Starting phenix.real_space_refine on Sat Sep 12 06:26:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wqz_21874/09_2026/6wqz_21874.cif" } resolution = 2.8 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= 0.010 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 9258 2.51 5 N 2324 2.21 5 O 2474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14128 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4393 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 514} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "F" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 175 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'TRANS': 34} Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'UNK:plan-1': 35} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4393 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 514} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4393 Classifications: {'peptide': 536} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 514} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 180 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'TRANS': 35} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'UNK:plan-1': 36} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 138 Unusual residues: {'LMN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.04, per 1000 atoms: 0.22 Number of scatterers: 14128 At special positions: 0 Unit cell: (129.32, 121.9, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2474 8.00 N 2324 7.00 C 9258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 524.9 milliseconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3274 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 6 sheets defined 79.9% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 42 through 56 removed outlier: 3.601A pdb=" N PHE C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 86 removed outlier: 3.618A pdb=" N PHE C 73 " --> pdb=" O GLU C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 94 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 118 through 128 removed outlier: 4.411A pdb=" N ALA C 124 " --> pdb=" O GLN C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 168 removed outlier: 4.287A pdb=" N GLU C 159 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE C 160 " --> pdb=" O CYS C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 194 removed outlier: 4.620A pdb=" N LYS C 192 " --> pdb=" O VAL C 188 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 225 removed outlier: 6.128A pdb=" N PHE C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N GLN C 216 " --> pdb=" O ILE C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 270 through 275 removed outlier: 3.530A pdb=" N LYS C 274 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 323 Proline residue: C 302 - end of helix removed outlier: 4.244A pdb=" N SER C 315 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 329 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 346 through 357 Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.910A pdb=" N ALA C 361 " --> pdb=" O GLY C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 398 Processing helix chain 'C' and resid 406 through 425 Processing helix chain 'C' and resid 433 through 446 Processing helix chain 'C' and resid 449 through 453 removed outlier: 3.575A pdb=" N TRP C 452 " --> pdb=" O PRO C 449 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 453 " --> pdb=" O ASP C 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 449 through 453' Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.839A pdb=" N GLN C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 481 Processing helix chain 'C' and resid 481 through 493 Proline residue: C 487 - end of helix Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 497 through 508 Processing helix chain 'C' and resid 520 through 524 removed outlier: 3.750A pdb=" N GLN C 523 " --> pdb=" O SER C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 564 Processing helix chain 'C' and resid 570 through 587 Processing helix chain 'F' and resid 690 through 700 Processing helix chain 'F' and resid 705 through 723 Processing helix chain 'B' and resid 42 through 56 removed outlier: 3.599A pdb=" N PHE B 46 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 86 removed outlier: 3.617A pdb=" N PHE B 73 " --> pdb=" O GLU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 94 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.409A pdb=" N ALA B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 168 removed outlier: 4.289A pdb=" N GLU B 159 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE B 160 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 194 removed outlier: 4.619A pdb=" N LYS B 192 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 removed outlier: 6.128A pdb=" N PHE B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN B 216 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.531A pdb=" N LYS B 274 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 314 Proline residue: B 302 - end of helix Processing helix chain 'B' and resid 315 through 323 Processing helix chain 'B' and resid 325 through 329 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 346 through 357 Processing helix chain 'B' and resid 357 through 366 removed outlier: 3.912A pdb=" N ALA B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 398 Processing helix chain 'B' and resid 406 through 425 Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 449 through 453 removed outlier: 3.576A pdb=" N TRP B 452 " --> pdb=" O PRO B 449 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN B 453 " --> pdb=" O ASP B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 453' Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.839A pdb=" N GLN B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 