714 (tp30) cc_final: 0.8432 (tp30) REVERT: C 232 LYS cc_start: 0.8975 (mtmt) cc_final: 0.8581 (mtmt) REVERT: C 255 MET cc_start: 0.8965 (mmt) cc_final: 0.8705 (mmm) REVERT: C 315 ARG cc_start: 0.7630 (mmt90) cc_final: 0.7331 (mmt90) REVERT: C 328 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8277 (mp) outliers start: 18 outliers final: 11 residues processed: 153 average time/residue: 0.0776 time to fit residues: 18.3513 Evaluate side-chains 137 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 0.6980 chunk 50 optimal weight: 8.9990 chunk 37 optimal weight: 0.2980 chunk 80 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.129265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.091077 restraints weight = 11546.857| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 1.61 r_work: 0.2680 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2540 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10428 Z= 0.135 Angle : 0.531 8.527 14088 Z= 0.270 Chirality : 0.040 0.140 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.314 63.239 1650 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.91 % Allowed : 16.52 % Favored : 81.57 % 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: 0.45 (0.25), residues: 1272 helix: 0.94 (0.18), residues: 948 sheet: -2.00 (0.67), residues: 60 loop : -1.22 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 310 TYR 0.009 0.001 TYR B 257 PHE 0.012 0.001 PHE B 159 TRP 0.017 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10428) covalent geometry : angle 0.53113 / 0.27 (14088) hydrogen bonds : bond 0.04528 / 2.99 ( 651) hydrogen bonds : angle 4.20507 / 2.80 ( 1944) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.360 Fit side-chains REVERT: A 232 LYS cc_start: 0.8815 (mtmt) cc_final: 0.8531 (mtmt) REVERT: A 235 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 255 MET cc_start: 0.8920 (mmt) cc_final: 0.8342 (mmt) REVERT: A 315 ARG cc_start: 0.7738 (mmt90) cc_final: 0.6450 (ttt90) REVERT: B 60 MET cc_start: 0.8931 (mmt) cc_final: 0.8687 (mmt) REVERT: B 231 GLU cc_start: 0.8742 (tp30) cc_final: 0.8499 (tp30) REVERT: B 255 MET cc_start: 0.9003 (mmt) cc_final: 0.8476 (mmt) REVERT: B 315 ARG cc_start: 0.7751 (mmt90) cc_final: 0.6508 (ttt90) REVERT: C 90 ILE cc_start: 0.8684 (tt) cc_final: 0.8382 (tt) REVERT: C 231 GLU cc_start: 0.8649 (tp30) cc_final: 0.8239 (tp30) REVERT: C 232 LYS cc_start: 0.8916 (mtmt) cc_final: 0.8498 (mtmt) REVERT: C 235 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8302 (tp) REVERT: C 255 MET cc_start: 0.8964 (mmt) cc_final: 0.8698 (mmm) REVERT: C 315 ARG cc_start: 0.7621 (mmt90) cc_final: 0.7308 (mmt90) REVERT: C 328 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8285 (mp) outliers start: 20 outliers final: 13 residues processed: 152 average time/residue: 0.0756 time to fit residues: 17.5629 Evaluate side-chains 147 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 62 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.129694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.090676 restraints weight = 11681.070| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.66 r_work: 0.2668 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10428 Z= 0.132 Angle : 0.526 6.639 14088 Z= 0.267 Chirality : 0.040 0.145 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.281 60.659 1650 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.10 % Allowed : 17.10 % Favored : 80.80 % 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: 0.68 (0.25), residues: 1272 helix: 1.06 (0.18), residues: 957 sheet: -1.68 (0.65), residues: 66 loop : -1.05 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 310 TYR 0.010 0.001 TYR B 257 PHE 0.018 0.001 PHE C 357 TRP 0.019 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (10428) covalent geometry : angle 0.52629 / 0.27 (14088) hydrogen bonds : bond 0.04455 / 2.94 ( 651) hydrogen bonds : angle 4.14859 / 2.77 ( 1944) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.382 Fit side-chains REVERT: A 232 LYS cc_start: 0.8841 (mtmt) cc_final: 0.8538 (mtmt) REVERT: A 235 