Starting phenix.real_space_refine on Mon Jul 28 21:43:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6s3q_10094/07_2025/6s3q_10094.cif Found real_map, /net/cci-nas-00/data/ceres_data/6s3q_10094/07_2025/6s3q_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6s3q_10094/07_2025/6s3q_10094.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6s3q_10094/07_2025/6s3q_10094.map" model { file = "/net/cci-nas-00/data/ceres_data/6s3q_10094/07_2025/6s3q_10094.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6s3q_10094/07_2025/6s3q_10094.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'ARG: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: 6.62, per 1000 atoms: 0.64 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: 2.39 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.92 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: 2.92 Time building geometry restraints manager: 2.85 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: 0.03 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: 0.370 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.800 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP A 19 HIS 0.001 0.001 HIS C 296 PHE 0.025 0.003 PHE A 159 TYR 0.028 0.003 TYR B 373 ARG 0.004 0.001 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.15504 ( 651) hydrogen bonds : angle 6.74530 ( 1944) covalent geometry : bond 0.01178 (10428) covalent geometry : angle 1.10505 (14088) *********************** 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 : 1.020 Fit side-chains REVERT: A 60 MET cc_start: 0.8678 (mmt) cc_final: 0.8205 (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: 0.8619 (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: 0.8394 (mmt) REVERT: B 315 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7012 (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: 0.8670 (tt) REVERT: C 232 LYS cc_start: 0.8398 (mtmt) cc_final: 0.8075 (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: 0.7500 (mmt90) outliers start: 6 outliers final: 0 residues processed: 144 average time/residue: 0.2198 time to fit residues: 45.4581 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 : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 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 = 0.3346 r_free = 0.3346 target = 0.128705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.090604 restraints weight = 11458.111| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 1.61 r_work: 0.2676 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10428 Z= 0.145 Angle : 0.575 5.738 14088 Z= 0.302 Chirality : 0.040 0.153 1746 Planarity : 0.004 0.034 1677 Dihedral : 10.069 69.355 1929 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.57 % Allowed : 13.18 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.23), residues: 1272 helix: -0.50 (0.17), residues: 930 sheet: -2.37 (0.65), residues: 60 loop : -1.93 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 441 HIS 0.000 0.000 HIS A 296 PHE 0.020 0.002 PHE A 357 TYR 0.011 0.001 TYR C 257 ARG 0.002 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.05302 ( 651) hydrogen bonds : angle 4.87344 ( 1944) covalent geometry : bond 0.00337 (10428) covalent geometry : angle 0.57523 (14088) *********************** 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 143 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 0.999 Fit side-chains REVERT: A 60 MET cc_start: 0.9144 (mmt) cc_final: 0.8818 (mmt) REVERT: A 232 LYS cc_start: 0.8844 (mtmt) cc_final: 0.8404 (mtmt) REVERT: A 315 ARG cc_start: 0.7800 (mmt90) cc_final: 0.6500 (ttt90) REVERT: B 60 MET cc_start: 0.9129 (mmt) cc_final: 0.8920 (mmt) REVERT: B 231 GLU cc_start: 0.8686 (tp30) cc_final: 0.8388 (tp30) REVERT: B 255 MET cc_start: 0.9045 (mmt) cc_final: 0.8455 (mmt) REVERT: B 315 ARG cc_start: 0.8004 (mmt90) cc_final: 0.6793 (ttt90) REVERT: C 90 ILE cc_start: 0.8794 (tt) cc_final: 0.8531 (tt) REVERT: C 232 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8535 (mtmt) REVERT: C 255 MET cc_start: 0.9002 (mmt) cc_final: 0.8702 (mmm) REVERT: C 286 MET cc_start: 0.7968 (mtm) cc_final: 0.7671 (mtp) REVERT: C 315 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7540 (mmt90) REVERT: C 449 MET cc_start: 0.8526 (ttp) cc_final: 0.8293 (ttp) outliers start: 6 outliers final: 6 residues processed: 143 average time/residue: 0.1787 time to fit residues: 38.6681 Evaluate side-chains 121 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 115 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 64 