Processing helix chain 'B' and resid 481 through 493 Proline residue: B 487 - end of helix Processing helix chain 'B' and resid 494 through 496 No H-bonds generated for 'chain 'B' and resid 494 through 496' Processing helix chain 'B' and resid 497 through 508 Processing helix chain 'B' and resid 520 through 524 removed outlier: 3.749A pdb=" N GLN B 523 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'B' and resid 570 through 587 Processing helix chain 'A' and resid 42 through 56 removed outlier: 3.599A pdb=" N PHE A 46 " --> pdb=" O ASN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 86 removed outlier: 3.616A pdb=" N PHE A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.411A pdb=" N ALA A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 168 removed outlier: 4.289A pdb=" N GLU A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 160 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 removed outlier: 4.620A pdb=" N LYS A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 6.129A pdb=" N PHE A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLN A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 256 Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.530A pdb=" N LYS A 274 " --> pdb=" O ALA A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 323 Proline residue: A 302 - end of helix removed outlier: 4.251A pdb=" N SER A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 329 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 346 through 357 Processing helix chain 'A' and resid 357 through 366 removed outlier: 3.913A pdb=" N ALA A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 398 Processing helix chain 'A' and resid 406 through 425 Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 449 through 453 removed outlier: 3.577A pdb=" N TRP A 452 " --> pdb=" O PRO A 449 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN A 453 " --> pdb=" O ASP A 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 449 through 453' Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.840A pdb=" N GLN A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 481 Processing helix chain 'A' and resid 481 through 493 Proline residue: A 487 - end of helix Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 497 through 508 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.750A pdb=" N GLN A 523 " --> pdb=" O SER A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 564 Processing helix chain 'A' and resid 570 through 587 Processing helix chain 'E' and resid 690 through 700 Processing helix chain 'E' and resid 706 through 724 Processing helix chain 'D' and resid 690 through 700 Processing helix chain 'D' and resid 706 through 724 Processing sheet with id=AA1, first strand: chain 'C' and resid 231 through 233 Processing sheet with id=AA2, first strand: chain 'C' and resid 510 through 512 Processing sheet with id=AA3, first strand: chain 'B' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'B' and resid 510 through 512 Processing sheet with id=AA5, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA6, first strand: chain 'A' and resid 510 through 512 900 hydrogen bonds defined for protein. 2619 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: 2.07 Time building geometry restraints manager: 1.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.03 - 1.18: 16 1.18 - 1.34: 4392 1.34 - 1.50: 4557 1.50 - 1.65: 5447 1.65 - 1.81: 100 Bond restraints: 14512 Sorted by residual: bond pdb=" C TYR B 311 " pdb=" O TYR B 311 " ideal model delta sigma weight residual 1.237 1.027 0.210 1.19e-02 7.06e+03 3.10e+02 bond pdb=" C TYR C 311 " pdb=" O TYR C 311 " ideal model delta sigma weight residual 1.237 1.053 0.184 1.17e-02 7.31e+03 2.47e+02 bond pdb=" C TYR A 311 " pdb=" O TYR A 311 " ideal model delta sigma weight residual 1.237 1.056 0.180 1.17e-02 7.31e+03 2.37e+02 bond pdb=" C PHE B 314 " pdb=" O PHE B 314 " ideal model delta sigma weight residual 1.235 1.041 0.194 1.33e-02 5.65e+03 2.14e+02 bond pdb=" C TYR C 447 " pdb=" O TYR C 447 " ideal model delta sigma weight residual 1.235 1.076 0.159 1.12e-02 7.97e+03 2.02e+02 ... (remaining 14507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.03: 19653 8.03 - 16.06: 72 16.06 - 24.09: 6 24.09 - 32.13: 0 32.13 - 40.16: 2 Bond angle restraints: 19733 Sorted by residual: angle pdb=" O CYS C 367 " pdb=" C CYS C 367 " pdb=" N PHE C 368 " ideal model delta sigma weight residual 122.12 81.96 40.16 1.06e+00 8.90e-01 1.44e+03 angle pdb=" O CYS B 367 " pdb=" C CYS B 367 " pdb=" N PHE B 368 " ideal model delta sigma weight residual 122.12 82.18 39.94 1.06e+00 8.90e-01 1.42e+03 angle pdb=" CA ASN A 366 " pdb=" C ASN A 366 " pdb=" N CYS A 367 " ideal model delta sigma weight residual 118.36 132.28 -13.92 1.33e+00 5.65e-01 1.09e+02 angle pdb=" CA TYR A 311 " pdb=" C TYR A 311 " pdb=" O TYR A 311 " ideal model delta sigma weight residual 120.55 109.81 10.74 1.06e+00 8.90e-01 1.03e+02 angle pdb=" CA CYS B 367 " pdb=" C CYS B 367 " pdb=" N PHE B 368 " ideal model delta sigma weight residual 117.30 105.74 11.56 1.16e+00 7.43e-01 9.93e+01 ... (remaining 19728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.46: 7792 29.46 - 58.93: 478 58.93 - 88.39: 47 88.39 - 117.85: 14 117.85 - 147.31: 9 Dihedral angle restraints: 8340 sinusoidal: 3303 harmonic: 5037 Sorted by residual: dihedral pdb=" CA UNK E 701 " pdb=" C UNK E 701 " pdb=" N UNK E 702 " pdb=" CA UNK E 702 " ideal model delta harmonic sigma weight residual 180.00 75.71 104.29 0 5.00e+00 4.00e-02 4.35e+02 dihedral pdb=" CA UNK F 702 " pdb=" C UNK F 702 " pdb=" N UNK F 703 " pdb=" CA UNK F 703 " ideal model delta harmonic sigma weight residual 180.00 86.83 93.17 0 5.00e+00 4.00e-02 3.47e+02 dihedral pdb=" CA UNK D 701 " pdb=" C UNK D 701 " pdb=" N UNK D 702 " pdb=" CA UNK D 702 " ideal model delta