Starting phenix.real_space_refine on Wed Mar 4 04:04:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3q_10094/03_2026/6s3q_10094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3q_10094/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6s3q_10094/03_2026/6s3q_10094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3q_10094/03_2026/6s3q_10094.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6s3q_10094/03_2026/6s3q_10094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3q_10094/03_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-dev-5986/lib/python3.9/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: 137 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: 137 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: 137 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: 2.35, per 1000 atoms: 0.23 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: 0.91 Conformation dependent library (CDL) restraints added in 449.1 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: 0.24 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: 1.26 Time building geometry restraints manager: 1.18 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: 5834 17.59 - 35.17: 511 35.17 - 52.76: 105 52.76 - 70.35: 30 70.35 - 87.94: 6 Dihedral angle restraints: 6486 sinusoidal: 2781 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 6483 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: 0.420 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 9.860 Find NCS groups from input model: 0.190 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: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 14.478 87.937 4092 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 covalent geometry : bond 0.01178 (10428) covalent geometry : angle 1.10505 (14088) hydrogen bonds : bond 0.15504 ( 651) hydrogen bonds : angle 6.74530 ( 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 : 0.359 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: 0.0950 time to fit residues: 19.7438 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 : 0.378 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 322 GLN A 347 ASN A 366 ASN A 385 ASN 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.129501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.091350 restraints weight = 11569.155| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.62 r_work: 0.2686 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1337 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= 0.132 Angle : 0.562 5.729 14088 Z= 0.296 Chirality : 0.039 0.147 1746 Planarity : 0.004 0.033 1677 Dihedral : 9.986 69.117 1929 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.26 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: -1.54 (0.22), residues: 1272 helix: -0.51 (0.17), residues: 930 sheet: -2.34 (0.65), residues: 60 loop : -1.94 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 280 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 covalent geometry : bond 0.00290 (10428) covalent geometry : angle 0.56232 (14088) hydrogen bonds : bond 0.05137 ( 651) hydrogen bonds : angle 4.86115 ( 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 : 0.228 Fit side-chains REVERT: A 60 MET cc_start: 0.9116 (mmt) cc_final: 0.8801 (mmt) REVERT: A 232 LYS cc_start: 0.8852 (mtmt) cc_final: 0.8410 (mtmt) REVERT: A 315 ARG cc_start: 0.7772 (mmt90) cc_final: 0.6467 (ttt90) REVERT: A 359 LEU cc_start: 0.8760 (mt) cc_final: 0.8543 (mt) REVERT: B 60 MET cc_start: 0.9101 (mmt) cc_final: 0.8874 (mmt) REVERT: B 231 GLU cc_start: 0.8680 (tp30) cc_final: 0.8386 (tp30) REVERT: B 255 MET cc_start: 0.9002 (mmt) cc_final: 0.8422 (mmt) REVERT: B 315 ARG cc_start: 0.7984 (mmt90) cc_final: 0.6767 (ttt90) REVERT: C 90 ILE cc_start: 0.8773 (tt) cc_final: 0.8514 (tt) REVERT: C 231 GLU cc_start: 0.8698 (tp30) cc_final: 0.8292 (tp30) REVERT: C 232 LYS cc_start: 0.8907 (mtmt) cc_final: 0.8518 (mtmt) REVERT: C 255 MET cc_start: 0.8974 (mmt) cc_final: 0.8680 (mmm) REVERT: C 286 MET cc_start: 0.7924 (mtm) cc_final: 0.7640 (mtp) REVERT: C 315 ARG cc_start: 0.7786 (mmt90) cc_final: 0.7518 (mmt90) REVERT: C 449 MET cc_start: 0.8471 (ttp) cc_final: 0.8238 (ttp) outliers start: 5 outliers final: 5 residues processed: 141 average time/residue: 0.0783 time to fit residues: 16.9718 Evaluate side-chains 119 