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.130944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092674 restraints weight = 11625.190| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.62 r_work: 0.2702 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10428 Z= 0.115 Angle : 0.523 5.547 14088 Z= 0.269 Chirality : 0.039 0.132 1746 Planarity : 0.003 0.030 1677 Dihedral : 9.455 68.096 1929 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.76 % Allowed : 14.61 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1272 helix: 0.44 (0.18), residues: 921 sheet: -2.19 (0.67), residues: 60 loop : -1.59 (0.34), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.010 0.001 PHE B 159 TYR 0.011 0.001 TYR C 257 ARG 0.001 0.000 ARG C 280 Details of bonding type rmsd hydrogen bonds : bond 0.04367 ( 651) hydrogen bonds : angle 4.43349 ( 1944) covalent geometry : bond 0.00255 (10428) covalent geometry : angle 0.52318 (14088) *********************** 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: 8 poor density : 135 time to evaluate : 1.182 Fit side-chains REVERT: A 232 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8406 (mtmt) REVERT: A 255 MET cc_start: 0.8888 (mmt) cc_final: 0.8224 (mmt) REVERT: A 309 VAL cc_start: 0.8998 (t) cc_final: 0.8723 (m) REVERT: A 315 ARG cc_start: 0.7792 (mmt90) cc_final: 0.6512 (ttt90) REVERT: B 60 MET cc_start: 0.9015 (mmt) cc_final: 0.8755 (mmt) REVERT: B 231 GLU cc_start: 0.8751 (tp30) cc_final: 0.8469 (tp30) REVERT: B 255 MET cc_start: 0.9007 (mmt) cc_final: 0.8448 (mmt) REVERT: B 286 MET cc_start: 0.7896 (mtt) cc_final: 0.7524 (mtp) REVERT: B 315 ARG cc_start: 0.7946 (mmt90) cc_final: 0.6725 (ttt90) REVERT: B 357 PHE cc_start: 0.8086 (t80) cc_final: 0.7803 (t80) REVERT: C 90 ILE cc_start: 0.8695 (tt) cc_final: 0.8396 (tt) REVERT: C 231 GLU cc_start: 0.8677 (tp30) cc_final: 0.8313 (tp30) REVERT: C 232 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8544 (mtmt) REVERT: C 255 MET cc_start: 0.8937 (mmt) cc_final: 0.8680 (mmm) REVERT: C 286 MET cc_start: 0.7806 (mtm) cc_final: 0.7535 (mtp) REVERT: C 315 ARG cc_start: 0.7725 (mmt90) cc_final: 0.7436 (mmt90) REVERT: C 343 CYS cc_start: 0.9223 (m) cc_final: 0.8916 (m) REVERT: C 449 MET cc_start: 0.8473 (ttp) cc_final: 0.8231 (ttp) outliers start: 8 outliers final: 6 residues processed: 142 average time/residue: 0.2062 time to fit residues: 44.7484 Evaluate side-chains 130 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 124 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain C residue 22 LEU 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 95 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.129397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.091036 restraints weight = 11486.136| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 1.61 r_work: 0.2674 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1873 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= 0.141 Angle : 0.537 5.554 14088 Z= 0.274 Chirality : 0.040 0.153 1746 Planarity : 0.003 0.030 1677 Dihedral : 9.465 66.200 1929 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.91 % Allowed : 15.28 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1272 helix: 0.66 (0.18), residues: 936 sheet: -2.08 (0.67), residues: 60 loop : -1.35 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.014 0.001 PHE B 159 TYR 0.011 0.001 TYR B 257 ARG 0.001 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 651) hydrogen bonds : angle 4.32067 ( 1944) covalent geometry : bond 0.00339 (10428) covalent geometry : angle 0.53683 (14088) *********************** 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 151 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.112 Fit side-chains REVERT: A 232 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8483 (mtmt) REVERT: A 255 MET cc_start: 0.8886 (mmt) cc_final: 0.8248 (mmt) REVERT: A 315 ARG cc_start: 0.7847 (mmt90) cc_final: 0.6523 (ttt90) REVERT: B 60 MET cc_start: 0.8987 (mmt) cc_final: 0.8749 (mmt) REVERT: B 231 GLU cc_start: 0.8755 (tp30) cc_final: 0.8493 (tp30) REVERT: B 235 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8244 (tp) REVERT: B 255 MET cc_start: 0.9035 (mmt) cc_final: 0.8501 (mmt) REVERT: B 315 ARG cc_start: 0.7840 (mmt90) cc_final: 0.6640 (ttt90) REVERT: C 90 ILE cc_start: 0.8711 (tt) cc_final: 0.8420 (tt) REVERT: C 232 LYS cc_start: 0.8949 (mtmt) cc_final: 0.8514 (mtmt) REVERT: C 255 MET cc_start: 0.8984 (mmt) cc_final: 0.8707 (mmm) REVERT: C 272 GLU cc_start: 0.7844 (mp0) cc_final: 0.7629 (mp0) REVERT: C 