harmonic sigma weight residual 180.00 97.05 82.95 0 5.00e+00 4.00e-02 2.75e+02 ... (remaining 8337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.200: 2209 0.200 - 0.401: 46 0.401 - 0.601: 15 0.601 - 0.801: 2 0.801 - 1.002: 1 Chirality restraints: 2273 Sorted by residual: chirality pdb=" CA UNK F 703 " pdb=" N UNK F 703 " pdb=" C UNK F 703 " pdb=" CB UNK F 703 " both_signs ideal model delta sigma weight residual False 2.52 1.52 1.00 2.00e-01 2.50e+01 2.51e+01 chirality pdb=" CG LEU B 310 " pdb=" CB LEU B 310 " pdb=" CD1 LEU B 310 " pdb=" CD2 LEU B 310 " both_signs ideal model delta sigma weight residual False -2.59 -1.89 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" CA TYR A 311 " pdb=" N TYR A 311 " pdb=" C TYR A 311 " pdb=" CB TYR A 311 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.12e+01 ... (remaining 2270 not shown) Planarity restraints: 2414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 367 " -0.158 2.00e-02 2.50e+03 2.47e-01 6.08e+02 pdb=" C CYS C 367 " 0.422 2.00e-02 2.50e+03 pdb=" O CYS C 367 " -0.183 2.00e-02 2.50e+03 pdb=" N PHE C 368 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 367 " -0.156 2.00e-02 2.50e+03 2.45e-01 6.01e+02 pdb=" C CYS B 367 " 0.420 2.00e-02 2.50e+03 pdb=" O CYS B 367 " -0.180 2.00e-02 2.50e+03 pdb=" N PHE B 368 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 447 " -0.108 2.00e-02 2.50e+03 6.18e-02 7.63e+01 pdb=" CG TYR B 447 " 0.123 2.00e-02 2.50e+03 pdb=" CD1 TYR B 447 " 0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR B 447 " 0.019 2.00e-02 2.50e+03 pdb=" CE1 TYR B 447 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR B 447 " -0.026 2.00e-02 2.50e+03 pdb=" CZ TYR B 447 " 0.017 2.00e-02 2.50e+03 pdb=" OH TYR B 447 " -0.034 2.00e-02 2.50e+03 ... (remaining 2411 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 63 2.40 - 3.02: 8455 3.02 - 3.65: 20586 3.65 - 4.27: 32098 4.27 - 4.90: 53722 Nonbonded interactions: 114924 Sorted by model distance: nonbonded pdb=" O UNK E 697 " pdb=" O UNK E 701 " model vdw 1.771 3.040 nonbonded pdb=" NE2 HIS C 39 " pdb=" O ILE C 198 " model vdw 2.057 3.120 nonbonded pdb=" NE2 HIS B 39 " pdb=" O ILE B 198 " model vdw 2.057 3.120 nonbonded pdb=" NE2 HIS A 39 " pdb=" O ILE A 198 " model vdw 2.059 3.120 nonbonded pdb=" CG1 VAL B 404 " pdb=" CG2 VAL B 407 " model vdw 2.068 3.880 ... (remaining 114919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 690 through 724) selection = (chain 'E' and resid 690 through 724) selection = chain 'F' } 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.470 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:7.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 0.016 0.210 14512 Z= 0.893 Angle : 1.443 40.157 19733 Z= 0.842 Chirality : 0.085 1.002 2273 Planarity : 0.010 0.247 2414 Dihedral : 19.307 147.314 5066 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 1.13 % Allowed : 8.55 % Favored : 90.31 % Rotamer: Outliers : 4.37 % Allowed : 10.92 % Favored : 84.71 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.19), residues: 1590 helix: -0.69 (0.15), residues: 1047 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 422 TYR 0.123 0.006 TYR B 447 PHE 0.026 0.003 PHE B 314 TRP 0.025 0.003 TRP C 180 HIS 0.009 0.002 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.01598 / 0.89 (14512) covalent geometry : angle 1.44305 / 0.84 (19733) hydrogen bonds : bond 0.14715 / 9.83 ( 900) hydrogen bonds : angle 6.28016 / 4.53 ( 2619) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 277 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 354 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7753 (mt) REVERT: B 61 CYS cc_start: 0.6384 (OUTLIER) cc_final: 0.6156 (m) REVERT: B 62 MET cc_start: 0.7957 (ttm) cc_final: 0.7680 (ttm) REVERT: B 69 GLU cc_start: 0.7084 (mt-10) cc_final: 0.6681 (mt-10) REVERT: B 90 ASP cc_start: 0.5933 (OUTLIER) cc_final: 0.5528 (p0) REVERT: B 249 TYR cc_start: 0.8433 (t80) cc_final: 0.8203 (t80) REVERT: B 387 ILE cc_start: 0.8179 (mt) cc_final: 0.7925 (mt) REVERT: A 90 ASP cc_start: 0.5651 (OUTLIER) cc_final: 0.5371 (p0) REVERT: A 225 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7440 (mtpp) REVERT: A 267 TRP cc_start: 0.7490 (p90) cc_final: 0.7117 (p90) REVERT: A 354 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7846 (mt) outliers start: 62 outliers final: 11 residues processed: 319 average time/residue: 0.5140 time to fit residues: 181.0259 Evaluate side-chains 202 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 186 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 61 CYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 61 CYS Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 455 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 GLN C 217 ASN C 308 GLN C 379 ASN C 428 GLN C 564 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 153 ASN B 217 ASN B 288 ASN B 308 GLN B 379 ASN B 428 GLN B 564 ASN A 42 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN A 217 ASN A 308 GLN A 379 ASN A 428 GLN A 564 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.217517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.168357 restraints weight = 15312.452| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.85 r_work: 0.3735 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14512 Z= 0.145 Angle : 0.681 7.365 19733 Z= 0.340 Chirality : 0.043 0.173 2273 Planarity : 0.005 0.052 2414 Dihedral : 12.758 172.433 1994 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 4.44 % Allowed : 19.17 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.21), residues: 1590 helix: 0.95 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -2.32 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 231 TYR 0.020 0.002 TYR C 471 PHE 0.018 0.001 PHE B 432 TRP 0.015 0.002 TRP B 257 HIS 0.007 0.001 