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8158 (tp) REVERT: A 255 MET cc_start: 0.8896 (mmt) cc_final: 0.8322 (mmt) REVERT: A 315 ARG cc_start: 0.7758 (mmt90) cc_final: 0.6473 (ttt90) REVERT: B 60 MET cc_start: 0.8898 (mmt) cc_final: 0.8667 (mmt) REVERT: B 231 GLU cc_start: 0.8769 (tp30) cc_final: 0.8533 (tp30) REVERT: B 235 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8269 (tp) REVERT: B 255 MET cc_start: 0.9024 (mmt) cc_final: 0.8518 (mmt) REVERT: B 315 ARG cc_start: 0.7737 (mmt90) cc_final: 0.6533 (ttt90) REVERT: C 90 ILE cc_start: 0.8691 (tt) cc_final: 0.8397 (tt) REVERT: C 231 GLU cc_start: 0.8663 (tp30) cc_final: 0.8250 (tp30) REVERT: C 232 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8510 (mtmt) REVERT: C 235 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8311 (tp) REVERT: C 255 MET cc_start: 0.8985 (mmt) cc_final: 0.8721 (mmm) REVERT: C 315 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7274 (mmt90) REVERT: C 328 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8301 (mp) outliers start: 22 outliers final: 17 residues processed: 153 average time/residue: 0.0826 time to fit residues: 19.3752 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 20 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 38 optimal weight: 0.0670 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.132183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.094193 restraints weight = 11496.566| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.60 r_work: 0.2726 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10428 Z= 0.102 Angle : 0.494 6.639 14088 Z= 0.251 Chirality : 0.038 0.149 1746 Planarity : 0.003 0.028 1677 Dihedral : 7.806 60.816 1650 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.10 % Allowed : 17.57 % Favored : 80.32 % 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: 1.08 (0.25), residues: 1272 helix: 1.39 (0.18), residues: 945 sheet: -1.42 (0.67), residues: 66 loop : -1.04 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 310 TYR 0.014 0.001 TYR A 257 PHE 0.008 0.001 PHE A 159 TRP 0.022 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (10428) covalent geometry : angle 0.49441 / 0.25 (14088) hydrogen bonds : bond 0.03851 / 2.55 ( 651) hydrogen bonds : angle 4.00821 / 2.67 ( 1944) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.326 Fit side-chains REVERT: A 232 LYS cc_start: 0.8807 (mtmt) cc_final: 0.8545 (mtmt) REVERT: A 235 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8073 (tp) REVERT: A 315 ARG cc_start: 0.7697 (mmt90) cc_final: 0.6444 (ttt90) REVERT: B 60 MET cc_start: 0.8814 (mmt) cc_final: 0.8557 (mmt) REVERT: B 231 GLU cc_start: 0.8713 (tp30) cc_final: 0.8481 (tp30) REVERT: B 235 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8205 (tp) REVERT: B 255 MET cc_start: 0.8960 (mmt) cc_final: 0.8428 (mmt) REVERT: B 315 ARG cc_start: 0.7732 (mmt90) cc_final: 0.6521 (ttt90) REVERT: B 440 ASP cc_start: 0.8041 (t70) cc_final: 0.7714 (t0) REVERT: C 90 ILE cc_start: 0.8598 (tt) cc_final: 0.8314 (tt) REVERT: C 231 GLU cc_start: 0.8613 (tp30) cc_final: 0.8232 (tp30) REVERT: C 232 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8470 (mtmt) REVERT: C 235 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8196 (tp) REVERT: C 255 MET cc_start: 0.8953 (mmt) cc_final: 0.8734 (mmm) REVERT: C 315 ARG cc_start: 0.7550 (mmt90) cc_final: 0.7212 (mmt90) REVERT: C 328 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8150 (mp) outliers start: 22 outliers final: 16 residues processed: 156 average time/residue: 0.0742 time to fit residues: 17.9852 Evaluate side-chains 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 127 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.132769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.094858 restraints weight = 11492.545| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.60 r_work: 0.2736 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10428 Z= 0.101 Angle : 0.493 6.974 14088 Z= 0.250 Chirality : 0.038 0.149 1746 Planarity : 0.003 0.028 1677 Dihedral : 7.550 60.819 1650 