315 ARG cc_start: 0.7618 (mmt90) cc_final: 0.7311 (mmt90) REVERT: C 328 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8233 (mp) REVERT: C 343 CYS cc_start: 0.9223 (m) cc_final: 0.8871 (m) outliers start: 20 outliers final: 15 residues processed: 147 average time/residue: 0.1817 time to fit residues: 40.4656 Evaluate side-chains 142 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 271 ILE Chi-restraints excluded: chain A residue 373 TYR 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 359 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 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 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 101 optimal weight: 6.9990 chunk 3 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- 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 = 0.3352 r_free = 0.3352 target = 0.129486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.090641 restraints weight = 11552.819| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 1.65 r_work: 0.2667 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1972 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= 0.136 Angle : 0.534 9.304 14088 Z= 0.270 Chirality : 0.040 0.135 1746 Planarity : 0.003 0.029 1677 Dihedral : 9.377 64.101 1929 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.29 % Allowed : 15.57 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1272 helix: 0.83 (0.18), residues: 942 sheet: -2.04 (0.67), residues: 60 loop : -1.22 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.013 0.001 PHE B 159 TYR 0.011 0.001 TYR B 257 ARG 0.001 0.000 ARG B 310 Details of bonding type rmsd hydrogen bonds : bond 0.04545 ( 651) hydrogen bonds : angle 4.22944 ( 1944) covalent geometry : bond 0.00325 (10428) covalent geometry : angle 0.53406 (14088) *********************** 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: 24 poor density : 134 time to evaluate : 1.179 Fit side-chains REVERT: A 232 LYS cc_start: 0.8821 (mtmt) cc_final: 0.8546 (mtmt) REVERT: A 235 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8176 (tp) REVERT: A 255 MET cc_start: 0.8922 (mmt) cc_final: 0.8317 (mmt) REVERT: A 315 ARG cc_start: 0.7841 (mmt90) cc_final: 0.6552 (ttt90) REVERT: B 60 MET cc_start: 0.8973 (mmt) cc_final: 0.8740 (mmt) REVERT: B 231 GLU cc_start: 0.8761 (tp30) cc_final: 0.8487 (tp30) REVERT: B 235 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8260 (tp) REVERT: B 255 MET cc_start: 0.9034 (mmt) cc_final: 0.8521 (mmt) REVERT: B 315 ARG cc_start: 0.7824 (mmt90) cc_final: 0.6660 (ttt90) REVERT: C 90 ILE cc_start: 0.8714 (tt) cc_final: 0.8399 (tt) REVERT: C 232 LYS cc_start: 0.8921 (mtmt) cc_final: 0.8557 (mtmt) REVERT: C 235 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8295 (tp) REVERT: C 255 MET cc_start: 0.8991 (mmt) cc_final: 0.8724 (mmm) REVERT: C 272 GLU cc_start: 0.7881 (mp0) cc_final: 0.7613 (mp0) REVERT: C 315 ARG cc_start: 0.7628 (mmt90) cc_final: 0.7307 (mmt90) REVERT: C 328 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8258 (mp) REVERT: C 343 CYS cc_start: 0.9178 (m) cc_final: 0.8828 (m) outliers start: 24 outliers final: 15 residues processed: 152 average time/residue: 0.1901 time to fit residues: 43.6682 Evaluate side-chains 150 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 373 TYR Chi-restraints excluded: chain A residue 387 LEU 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 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 271 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 373 TYR 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 65 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.131453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.092564 restraints weight = 11537.641| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 1.65 r_work: 0.2697 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2157 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= 0.111 Angle : 0.505 7.213 14088 Z= 0.256 Chirality : 0.039 0.143 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.994 61.708 1929 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.81 % Allowed : 16.52 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.25), residues: 1272 helix: 1.23 (0.18), residues: 930 sheet: -1.70 (0.64), residues: 66 loop : -1.18 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.021 0.001 PHE A 357 TYR 0.010 0.001 TYR B 257 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 651) hydrogen bonds : angle 4.09002 ( 1944) covalent geometry : bond 0.00250 (10428) covalent geometry : angle 