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 6.9990 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: 6.9990 chunk 111 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.089421 restraints weight = 11680.735| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.66 r_work: 0.2649 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10428 Z= 0.158 Angle : 0.568 5.654 14088 Z= 0.291 Chirality : 0.041 0.162 1746 Planarity : 0.003 0.031 1677 Dihedral : 9.757 67.800 1929 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.05 % Allowed : 14.23 % Favored : 84.72 % 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: -0.54 (0.24), residues: 1272 helix: 0.22 (0.18), residues: 936 sheet: -2.24 (0.66), residues: 60 loop : -1.55 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 61 TYR 0.009 0.001 TYR C 257 PHE 0.017 0.002 PHE B 159 TRP 0.014 0.001 TRP C 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00385 (10428) covalent geometry : angle 0.56794 (14088) hydrogen bonds : bond 0.05063 ( 651) hydrogen bonds : angle 4.51360 ( 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 143 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.298 Fit side-chains REVERT: A 60 MET cc_start: 0.9093 (mmt) cc_final: 0.8862 (mmt) REVERT: A 232 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8463 (mtmt) REVERT: A 255 MET cc_start: 0.8947 (mmt) cc_final: 0.8232 (mmt) REVERT: A 315 ARG cc_start: 0.7871 (mmt90) cc_final: 0.6519 (ttt90) REVERT: B 60 MET cc_start: 0.9036 (mmt) cc_final: 0.8784 (mmt) REVERT: B 231 GLU cc_start: 0.8807 (tp30) cc_final: 0.8483 (tp30) REVERT: B 255 MET cc_start: 0.9029 (mmt) cc_final: 0.8444 (mmt) REVERT: B 315 ARG cc_start: 0.7988 (mmt90) cc_final: 0.6773 (ttt90) REVERT: C 90 ILE cc_start: 0.8735 (tt) cc_final: 0.8398 (tt) REVERT: C 231 GLU cc_start: 0.8738 (tp30) cc_final: 0.8507 (tp30) REVERT: C 232 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8601 (mtmt) REVERT: C 255 MET cc_start: 0.9011 (mmt) cc_final: 0.8729 (mmm) REVERT: C 315 ARG cc_start: 0.7800 (mmt90) cc_final: 0.7515 (mmt90) REVERT: C 449 MET cc_start: 0.8513 (ttp) cc_final: 0.8262 (tmm) outliers start: 11 outliers final: 10 residues processed: 142 average time/residue: 0.0796 time to fit residues: 17.3509 Evaluate side-chains 136 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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: 0.9990 chunk 43 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.130940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.092486 restraints weight = 11598.783| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.63 r_work: 0.2695 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10428 Z= 0.115 Angle : 0.510 5.506 14088 Z= 0.261 Chirality : 0.039 0.131 1746 Planarity : 0.003 0.030 1677 Dihedral : 9.376 65.732 1929 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.24 % Allowed : 15.66 % 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: 0.17 (0.25), residues: 1272 helix: 0.79 (0.18), residues: 924 sheet: -2.09 (0.67), residues: 60 loop : -1.37 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 310 TYR 0.013 0.001 TYR B 257 PHE 0.010 0.001 PHE B 159 TRP 0.016 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00257 (10428) covalent geometry : angle 0.50969 (14088) hydrogen bonds : bond 0.04266 ( 651) hydrogen bonds : angle 4.27115 ( 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 149 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.229 Fit side-chains REVERT: A 232 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8499 (mtmt) REVERT: A 255 MET cc_start: 0.8889 (mmt) cc_final: 0.8299 (mmt) REVERT: A 315 ARG cc_start: 0.7853 (mmt90) cc_final: 0.6539 (ttt90) REVERT: A 440 ASP cc_start: 0.7721 (t0) cc_final: 0.7422 (t0) REVERT: B 60 MET cc_start: 0.8951 (mmt) cc_final: 0.8714 (mmt) REVERT: B 231 GLU cc_start: 0.8770 (tp30) cc_final: 0.8491 (tp30) REVERT: B 255 MET cc_start: 0.9003 (mmt) cc_final: 0.8482 (mmt) REVERT: B 315 ARG cc_start: 0.7941 (mmt90) cc_final: 0.6730 (ttt90) REVERT: C 90 ILE cc_start: 0.8707 (tt) cc_final: 0.8409 (tt) REVERT: C 231 GLU cc_start: 0.8713 (tp30) cc_final: 0.8439 (tp30) REVERT: C 232 LYS cc_start: 0.8976 (mtmt) cc_final: 0.8582 (mtmt) REVERT: C 235 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (tp) REVERT: C 255 MET cc_start: 0.8969 (mmt) cc_final: 