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (14512) covalent geometry : angle 0.68121 / 0.34 (19733) hydrogen bonds : bond 0.04754 / 3.11 ( 900) hydrogen bonds : angle 4.37586 / 3.12 ( 2619) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8435 (ttp) cc_final: 0.8158 (ttm) REVERT: C 181 GLN cc_start: 0.7766 (mm110) cc_final: 0.7352 (mm-40) REVERT: C 225 LYS cc_start: 0.7799 (mtpp) cc_final: 0.7561 (mtpt) REVERT: C 424 PHE cc_start: 0.7838 (m-80) cc_final: 0.7562 (m-80) REVERT: C 524 MET cc_start: 0.6780 (mtt) cc_final: 0.6037 (mtt) REVERT: C 558 MET cc_start: 0.4165 (OUTLIER) cc_final: 0.3542 (tpt) REVERT: B 62 MET cc_start: 0.8447 (ttm) cc_final: 0.8111 (ttm) REVERT: B 69 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7093 (mt-10) REVERT: B 193 GLU cc_start: 0.7258 (mp0) cc_final: 0.7033 (mp0) REVERT: B 205 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5990 (tt0) REVERT: B 249 TYR cc_start: 0.8733 (t80) cc_final: 0.8493 (t80) REVERT: B 250 ASN cc_start: 0.8507 (m-40) cc_final: 0.8302 (m110) REVERT: B 290 ILE cc_start: 0.7940 (tt) cc_final: 0.7361 (mt) REVERT: B 354 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 379 ASN cc_start: 0.8022 (m-40) cc_final: 0.7768 (m110) REVERT: B 497 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6837 (tpp80) REVERT: B 558 MET cc_start: 0.4198 (OUTLIER) cc_final: 0.3256 (tmt) REVERT: A 90 ASP cc_start: 0.5870 (OUTLIER) cc_final: 0.5290 (p0) REVERT: A 149 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7640 (ttmm) REVERT: A 225 LYS cc_start: 0.7654 (mtpp) cc_final: 0.7335 (mtpt) REVERT: A 354 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8126 (mt) REVERT: A 376 LEU cc_start: 0.7414 (OUTLIER) cc_final: 0.7123 (mt) REVERT: A 453 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6788 (pt0) REVERT: A 484 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8500 (mt) REVERT: A 558 MET cc_start: 0.4740 (OUTLIER) cc_final: 0.4150 (tpt) outliers start: 63 outliers final: 21 residues processed: 264 average time/residue: 0.5009 time to fit residues: 146.2682 Evaluate side-chains 212 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 164 TYR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 453 GLN Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 484 ILE Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 76 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 114 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN C 529 HIS B 52 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 181 GLN B 288 ASN B 529 HIS B 564 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 181 GLN A 288 ASN A 379 ASN A 529 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.215740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172133 restraints weight = 15392.128| |-----------------------------------------------------------------------------| r_work (start): 0.3917 rms_B_bonded: 1.62 r_work: 0.3659 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14512 Z= 0.183 Angle : 0.696 7.049 19733 Z= 0.346 Chirality : 0.045 0.221 2273 Planarity : 0.005 0.058 2414 Dihedral : 11.645 177.807 1983 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.18 % Favored : 91.82 % Rotamer: Outliers : 5.00 % Allowed : 20.51 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: 0.32 (0.21), residues: 1590 helix: 1.23 (0.16), residues: 1074 sheet: None (None), residues: 0 loop : -2.03 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 231 TYR 0.014 0.002 TYR C 316 PHE 0.018 0.002 PHE A 432 TRP 0.018 0.002 TRP A 180 HIS 0.006 0.002 HIS A 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (14512) covalent geometry : angle 0.69639 / 0.35 (19733) hydrogen bonds : bond 0.05131 / 3.40 ( 900) hydrogen bonds : angle 4.34934 / 3.12 ( 2619) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 182 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8542 (ttp) cc_final: 0.8086 (ttm) REVERT: C 193 GLU cc_start: 0.7285 (mp0) cc_final: 0.6996 (mt-10) REVERT: C 225 LYS cc_start: 0.7919 (mtpp) cc_final: 0.7644 (mtpt) REVERT: C 290 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7518 (mt) REVERT: C 375 LEU cc_start: 0.7580 (mp) cc_final: 0.7337 (mt) REVERT: C 489 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7343 (mt) REVERT: C 497 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7194 (tpp80) REVERT: C 506 ARG cc_start: 0.8419 (ttp-110) cc_final: 0.8034 (ttp-110) REVERT: C 524 MET cc_start: 0.6604 (mtt) cc_final: 0.6246 (mtt) REVERT: C 558 MET cc_start: 0.4328 (OUTLIER) cc_final: 0.3076 (tmt) REVERT: B 69 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 222 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7620 (tp) REVERT: B 233 ARG cc_start: 0.7718 (mmm160) cc_final: 0.7145 (mtm180) REVERT: B 290 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7627 (mt) REVERT: B 354 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7962 (mt) REVERT: B 375 LEU cc_start: 0.7686 (mp) cc_final: 0.7477 (mt) REVERT: B 453 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6722 (pt0) REVERT: B 558 MET cc_start: 0.4537 (OUTLIER) cc_final: 0.3531 (tmt) REVERT: A 63 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8500 (tt) REVERT: A 224 ASN cc_start: 0.7719 (t0) cc_final: 0.7494 (t0) REVERT: A 225 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7525 (mtpt) REVERT: A 290 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 345 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: A 375 LEU cc_start: 0.7566 (mp) cc_final: 0.7320 (mt) REVERT: A 445 ILE cc_start: 0.7369 (OUTLIER) cc_final: 0.7159 (tp) REVERT: A 489 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7272 (mt) REVERT: A 518 THR cc_start: 0.8136 (p) cc_final: 0.7930 (m) REVERT: A 558 MET cc_start: 0.4280 (OUTLIER) cc_final: 0.3468 (tpt) outliers start: 71 outliers final: 16 residues processed: 228 