0.50495 (14088) *********************** 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 160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.041 Fit side-chains REVERT: A 232 LYS cc_start: 0.8842 (mtmt) cc_final: 0.8511 (mtmt) REVERT: A 235 ILE cc_start: 0.8451 (OUTLIER) cc_final: 0.8141 (tp) REVERT: A 258 MET cc_start: 0.8342 (tmm) cc_final: 0.8118 (tmm) REVERT: A 315 ARG cc_start: 0.7749 (mmt90) cc_final: 0.6471 (ttt90) REVERT: A 347 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8486 (m-40) REVERT: B 60 MET cc_start: 0.8916 (mmt) cc_final: 0.8671 (mmt) REVERT: B 231 GLU cc_start: 0.8746 (tp30) cc_final: 0.8498 (tp30) REVERT: B 235 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8284 (tp) REVERT: B 255 MET cc_start: 0.8995 (mmt) cc_final: 0.8462 (mmt) REVERT: B 315 ARG cc_start: 0.7798 (mmt90) cc_final: 0.6645 (ttt90) REVERT: B 440 ASP cc_start: 0.8061 (t0) cc_final: 0.7734 (t0) REVERT: C 90 ILE cc_start: 0.8657 (tt) cc_final: 0.8365 (tt) REVERT: C 232 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8564 (mtmt) REVERT: C 235 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8273 (tp) REVERT: C 272 GLU cc_start: 0.7739 (mp0) cc_final: 0.7460 (mp0) REVERT: C 315 ARG cc_start: 0.7551 (mmt90) cc_final: 0.7219 (mmt90) REVERT: C 328 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8284 (mp) outliers start: 19 outliers final: 12 residues processed: 154 average time/residue: 0.2298 time to fit residues: 53.0358 Evaluate side-chains 154 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 137 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.127973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.089299 restraints weight = 11732.289| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.62 r_work: 0.2652 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10428 Z= 0.172 Angle : 0.568 6.468 14088 Z= 0.288 Chirality : 0.041 0.146 1746 Planarity : 0.003 0.029 1677 Dihedral : 9.300 59.712 1929 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.10 % Allowed : 17.00 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1272 helix: 1.09 (0.18), residues: 939 sheet: -1.71 (0.65), residues: 66 loop : -1.14 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 441 HIS 0.001 0.000 HIS A 296 PHE 0.017 0.002 PHE B 159 TYR 0.013 0.001 TYR A 257 ARG 0.002 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.05009 ( 651) hydrogen bonds : angle 4.21560 ( 1944) covalent geometry : bond 0.00428 (10428) covalent geometry : angle 0.56810 (14088) *********************** 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 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.388 Fit side-chains REVERT: A 232 LYS cc_start: 0.8712 (mtmt) cc_final: 0.8504 (mtmt) REVERT: A 235 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8262 (tp) REVERT: A 315 ARG cc_start: 0.7722 (mmt90) cc_final: 0.6446 (ttt90) REVERT: B 60 MET cc_start: 0.8967 (mmt) cc_final: 0.8733 (mmt) REVERT: B 231 GLU cc_start: 0.8756 (tp30) cc_final: 0.8548 (tm-30) REVERT: B 255 MET cc_start: 0.9040 (mmt) cc_final: 0.8490 (mmt) REVERT: B 315 ARG cc_start: 0.7794 (mmt90) cc_final: 0.6658 (ttt90) REVERT: C 90 ILE cc_start: 0.8696 (tt) cc_final: 0.8401 (tt) REVERT: C 232 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8449 (mtmt) REVERT: C 235 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8349 (tp) REVERT: C 255 MET cc_start: 0.9014 (mmt) cc_final: 0.8736 (mmm) REVERT: C 272 GLU cc_start: 0.7826 (mp0) cc_final: 0.7477 (mp0) REVERT: C 315 ARG cc_start: 0.7594 (mmt90) cc_final: 0.7252 (mmt90) REVERT: C 328 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8324 (mp) REVERT: C 343 CYS cc_start: 0.9149 (m) cc_final: 0.8805 (m) outliers start: 22 outliers final: 17 residues processed: 154 average time/residue: 0.2001 time to fit residues: 46.4239 Evaluate side-chains 155 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 1.495 ------------------------------------------------------------------------------- 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 A residue 402 THR Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 270 ILE 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 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 Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 92 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.131480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.092976 restraints weight = 11547.963| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 1.61 r_work: 0.2707 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2264 