0.8710 (mmm) REVERT: C 315 ARG cc_start: 0.7727 (mmt90) cc_final: 0.7429 (mmt90) REVERT: C 328 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8319 (mp) REVERT: C 449 MET cc_start: 0.8480 (ttp) cc_final: 0.8234 (ttp) outliers start: 13 outliers final: 8 residues processed: 147 average time/residue: 0.0767 time to fit residues: 17.2469 Evaluate side-chains 131 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 373 TYR 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 235 ILE 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: 3.9990 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 111 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.127348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.088860 restraints weight = 11586.704| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.61 r_work: 0.2645 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 10428 Z= 0.182 Angle : 0.582 8.874 14088 Z= 0.295 Chirality : 0.042 0.159 1746 Planarity : 0.003 0.030 1677 Dihedral : 9.720 63.887 1929 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.39 % Allowed : 15.85 % Favored : 81.76 % 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: 0.73 (0.18), residues: 939 sheet: -2.10 (0.66), residues: 60 loop : -1.22 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 310 TYR 0.010 0.001 TYR B 257 PHE 0.017 0.002 PHE B 159 TRP 0.016 0.001 TRP C 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00453 (10428) covalent geometry : angle 0.58239 (14088) hydrogen bonds : bond 0.05147 ( 651) hydrogen bonds : angle 4.32812 ( 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 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.362 Fit side-chains REVERT: A 232 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8521 (mtmt) REVERT: A 235 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8244 (tp) REVERT: A 255 MET cc_start: 0.8893 (mmt) cc_final: 0.8226 (mmt) REVERT: A 315 ARG cc_start: 0.7845 (mmt90) cc_final: 0.6550 (ttt90) REVERT: B 60 MET cc_start: 0.8998 (mmt) cc_final: 0.8764 (mmt) REVERT: B 231 GLU cc_start: 0.8782 (tp30) cc_final: 0.8484 (tp30) REVERT: B 235 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (tp) REVERT: B 255 MET cc_start: 0.9032 (mmt) cc_final: 0.8436 (mmt) REVERT: B 315 ARG cc_start: 0.7954 (mmt90) cc_final: 0.6713 (ttt90) REVERT: C 90 ILE cc_start: 0.8751 (tt) cc_final: 0.8426 (tt) REVERT: C 231 GLU cc_start: 0.8677 (tp30) cc_final: 0.8237 (tp30) REVERT: C 232 LYS cc_start: 0.8929 (mtmt) cc_final: 0.8543 (mtmt) REVERT: C 255 MET cc_start: 0.9009 (mmt) cc_final: 0.8729 (mmm) REVERT: C 315 ARG cc_start: 0.7625 (mmt90) cc_final: 0.7315 (mmt90) REVERT: C 328 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8309 (mp) outliers start: 25 outliers final: 17 residues processed: 154 average time/residue: 0.0790 time to fit residues: 18.6593 Evaluate side-chains 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain A residue 347 ASN 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 260 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 359 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 373 TYR Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.130231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.091705 restraints weight = 11608.921| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 1.62 r_work: 0.2686 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2083 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 : 0.519 7.093 14088 Z= 0.263 Chirality : 0.039 0.144 1746 Planarity : 0.003 0.029 1677 Dihedral : 9.193 61.232 1929 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.01 % Allowed : 16.52 % Favored : 81.47 % 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: 0.59 (0.25), residues: 1272 helix: 1.03 (0.18), residues: 939 sheet: -1.91 (0.68), residues: 60 loop : -1.09 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.011 0.001 TYR B 257 PHE 0.010 0.001 PHE B 159 TRP 0.020 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00275 (10428) covalent geometry : angle 0.51908 (14088) hydrogen bonds : bond 0.04294 ( 651) hydrogen bonds : angle 4.15513 ( 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 161 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.291 Fit side-chains REVERT: A 232 LYS cc_start: 0.8839 (mtmt) cc_final: 0.8534 (mtmt) REVERT: A 235 