average time/residue: 0.4948 time to fit residues: 125.6948 Evaluate side-chains 194 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 445 ILE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 116 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 278 GLN A 507 ASN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.215924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164022 restraints weight = 15256.203| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.21 r_work: 0.3690 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14512 Z= 0.133 Angle : 0.621 6.906 19733 Z= 0.310 Chirality : 0.041 0.180 2273 Planarity : 0.005 0.048 2414 Dihedral : 10.176 140.490 1973 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.88 % Allowed : 22.76 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: 0.90 (0.22), residues: 1590 helix: 1.72 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : -1.90 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.013 0.001 TYR C 152 PHE 0.016 0.001 PHE B 432 TRP 0.012 0.001 TRP B 180 HIS 0.005 0.001 HIS C 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (14512) covalent geometry : angle 0.62061 / 0.31 (19733) hydrogen bonds : bond 0.04335 / 2.87 ( 900) hydrogen bonds : angle 4.15541 / 2.97 ( 2619) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8431 (ttp) cc_final: 0.7916 (ttm) REVERT: C 193 GLU cc_start: 0.7175 (mp0) cc_final: 0.6931 (mt-10) REVERT: C 250 ASN cc_start: 0.8569 (m-40) cc_final: 0.8351 (m110) REVERT: C 375 LEU cc_start: 0.7388 (mp) cc_final: 0.7105 (mt) REVERT: C 462 ARG cc_start: 0.7723 (tmm160) cc_final: 0.7157 (tmt-80) REVERT: C 489 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7200 (mt) REVERT: C 497 ARG cc_start: 0.7358 (OUTLIER) cc_final: 0.7053 (tpp80) REVERT: C 506 ARG cc_start: 0.8353 (ttp-110) cc_final: 0.7987 (ttp-110) REVERT: C 524 MET cc_start: 0.6625 (mtt) cc_final: 0.6288 (mtt) REVERT: C 558 MET cc_start: 0.4135 (OUTLIER) cc_final: 0.2986 (tmt) REVERT: B 40 ILE cc_start: 0.3387 (OUTLIER) cc_final: 0.3143 (pp) REVERT: B 62 MET cc_start: 0.8522 (ttm) cc_final: 0.8106 (ttm) REVERT: B 224 ASN cc_start: 0.7322 (t0) cc_final: 0.6970 (t0) REVERT: B 233 ARG cc_start: 0.7555 (mmm160) cc_final: 0.7028 (mtm180) REVERT: B 290 ILE cc_start: 0.7958 (tt) cc_final: 0.7459 (mt) REVERT: B 327 LEU cc_start: 0.8194 (mt) cc_final: 0.7774 (mm) REVERT: B 354 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7896 (mt) REVERT: B 445 ILE cc_start: 0.7543 (OUTLIER) cc_final: 0.7267 (tp) REVERT: B 558 MET cc_start: 0.4393 (OUTLIER) cc_final: 0.3558 (tmt) REVERT: A 63 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8353 (tp) REVERT: A 149 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7631 (ttmm) REVERT: A 193 GLU cc_start: 0.7027 (mp0) cc_final: 0.6521 (mt-10) REVERT: A 224 ASN cc_start: 0.7512 (t0) cc_final: 0.7310 (t0) REVERT: A 225 LYS cc_start: 0.7793 (mtpp) cc_final: 0.7374 (mtpt) REVERT: A 233 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7200 (mpp-170) REVERT: A 264 LEU cc_start: 0.6311 (OUTLIER) cc_final: 0.5580 (tt) REVERT: A 345 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 375 LEU cc_start: 0.7428 (mp) cc_final: 0.7185 (mt) REVERT: A 489 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7107 (mt) REVERT: A 518 THR cc_start: 0.8123 (p) cc_final: 0.7876 (m) REVERT: A 558 MET cc_start: 0.4052 (OUTLIER) cc_final: 0.3328 (tpt) outliers start: 55 outliers final: 16 residues processed: 234 average time/residue: 0.4440 time to fit residues: 116.7612 Evaluate side-chains 199 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 88 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.216083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.169240 restraints weight = 15176.886| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.94 r_work: 0.3649 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14512 Z= 0.143 Angle : 0.629 7.907 19733 Z= 0.312 Chirality : 0.042 0.199 2273 Planarity : 0.005 0.046 2414 Dihedral : 9.586 115.096 1973 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.51 % Allowed : 22.62 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.03 (0.21), residues: 1590 helix: 1.96 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.014 0.002 TYR C 152 PHE 0.014 0.001 PHE A 432 TRP 0.016 0.002 TRP A 158 HIS 0.005 0.001 HIS C 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14512) covalent geometry : angle 0.62876 / 0.31 (19733) hydrogen bonds : bond 0.04499 / 2.98 ( 900) hydrogen bonds : angle 4.17386 / 2.98 ( 2619) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8022 (ttm) REVERT: C 193 GLU cc_start: 0.7371 (mp0) cc_final: 0.7040 (mt-10) REVERT: C 290 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7465 (mt) REVERT: C 375 LEU cc_start: 0.7575 (mp) cc_final: 0.7290 (mt) REVERT: C 470 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.6057 (tm-30) REVERT: C 489 ILE cc_start: 0.7623 (OUTLIER) cc_final: 0.7229 (mt) REVERT: C 497 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7070 (tpp80) REVERT: C 506 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8105 (ttp-110) REVERT: C 524 MET cc_start: 0.6676 (mtt) cc_final: 0.6405 (mtt) REVERT: C 558 MET cc_start: 0.4224 (OUTLIER) cc_final: 0.2982 (tmt) REVERT: B 40 ILE cc_start: 0.3396 (OUTLIER) cc_final: 0.3110 (pp) REVERT: B 191 GLN cc_start: 0.6456 (OUTLIER) cc_final: 0.6096 (pp30) REVERT: B 222 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7618 (tp) REVERT: B 224 ASN cc_start: 0.7448 (t0) cc_final: 0.7093 (t0) REVERT: B 233 ARG cc_start: 0.7590 (mmm160) cc_final: 0.7016 (mtm180) REVERT: B 290 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7591 (mt) REVERT: B 327 LEU cc_start: 0.8127 (mt) cc_final: 0.7829 (mm) REVERT: B 354 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7843 (mt) REVERT: B 445 