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= 0.110 Angle : 0.505 6.908 14088 Z= 0.256 Chirality : 0.039 0.150 1746 Planarity : 0.003 0.029 1677 Dihedral : 8.785 59.881 1929 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.72 % Allowed : 17.48 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.25), residues: 1272 helix: 1.41 (0.18), residues: 927 sheet: -1.50 (0.66), residues: 66 loop : -1.11 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.020 0.001 PHE A 357 TYR 0.010 0.001 TYR C 257 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 651) hydrogen bonds : angle 4.05573 ( 1944) covalent geometry : bond 0.00243 (10428) covalent geometry : angle 0.50490 (14088) *********************** 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 158 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 1.175 Fit side-chains REVERT: A 232 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8523 (mtmt) REVERT: A 235 ILE cc_start: 0.8448 (OUTLIER) cc_final: 0.8120 (tp) REVERT: A 315 ARG cc_start: 0.7681 (mmt90) cc_final: 0.6413 (ttt90) REVERT: A 347 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8462 (m-40) REVERT: B 60 MET cc_start: 0.8868 (mmt) cc_final: 0.8621 (mmt) REVERT: B 231 GLU cc_start: 0.8694 (tp30) cc_final: 0.8483 (tm-30) REVERT: B 255 MET cc_start: 0.8986 (mmt) cc_final: 0.8509 (mmt) REVERT: B 315 ARG cc_start: 0.7766 (mmt90) cc_final: 0.6526 (ttt90) REVERT: B 440 ASP cc_start: 0.8086 (t0) cc_final: 0.7727 (t0) REVERT: C 90 ILE cc_start: 0.8620 (tt) cc_final: 0.8330 (tt) REVERT: C 232 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8431 (mtmt) REVERT: C 235 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8242 (tp) REVERT: C 255 MET cc_start: 0.8946 (mmt) cc_final: 0.8718 (mmm) REVERT: C 272 GLU cc_start: 0.7759 (mp0) cc_final: 0.7431 (mp0) REVERT: C 315 ARG cc_start: 0.7525 (mmt90) cc_final: 0.7172 (mmt90) REVERT: C 328 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8247 (mp) outliers start: 18 outliers final: 13 residues processed: 152 average time/residue: 0.1837 time to fit residues: 42.4725 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 : 1.101 ------------------------------------------------------------------------------- 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 270 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 119 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3368 r_free = 0.3368 target = 0.131024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.092663 restraints weight = 11584.157| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.61 r_work: 0.2701 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2562 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2312 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= 0.114 Angle : 0.508 7.327 14088 Z= 0.258 Chirality : 0.039 0.154 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.630 59.533 1929 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.81 % Allowed : 17.67 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.25), residues: 1272 helix: 1.47 (0.18), residues: 930 sheet: -1.32 (0.67), residues: 66 loop : -1.11 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 441 HIS 0.000 0.000 HIS B 296 PHE 0.019 0.001 PHE A 357 TYR 0.010 0.001 TYR C 257 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 651) hydrogen bonds : angle 4.02562 ( 1944) covalent geometry : bond 0.00258 (10428) covalent geometry : angle 0.50842 (14088) *********************** 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 160 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 141 time to evaluate : 1.434 Fit side-chains REVERT: A 232 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8486 (mtmt) REVERT: A 235 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8112 (tp) REVERT: A 315 ARG cc_start: 0.7649 (mmt90) cc_final: 0.6374 (ttt90) REVERT: A 347 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8464 (m-40) REVERT: B 60 MET cc_start: 0.8864 (mmt) cc_final: 0.8615 (mmt) REVERT: B 235 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8232 (tp) REVERT: B 255 MET cc_start: 0.8974 (mmt) cc_final: 0.8430 (mmt) REVERT: B 258 MET cc_start: 0.8277 (tmm) cc_final: 0.8043 (tmm) REVERT: B 315 ARG cc_start: 0.7769 (mmt90) cc_final: 0.6533 (ttt90) REVERT: B 440 ASP cc_start: 0.8099 (t0) cc_final: 0.7742 (t0) REVERT: C 90 ILE cc_start: 0.8573 (tt) cc_final: 0.8301 (tt) REVERT: C 232 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8434 (mtmt) REVERT: C 235 ILE cc_start: 0.8525 (OUTLIER) cc_final: 