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 255 MET cc_start: 0.8894 (mmt) cc_final: 0.8336 (mmt) REVERT: A 315 ARG cc_start: 0.7735 (mmt90) cc_final: 0.6456 (ttt90) REVERT: B 60 MET cc_start: 0.8883 (mmt) cc_final: 0.8645 (mmt) REVERT: B 231 GLU cc_start: 0.8743 (tp30) cc_final: 0.8421 (tp30) REVERT: B 235 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8229 (tp) REVERT: B 255 MET cc_start: 0.8972 (mmt) cc_final: 0.8472 (mmt) REVERT: B 315 ARG cc_start: 0.7820 (mmt90) cc_final: 0.6650 (ttt90) REVERT: C 90 ILE cc_start: 0.8699 (tt) cc_final: 0.8386 (tt) REVERT: C 231 GLU cc_start: 0.8650 (tp30) cc_final: 0.8250 (tp30) REVERT: C 232 LYS cc_start: 0.8854 (mtmt) cc_final: 0.8482 (mtmt) REVERT: C 235 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8218 (tp) REVERT: C 255 MET cc_start: 0.8961 (mmt) cc_final: 0.8700 (mmm) REVERT: C 315 ARG cc_start: 0.7600 (mmt90) cc_final: 0.7274 (mmt90) REVERT: C 328 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8291 (mp) outliers start: 21 outliers final: 15 residues processed: 154 average time/residue: 0.0770 time to fit residues: 18.2917 Evaluate side-chains 153 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 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 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 260 LEU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.093774 restraints weight = 11464.148| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.61 r_work: 0.2718 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10428 Z= 0.105 Angle : 0.497 6.552 14088 Z= 0.252 Chirality : 0.038 0.146 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.738 59.763 1929 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.81 % Allowed : 17.00 % Favored : 81.18 % 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: 0.96 (0.25), residues: 1272 helix: 1.36 (0.18), residues: 927 sheet: -1.48 (0.66), residues: 66 loop : -1.14 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 356 TYR 0.011 0.001 TYR B 257 PHE 0.023 0.001 PHE A 357 TRP 0.022 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00229 (10428) covalent geometry : angle 0.49717 (14088) hydrogen bonds : bond 0.03909 ( 651) hydrogen bonds : angle 4.02394 ( 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 162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 0.376 Fit side-chains REVERT: A 232 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8513 (mtmt) REVERT: A 235 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8104 (tp) REVERT: A 315 ARG cc_start: 0.7690 (mmt90) cc_final: 0.6428 (ttt90) REVERT: A 347 ASN cc_start: 0.8925 (OUTLIER) cc_final: 0.8486 (m-40) REVERT: B 60 MET cc_start: 0.8833 (mmt) cc_final: 0.8590 (mmt) REVERT: B 231 GLU cc_start: 0.8728 (tp30) cc_final: 0.8473 (tp30) REVERT: B 235 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8224 (tp) REVERT: B 255 MET cc_start: 0.8953 (mmt) cc_final: 0.8424 (mmt) REVERT: B 315 ARG cc_start: 0.7724 (mmt90) cc_final: 0.6502 (ttt90) REVERT: C 90 ILE cc_start: 0.8579 (tt) cc_final: 0.8294 (tt) REVERT: C 231 GLU cc_start: 0.8625 (tp30) cc_final: 0.8221 (tp30) REVERT: C 232 LYS cc_start: 0.8830 (mtmt) cc_final: 0.8489 (mtmt) REVERT: C 235 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8087 (tp) REVERT: C 255 MET cc_start: 0.8935 (mmt) cc_final: 0.8714 (mmm) REVERT: C 315 ARG cc_start: 0.7533 (mmt90) cc_final: 0.7201 (mmt90) REVERT: C 328 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8258 (mp) outliers start: 19 outliers final: 12 residues processed: 155 average time/residue: 0.0746 time to fit residues: 17.9836 Evaluate side-chains 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 286 MET Chi-restraints excluded: chain A residue 347 ASN 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 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: 2.