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.7251 (tp) REVERT: B 453 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6719 (pt0) REVERT: B 470 GLN cc_start: 0.7699 (OUTLIER) cc_final: 0.6735 (tm-30) REVERT: B 558 MET cc_start: 0.4543 (OUTLIER) cc_final: 0.3630 (tmt) REVERT: A 63 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8454 (tp) REVERT: A 149 LYS cc_start: 0.7989 (OUTLIER) cc_final: 0.7704 (ttmm) REVERT: A 186 ARG cc_start: 0.7834 (tpt90) cc_final: 0.6963 (tpt-90) REVERT: A 224 ASN cc_start: 0.7624 (t0) cc_final: 0.7375 (t0) REVERT: A 225 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7520 (mtpt) REVERT: A 233 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.6962 (mpp-170) REVERT: A 264 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.5738 (tt) REVERT: A 345 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7726 (tm-30) REVERT: A 375 LEU cc_start: 0.7551 (mp) cc_final: 0.7325 (mt) REVERT: A 432 PHE cc_start: 0.7609 (t80) cc_final: 0.6952 (t80) REVERT: A 489 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7143 (mt) REVERT: A 518 THR cc_start: 0.8147 (p) cc_final: 0.7934 (m) REVERT: A 558 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3291 (tpt) outliers start: 64 outliers final: 17 residues processed: 220 average time/residue: 0.4953 time to fit residues: 121.0227 Evaluate side-chains 205 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 484 ILE Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 169 ARG Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.216206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165341 restraints weight = 15134.665| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.90 r_work: 0.3684 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14512 Z= 0.143 Angle : 0.625 7.868 19733 Z= 0.310 Chirality : 0.042 0.206 2273 Planarity : 0.004 0.045 2414 Dihedral : 8.839 79.112 1973 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 4.37 % Allowed : 23.11 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.09 (0.22), residues: 1590 helix: 2.01 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 231 TYR 0.013 0.002 TYR C 152 PHE 0.013 0.001 PHE C 432 TRP 0.020 0.002 TRP C 158 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14512) covalent geometry : angle 0.62517 / 0.31 (19733) hydrogen bonds : bond 0.04463 / 2.95 ( 900) hydrogen bonds : angle 4.15014 / 2.97 ( 2619) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 179 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8073 (ttm) REVERT: C 193 GLU cc_start: 0.7343 (mp0) cc_final: 0.6984 (mt-10) REVERT: C 225 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7731 (mtpt) REVERT: C 290 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.7501 (mt) REVERT: C 375 LEU cc_start: 0.7538 (mp) cc_final: 0.7241 (mt) REVERT: C 489 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7226 (mt) REVERT: C 497 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7209 (tpp80) REVERT: C 506 ARG cc_start: 0.8511 (ttp-110) cc_final: 0.8209 (ttp-110) REVERT: C 558 MET cc_start: 0.4229 (OUTLIER) cc_final: 0.3007 (tmt) REVERT: B 40 ILE cc_start: 0.3477 (OUTLIER) cc_final: 0.3195 (pp) REVERT: B 62 MET cc_start: 0.8658 (ttm) cc_final: 0.8003 (ttm) REVERT: B 205 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6063 (tt0) REVERT: B 222 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7623 (tp) REVERT: B 224 ASN cc_start: 0.7559 (t0) cc_final: 0.7195 (t0) REVERT: B 225 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7852 (mtpt) REVERT: B 233 ARG cc_start: 0.7700 (mmm160) cc_final: 0.6937 (mtm180) REVERT: B 290 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7620 (mt) REVERT: B 354 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7825 (mt) REVERT: B 375 LEU cc_start: 0.7535 (mp) cc_final: 0.7311 (mt) REVERT: B 445 ILE cc_start: 0.7545 (OUTLIER) cc_final: 0.7256 (tp) REVERT: B 453 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.6845 (pt0) REVERT: B 558 MET cc_start: 0.4527 (OUTLIER) cc_final: 0.3619 (tmt) REVERT: A 149 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7675 (ttmm) REVERT: A 162 SER cc_start: 0.7118 (p) cc_final: 0.6688 (m) REVERT: A 186 ARG cc_start: 0.7893 (tpt90) cc_final: 0.6937 (tpt-90) REVERT: A 191 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: A 224 ASN cc_start: 0.7770 (t0) cc_final: 0.7550 (t0) REVERT: A 225 LYS cc_start: 0.8048 (mtpp) cc_final: 0.7652 (mtpt) REVERT: A 233 ARG cc_start: 0.7431 (tpp-160) cc_final: 0.7011 (mpp-170) REVERT: A 264 LEU cc_start: 0.6603 (OUTLIER) cc_final: 0.5797 (tt) REVERT: A 290 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7652 (mt) REVERT: A 345 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: A 375 LEU cc_start: 0.7634 (mp) cc_final: 0.7393 (mt) REVERT: A 432 PHE cc_start: 0.7583 (t80) cc_final: 0.7210 (t80) REVERT: A 489 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7160 (mt) REVERT: A 507 ASN cc_start: 0.7486 (OUTLIER) cc_final: 0.7207 (m110) REVERT: A 558 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.3194 (tpt) outliers start: 62 outliers final: 21 residues processed: 221 average time/residue: 0.4812 time to fit residues: 118.3322 Evaluate side-chains 214 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 117 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 162 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 379 ASN C 531 HIS ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 531 HIS A 52 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 531 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.210077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.156320 restraints weight = 15198.705| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.86 r_work: 0.3547 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 14512 Z= 0.232 Angle : 0.745 8.287 19733 