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.91 % Allowed : 18.15 % Favored : 79.94 % 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: 1.27 (0.25), residues: 1272 helix: 1.51 (0.18), residues: 948 sheet: -1.23 (0.68), residues: 66 loop : -0.97 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.011 0.001 TYR A 257 PHE 0.008 0.001 PHE B 159 TRP 0.022 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (10428) covalent geometry : angle 0.49281 / 0.25 (14088) hydrogen bonds : bond 0.03829 / 2.53 ( 651) hydrogen bonds : angle 3.95726 / 2.63 ( 1944) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.412 Fit side-chains REVERT: A 232 LYS cc_start: 0.8788 (mtmt) cc_final: 0.8491 (mtmt) REVERT: A 235 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8070 (tp) REVERT: A 315 ARG cc_start: 0.7649 (mmt90) cc_final: 0.6394 (ttt90) REVERT: A 347 ASN cc_start: 0.8852 (OUTLIER) cc_final: 0.8425 (m-40) REVERT: B 60 MET cc_start: 0.8701 (mmt) cc_final: 0.8459 (mmt) REVERT: B 231 GLU cc_start: 0.8666 (tp30) cc_final: 0.8434 (tp30) REVERT: B 235 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8163 (tp) REVERT: B 255 MET cc_start: 0.8974 (mmt) cc_final: 0.8444 (mmt) REVERT: B 258 MET cc_start: 0.8272 (tmm) cc_final: 0.8035 (tmm) REVERT: B 315 ARG cc_start: 0.7784 (mmt90) cc_final: 0.6566 (ttt90) REVERT: B 440 ASP cc_start: 0.8005 (t70) cc_final: 0.7690 (t0) REVERT: C 90 ILE cc_start: 0.8526 (tt) cc_final: 0.8267 (tt) REVERT: C 231 GLU cc_start: 0.8581 (tp30) cc_final: 0.8203 (tp30) REVERT: C 232 LYS cc_start: 0.8789 (mtmt) cc_final: 0.8435 (mtmt) REVERT: C 235 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8160 (tp) REVERT: C 255 MET cc_start: 0.8920 (mmt) cc_final: 0.8702 (mmm) REVERT: C 315 ARG cc_start: 0.7518 (mmt90) cc_final: 0.7169 (mmt90) REVERT: C 328 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7954 (mp) outliers start: 20 outliers final: 14 residues processed: 155 average time/residue: 0.0748 time to fit residues: 17.9390 Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 20 optimal weight: 0.5980 chunk 116 optimal weight: 2.9990 chunk 4 optimal weight: 0.0370 chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.131031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.092419 restraints weight = 11521.360| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.64 r_work: 0.2693 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10428 Z= 0.120 Angle : 0.509 7.333 14088 Z= 0.257 Chirality : 0.039 0.150 1746 Planarity : 0.003 0.027 1677 Dihedral : 7.758 62.247 1650 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.91 % Allowed : 18.43 % Favored : 79.66 % 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: 1.30 (0.25), residues: 1272 helix: 1.52 (0.18), residues: 951 sheet: -1.17 (0.68), residues: 66 loop : -0.93 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 61 TYR 0.010 0.001 TYR C 257 PHE 0.011 0.001 PHE B 159 TRP 0.029 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10428) covalent geometry : angle 0.50937 / 0.26 (14088) hydrogen bonds : bond 0.04141 / 2.73 ( 651) hydrogen bonds : angle 3.98259 / 2.66 ( 1944) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.400 Fit side-chains REVERT: A 232 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8479 (mtmt) REVERT: A 235 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8116 (tp) REVERT: A 315 ARG cc_start: 0.7685 (mmt90) cc_final: 0.6423 (ttt90) REVERT: B 60 MET cc_start: 0.8827 (mmt) cc_final: 0.8587 (mmt) REVERT: B 235 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8238 (tp) REVERT: B 255 MET cc_start: 0.8976 (mmt) cc_final: 0.8439 (mmt) REVERT: B 315 ARG cc_start: 0.7810 (mmt90) cc_final: 0.6551 (ttt90) REVERT: B 440 ASP cc_start: 0.8095 (t70) cc_final: 0.7756 (t0) REVERT: C 90 ILE cc_start: 0.8592 (tt) cc_final: 0.8318 (tt) REVERT: C 231 GLU cc_start: 0.8594 (tp30) cc_final: 0.8204 (tp30) REVERT: C 232 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8453 (mtmt) REVERT: C 235 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8220 (tp) REVERT: C 255 MET cc_start: 0.8968 (mmt) cc_final: 