0.8211 (tp) REVERT: C 272 GLU cc_start: 0.7788 (mp0) cc_final: 0.7529 (mp0) REVERT: C 315 ARG cc_start: 0.7522 (mmt90) cc_final: 0.7169 (mmt90) REVERT: C 328 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8171 (mp) REVERT: C 433 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (t) outliers start: 19 outliers final: 13 residues processed: 154 average time/residue: 0.1975 time to fit residues: 46.5038 Evaluate side-chains 159 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 270 ILE 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 138 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 20 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 99 optimal weight: 0.2980 chunk 115 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.132006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.093694 restraints weight = 11571.540| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.61 r_work: 0.2717 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10428 Z= 0.107 Angle : 0.507 7.673 14088 Z= 0.256 Chirality : 0.039 0.158 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.434 59.580 1929 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.62 % Allowed : 17.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.25), residues: 1272 helix: 1.57 (0.18), residues: 930 sheet: -1.17 (0.69), residues: 66 loop : -1.09 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.022 0.001 PHE A 357 TYR 0.014 0.001 TYR C 257 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 651) hydrogen bonds : angle 3.97531 ( 1944) covalent geometry : bond 0.00236 (10428) covalent geometry : angle 0.50681 (14088) ********************** 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 157 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.165 Fit side-chains REVERT: A 232 LYS cc_start: 0.8782 (mtmt) cc_final: 0.8471 (mtmt) REVERT: A 235 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8104 (tp) REVERT: A 315 ARG cc_start: 0.7637 (mmt90) cc_final: 0.6377 (ttt90) REVERT: A 347 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8445 (m-40) REVERT: B 60 MET cc_start: 0.8811 (mmt) cc_final: 0.8597 (mmt) REVERT: B 235 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8201 (tp) REVERT: B 255 MET cc_start: 0.8949 (mmt) cc_final: 0.8430 (mmt) REVERT: B 315 ARG cc_start: 0.7809 (mmt90) cc_final: 0.6549 (ttt90) REVERT: B 440 ASP cc_start: 0.8074 (t0) cc_final: 0.7726 (t0) REVERT: C 90 ILE cc_start: 0.8529 (tt) cc_final: 0.8259 (tt) REVERT: C 232 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8445 (mtmt) REVERT: C 235 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8181 (tp) REVERT: C 255 MET cc_start: 0.8947 (mmt) cc_final: 0.8734 (mmm) REVERT: C 272 GLU cc_start: 0.7767 (mp0) cc_final: 0.7509 (mp0) REVERT: C 315 ARG cc_start: 0.7515 (mmt90) cc_final: 0.7156 (mmt90) REVERT: C 328 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8020 (mp) outliers start: 17 outliers final: 12 residues processed: 152 average time/residue: 0.2320 time to fit residues: 54.0785 Evaluate side-chains 157 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.119 ------------------------------------------------------------------------------- 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 270 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 93 optimal weight: 7.9990 chunk 104 optimal weight: 0.0470 chunk 18 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.3390 r_free = 0.3390 target = 0.133120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.094383 restraints weight = 11413.430| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.64 r_work: 0.2722 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2488 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= 0.103 Angle : 0.498 7.722 14088 Z= 0.252 Chirality : 0.039 0.153 1746 Planarity : 0.003 0.028 1677 Dihedral : 8.118 59.660 1929 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.72 % Allowed : 17.77 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1272 helix: 1.69 (0.18), residues: 927 sheet: -1.05 (0.69), residues: 66 loop : -1.07 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP C 441 HIS 0.001 0.000 HIS B 296 PHE 0.019 0.001 PHE A 357 TYR 0.009 0.001 TYR C 257 ARG 0.001 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 651) hydrogen bonds : angle 3.91670 ( 1944) covalent geometry : bond 0.00224 (10428) covalent geometry : angle 0.49767 (14088) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5557.38 seconds wall clock time: 100 minutes 28.90 seconds (6028.90 seconds total)