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 127 optimal weight: 0.8980 chunk 36 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.131958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.093166 restraints weight = 11480.190| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.64 r_work: 0.2706 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2565 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10428 Z= 0.108 Angle : 0.501 6.997 14088 Z= 0.254 Chirality : 0.039 0.150 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.572 59.853 1929 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.81 % Allowed : 17.57 % Favored : 80.61 % 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: 1.10 (0.25), residues: 1272 helix: 1.45 (0.18), residues: 930 sheet: -1.28 (0.68), residues: 66 loop : -1.13 (0.37), residues: 276 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 0.018 0.001 PHE A 357 TRP 0.023 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00241 (10428) covalent geometry : angle 0.50074 (14088) hydrogen bonds : bond 0.03995 ( 651) hydrogen bonds : angle 4.00627 ( 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: 19 poor density : 141 time to evaluate : 0.568 Fit side-chains REVERT: A 232 LYS cc_start: 0.8824 (mtmt) cc_final: 0.8509 (mtmt) REVERT: A 235 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8129 (tp) REVERT: A 315 ARG cc_start: 0.7676 (mmt90) cc_final: 0.6420 (ttt90) REVERT: A 347 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8388 (m-40) REVERT: B 60 MET cc_start: 0.8816 (mmt) cc_final: 0.8581 (mmt) REVERT: B 235 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.8240 (tp) REVERT: B 255 MET cc_start: 0.8964 (mmt) cc_final: 0.8444 (mmt) REVERT: B 315 ARG cc_start: 0.7766 (mmt90) cc_final: 0.6530 (ttt90) REVERT: B 440 ASP cc_start: 0.8100 (t0) cc_final: 0.7763 (t0) REVERT: C 90 ILE cc_start: 0.8565 (tt) cc_final: 0.8286 (tt) REVERT: C 231 GLU cc_start: 0.8606 (tp30) cc_final: 0.8216 (tp30) REVERT: C 232 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8454 (mtmt) REVERT: C 235 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8097 (tp) REVERT: C 255 MET cc_start: 0.8958 (mmt) cc_final: 0.8743 (mmm) REVERT: C 315 ARG cc_start: 0.7527 (mmt90) cc_final: 0.7185 (mmt90) REVERT: C 328 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8203 (mp) outliers start: 19 outliers final: 14 residues processed: 153 average time/residue: 0.0769 time to fit residues: 17.9352 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 : 0.344 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 20 optimal weight: 0.9990 chunk 116 optimal weight: 0.0470 chunk 4 optimal weight: 0.2980 chunk 41 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 46 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.134724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.096760 restraints weight = 11394.274| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.59 r_work: 0.2762 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10428 Z= 0.096 Angle : 0.487 7.456 14088 Z= 0.246 Chirality : 0.038 0.153 1746 Planarity : 0.003 0.027 1677 Dihedral : 8.235 58.895 1929 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.91 % Allowed : 18.24 % Favored : 79.85 % 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: 1.67 (0.18), residues: 927 sheet: -1.07 (0.69), residues: 66 loop : -1.07 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 280 TYR 0.009 0.001 TYR B 257 PHE 0.016 0.001 PHE A 357 TRP 0.033 0.002 TRP C 441 HIS 0.001 0.000 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00195 (10428) covalent geometry : angle 0.48721 (14088) hydrogen bonds : bond 0.03544 ( 651) hydrogen bonds : angle 3.88817 ( 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 162 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.356 Fit side-chains REVERT: A 232 LYS cc_start: 0.8763 (mtmt) cc_final: 0.8467 (mtmt) REVERT: A 235 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7920 (tp) REVERT: A 315 ARG cc_start: 0.7638 (mmt90) cc_final: 0.6357 (ttt90) REVERT: A 347 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8370 (m-40) REVERT: B 235 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8147 (tp) REVERT: B 315 ARG cc_start: 0.7874 (mmt90) cc_final: 0.6669 (ttt90) REVERT: C 90 ILE cc_start: 0.8491 (tt) cc_final: 0.8251 (tt) REVERT: C 231 GLU cc_start: 0.8553 (tp30) cc_final: 0.8186 (tp30) REVERT: C 232 LYS cc_start: 0.8777 (mtmt) cc_final: 0.8452 (mtmt) REVERT: C 235 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7962 (tp) REVERT: C 255 MET cc_start: 0.8835 (mmt) cc_final: 0.8615 (mmm) REVERT: C 315 ARG cc_start: 0.7524 (mmt90) cc_final: 0.7180 (mmt90) REVERT: C 328 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8060 (mp) outliers start: 20 outliers final: 9 residues processed: 156 average