0.8762 (mmm) REVERT: C 315 ARG cc_start: 0.7543 (mmt90) cc_final: 0.7194 (mmt90) REVERT: C 328 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7980 (mp) outliers start: 20 outliers final: 16 residues processed: 154 average time/residue: 0.0827 time to fit residues: 19.6879 Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.131536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.092951 restraints weight = 11436.863| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.64 r_work: 0.2704 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10428 Z= 0.113 Angle : 0.509 7.619 14088 Z= 0.258 Chirality : 0.039 0.155 1746 Planarity : 0.003 0.027 1677 Dihedral : 7.698 62.590 1650 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.81 % Allowed : 18.72 % Favored : 79.47 % 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: 1.39 (0.25), residues: 1272 helix: 1.57 (0.18), residues: 951 sheet: -1.07 (0.69), residues: 66 loop : -0.90 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 61 TYR 0.014 0.001 TYR C 257 PHE 0.009 0.001 PHE B 159 TRP 0.029 0.002 TRP C 441 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (10428) covalent geometry : angle 0.50936 / 0.26 (14088) hydrogen bonds : bond 0.04042 / 2.67 ( 651) hydrogen bonds : angle 3.97261 / 2.65 ( 1944) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 0.368 Fit side-chains REVERT: A 232 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8470 (mtmt) REVERT: A 235 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8140 (tp) REVERT: A 315 ARG cc_start: 0.7665 (mmt90) cc_final: 0.6423 (ttt90) REVERT: B 60 MET cc_start: 0.8819 (mmt) cc_final: 0.8577 (mmt) REVERT: B 235 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8221 (tp) REVERT: B 255 MET cc_start: 0.8966 (mmt) cc_final: 0.8437 (mmt) REVERT: B 315 ARG cc_start: 0.7809 (mmt90) cc_final: 0.6551 (ttt90) REVERT: B 440 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7721 (t0) REVERT: C 90 ILE cc_start: 0.8559 (tt) cc_final: 0.8298 (tt) REVERT: C 231 GLU cc_start: 0.8557 (tp30) cc_final: 0.8169 (tp30) REVERT: C 232 LYS cc_start: 0.8783 (mtmt) cc_final: 0.8447 (mtmt) REVERT: C 235 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8197 (tp) REVERT: C 255 MET cc_start: 0.8964 (mmt) cc_final: 0.8756 (mmm) REVERT: C 315 ARG cc_start: 0.7539 (mmt90) cc_final: 0.7187 (mmt90) REVERT: C 328 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7990 (mp) outliers start: 19 outliers final: 14 residues processed: 152 average time/residue: 0.0803 time to fit residues: 18.8644 Evaluate side-chains 156 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 208 ASP Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 286 MET Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 ILE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 387 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 126 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 46 optimal weight: 0.2980 chunk 50 optimal weight: 7.9990 chunk 16 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.133448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.094999 restraints weight = 11523.395| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.64 r_work: 0.2734 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10428 Z= 0.101 Angle : 0.496 7.643 14088 Z= 0.250 Chirality : 0.038 0.149 1746 Planarity : 0.003 0.027 1677 Dihedral : 7.459 63.671 1650 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.01 % Allowed : 18.62 % Favored : 79.37 % 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: 1.56 (0.25), residues: 1272 helix: 1.70 (0.18), residues: 948 sheet: -0.98 (0.70), residues: 66 loop : -0.81 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.010 0.001 TYR B 257 PHE 0.007 0.001 PHE C 159 TRP 0.028 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (10428) covalent geometry : angle 0.49574 / 0.25 (14088) hydrogen bonds : bond 0.03723 / 2.46 ( 651) hydrogen bonds : angle 3.89435 / 2.60 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2413.96 seconds wall clock time: 41 minutes 56.89 seconds (2516.89 seconds total)