time/residue: 0.0754 time to fit residues: 18.0232 Evaluate side-chains 148 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 347 ASN Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain B residue 235 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 328 LEU Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 0.0970 chunk 30 optimal weight: 6.9990 chunk 91 optimal weight: 0.1980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.131978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.093852 restraints weight = 11426.760| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.60 r_work: 0.2720 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2449 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= 0.118 Angle : 0.517 7.542 14088 Z= 0.260 Chirality : 0.039 0.154 1746 Planarity : 0.003 0.027 1677 Dihedral : 8.332 59.592 1929 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.62 % Allowed : 18.62 % Favored : 79.75 % 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 (0.25), residues: 1272 helix: 1.60 (0.18), residues: 933 sheet: -1.04 (0.69), residues: 66 loop : -1.00 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.013 0.001 TYR C 257 PHE 0.014 0.001 PHE A 357 TRP 0.029 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00274 (10428) covalent geometry : angle 0.51694 (14088) hydrogen bonds : bond 0.04061 ( 651) hydrogen bonds : angle 3.95053 ( 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 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 138 time to evaluate : 0.230 Fit side-chains REVERT: A 232 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8420 (mtmt) REVERT: A 235 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8090 (tp) REVERT: A 315 ARG cc_start: 0.7617 (mmt90) cc_final: 0.6358 (ttt90) REVERT: B 235 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8208 (tp) REVERT: B 255 MET cc_start: 0.8942 (mmt) cc_final: 0.8426 (mmt) REVERT: B 315 ARG cc_start: 0.7887 (mmt90) cc_final: 0.6703 (ttt90) REVERT: C 90 ILE cc_start: 0.8537 (tt) cc_final: 0.8271 (tt) REVERT: C 231 GLU cc_start: 0.8519 (tp30) cc_final: 0.8148 (tp30) REVERT: C 232 LYS cc_start: 0.8770 (mtmt) cc_final: 0.8446 (mtmt) REVERT: C 235 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8093 (tp) REVERT: C 255 MET cc_start: 0.8936 (mmt) cc_final: 0.8729 (mmm) REVERT: C 315 ARG cc_start: 0.7515 (mmt90) cc_final: 0.7168 (mmt90) REVERT: C 328 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8003 (mp) outliers start: 17 outliers final: 11 residues processed: 150 average time/residue: 0.0790 time to fit residues: 18.2734 Evaluate side-chains 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 347 ASN Chi-restraints excluded: chain A residue 373 TYR Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain B residue 235 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 328 LEU Chi-restraints excluded: chain C residue 373 TYR 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: 0.6980 chunk 87 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 117 optimal weight: 0.0070 chunk 101 optimal weight: 4.9990 chunk 38 optimal weight: 0.0970 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.134524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.096295 restraints weight = 11481.085| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.61 r_work: 0.2751 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2611 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10428 Z= 0.099 Angle : 0.492 7.675 14088 Z= 0.247 Chirality : 0.038 0.153 1746 Planarity : 0.003 0.036 1677 Dihedral : 7.981 58.542 1929 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.53 % Allowed : 18.62 % Favored : 79.85 % 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: 1.52 (0.25), residues: 1272 helix: 1.74 (0.18), residues: 930 sheet: -1.03 (0.69), residues: 66 loop : -0.93 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 447 TYR 0.011 0.001 TYR C 257 PHE 0.014 0.001 PHE A 357 TRP 0.029 0.002 TRP C 441 HIS 0.001 0.000 HIS B 296 Details of bonding type rmsd covalent geometry : bond 0.00206 (10428) covalent geometry : angle 0.49155 (14088) hydrogen bonds : bond 0.03626 ( 651) hydrogen bonds : angle 3.87100 ( 1944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2358.85 seconds wall clock time: 40 minutes 56.15 seconds (2456.15 seconds total)