Z= 0.370 Chirality : 0.048 0.325 2273 Planarity : 0.005 0.053 2414 Dihedral : 9.404 80.973 1973 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.65 % Allowed : 23.26 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 0.51 (0.21), residues: 1590 helix: 1.53 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -2.19 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 506 TYR 0.017 0.003 TYR A 157 PHE 0.022 0.002 PHE C 469 TRP 0.025 0.003 TRP C 158 HIS 0.008 0.002 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.23 (14512) covalent geometry : angle 0.74486 / 0.37 (19733) hydrogen bonds : bond 0.05588 / 3.72 ( 900) hydrogen bonds : angle 4.44617 / 3.18 ( 2619) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 161 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8548 (ttp) cc_final: 0.8158 (ttm) REVERT: C 225 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7778 (mtpt) REVERT: C 264 LEU cc_start: 0.6619 (OUTLIER) cc_final: 0.6301 (pp) REVERT: C 290 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7530 (mt) REVERT: C 375 LEU cc_start: 0.7724 (mp) cc_final: 0.7471 (mt) REVERT: C 489 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7381 (mt) REVERT: C 524 MET cc_start: 0.6756 (mtt) cc_final: 0.6346 (mtt) REVERT: C 558 MET cc_start: 0.4311 (OUTLIER) cc_final: 0.3054 (tmt) REVERT: B 40 ILE cc_start: 0.3803 (OUTLIER) cc_final: 0.3538 (pp) REVERT: B 69 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7528 (mt-10) REVERT: B 191 GLN cc_start: 0.7322 (tm-30) cc_final: 0.6698 (pp30) REVERT: B 205 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6376 (mt-10) REVERT: B 222 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7659 (tp) REVERT: B 233 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7031 (mtm180) REVERT: B 290 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7652 (mt) REVERT: B 354 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7939 (mt) REVERT: B 375 LEU cc_start: 0.7858 (mp) cc_final: 0.7608 (mt) REVERT: B 453 GLN cc_start: 0.6994 (OUTLIER) cc_final: 0.6674 (pt0) REVERT: B 470 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: B 558 MET cc_start: 0.4549 (OUTLIER) cc_final: 0.3686 (tmt) REVERT: A 224 ASN cc_start: 0.7761 (t0) cc_final: 0.7533 (t0) REVERT: A 225 LYS cc_start: 0.8104 (mtpp) cc_final: 0.7671 (mtpt) REVERT: A 233 ARG cc_start: 0.7441 (tpp-160) cc_final: 0.7199 (mpp-170) REVERT: A 290 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7702 (mt) REVERT: A 345 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: A 391 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.5479 (mp) REVERT: A 470 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7212 (tm-30) REVERT: A 489 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7536 (mt) REVERT: A 558 MET cc_start: 0.4247 (OUTLIER) cc_final: 0.3326 (tpt) outliers start: 66 outliers final: 26 residues processed: 206 average time/residue: 0.4519 time to fit residues: 104.1130 Evaluate side-chains 198 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 154 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 470 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 550 ASP Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 239 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 141 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.220463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179633 restraints weight = 15004.205| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.81 r_work: 0.3652 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14512 Z= 0.131 Angle : 0.622 7.921 19733 Z= 0.310 Chirality : 0.041 0.205 2273 Planarity : 0.005 0.048 2414 Dihedral : 8.722 70.117 1973 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 3.45 % Allowed : 24.74 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.07 (0.22), residues: 1590 helix: 1.97 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 330 TYR 0.016 0.001 TYR C 152 PHE 0.014 0.001 PHE B 432 TRP 0.023 0.002 TRP A 158 HIS 0.005 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14512) covalent geometry : angle 0.62203 / 0.31 (19733) hydrogen bonds : bond 0.04317 / 2.86 ( 900) hydrogen bonds : angle 4.17991 / 2.99 ( 2619) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 173 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8554 (ttp) cc_final: 0.7964 (ttm) REVERT: C 225 LYS cc_start: 0.7982 (mtpp) cc_final: 0.7677 (mtpt) REVERT: C 264 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.5855 (tt) REVERT: C 290 ILE cc_start: 0.8066 (OUTLIER) cc_final: 0.7454 (mt) REVERT: C 375 LEU cc_start: 0.7530 (mp) cc_final: 0.7240 (mt) REVERT: C 489 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7234 (mt) REVERT: C 497 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.7244 (tpp80) REVERT: C 506 ARG cc_start: 0.8531 (ttp-110) cc_final: 0.8276 (ttp-110) REVERT: C 524 MET cc_start: 0.6790 (mtt) cc_final: 0.6483 (mtt) REVERT: C 558 MET cc_start: 0.4171 (OUTLIER) cc_final: 0.2977 (tmt) REVERT: B 40 ILE cc_start: 0.3100 (OUTLIER) cc_final: 0.2866 (pp) REVERT: B 62 MET cc_start: 0.8450 (ttm) cc_final: 0.7949 (ttm) REVERT: B 69 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7480 (mt-10) REVERT: B 205 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5995 (tt0) REVERT: B 222 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7606 (tp) REVERT: B 224 ASN cc_start: 0.7461 (t0) cc_final: 0.7163 (t0) REVERT: B 225 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7799 (mtpt) REVERT: B 233 ARG cc_start: 0.7553 (mmm160) cc_final: 0.6997 (mtm180) REVERT: B 290 ILE cc_start: 0.8087 (OUTLIER) cc_final: 0.7592 (mt) REVERT: B 327 LEU cc_start: 0.7974 (mt) cc_final: 0.7498 (mm) REVERT: B 354 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7869 (mt) REVERT: B 445 ILE cc_start: 0.7444 (OUTLIER) cc_final: 0.7179 (tp) REVERT: B 453 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6692 (pt0) REVERT: B 558 MET cc_start: 0.4559 (OUTLIER) cc_final: 0.3652 (tmt) REVERT: A 186 ARG cc_start: 0.7830 (tpt90) cc_final: 0.6911 (tpt-90) REVERT: A 224 ASN cc_start: 0.7668 (t0) cc_final: 0.7440 (t0) REVERT: A 225 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7571 (mtpt) REVERT: A 233 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.7090 (mpp-170) REVERT: A 264 LEU cc_start: 0.6609 (OUTLIER) cc_final: 0.5992 (tt) REVERT: A 290 ILE cc_start: 0.8049 (OUTLIER) cc_final: 0.7577 (mt) REVERT: A 470 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6670 (tm-30) REVERT: A 489 ILE cc_start: 0.7646 (OUTLIER) cc_final: 0.7179 (mt) REVERT: A 558 MET cc_start: 0.4138 (OUTLIER) cc_final: 0.3324 (tpt) outliers start: 49 outliers final: 13 residues processed: 208 average time/residue: 0.4699 time to fit residues: 108.6981 Evaluate side-chains 193 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 68 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 134 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.220332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.180143 restraints weight = 15037.537| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 2.60 r_work: 0.3677 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3547 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14512 Z= 0.135 Angle : 0.627 8.214 19733 Z= 0.313 Chirality : 0.042 0.211 2273 Planarity : 0.004 0.045 2414 Dihedral : 8.567 63.894 1973 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.75 % Allowed : 25.72 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.18 (0.22), residues: 1590 helix: 2.05 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.94 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 186 TYR 0.016 0.001 TYR C 152 PHE 0.025 0.001 PHE A 432 TRP 0.023 0.002 TRP A 158 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14512) covalent geometry : angle 0.62748 / 0.31 (19733) hydrogen bonds : bond 0.04325 / 2.87 ( 900) hydrogen bonds : angle 4.16140 / 2.98 ( 2619) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7995 (ttm) REVERT: C 193 GLU cc_start: 0.7257 (mp0) cc_final: 0.6865 (mt-10) REVERT: C 225 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7680 (mtpt) REVERT: C 264 LEU cc_start: 0.6488 (OUTLIER) cc_final: 0.5818 (tt) REVERT: C 290 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7466 (mt) REVERT: C 375 LEU cc_start: 0.7456 (mp) cc_final: 0.7134 (mt) REVERT: C 489 ILE cc_start: 0.7589 (OUTLIER) cc_final: 0.7142 (mt) REVERT: C 497 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7260 (tpp80) REVERT: C 524 MET cc_start: 0.6731 (mtt) cc_final: 0.6352 (mtt) REVERT: C 558 MET cc_start: 0.4111 (OUTLIER) cc_final: 0.2896 (tmt) REVERT: B 40 ILE cc_start: 0.3381 (OUTLIER) cc_final: 0.3106 (pp) REVERT: B 62 MET cc_start: 0.8411 (ttm) cc_final: 0.7931 (ttm) REVERT: B 69 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7599 (mt-10) REVERT: B 191 GLN cc_start: 0.7247 (tm-30) cc_final: 0.6628 (pp30) REVERT: B 205 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6144 (tt0) REVERT: B 222 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7550 (tp) REVERT: B 224 ASN cc_start: 0.7520 (t0) cc_final: 0.7160 (t0) REVERT: B 233 ARG cc_start: 0.7733 (mmm160) cc_final: 0.6919 (mtm180) REVERT: B 290 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7594 (mt) REVERT: B 327 LEU cc_start: 0.7981 (mt) cc_final: 0.7614 (mm) REVERT: B 354 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7826 (mt) REVERT: B 375 LEU cc_start: 0.7387 (mp) cc_final: 0.7143 (mt) REVERT: B 445 ILE cc_start: 0.7574 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 453 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6753 (pt0) REVERT: B 558 MET cc_start: 0.4343 (OUTLIER) cc_final: 0.3486 (tmt) REVERT: A 186 ARG cc_start: 0.7825 (tpt90) cc_final: 0.6808 (tpt-90) REVERT: A 224 ASN cc_start: 0.7729 (t0) cc_final: 0.7515 (t0) REVERT: A 225 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7627 (mtpt) REVERT: A 264 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.5908 (tt) REVERT: A 290 ILE cc_start: 0.8038 (OUTLIER) cc_final: 0.7613 (mt) REVERT: A 372 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7912 (tt) REVERT: A 470 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.6903 (tm-30) REVERT: A 489 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7078 (mt) REVERT: A 558 MET cc_start: 0.4057 (OUTLIER) cc_final: 0.3067 (tpt) outliers start: 39 outliers final: 15 residues processed: 197 average time/residue: 0.4589 time to fit residues: 101.2756 Evaluate side-chains 195 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 191 GLN Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 0.0270 chunk 132 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 44 optimal weight: 0.0050 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 142 optimal weight: 0.5980 chunk 137 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.220925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.181256 restraints weight = 15010.963| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 2.61 r_work: 0.3687 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14512 Z= 0.135 Angle : 0.626 7.903 19733 Z= 0.312 Chirality : 0.042 0.214 2273 Planarity : 0.004 0.044 2414 Dihedral : 8.424 59.457 1973 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.68 % Allowed : 25.86 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.24 (0.22), residues: 1590 helix: 2.06 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -1.85 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 330 TYR 0.015 0.001 TYR C 152 PHE 0.023 0.001 PHE A 432 TRP 0.022 0.002 TRP A 158 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 (14512) covalent geometry : angle 0.62591 / 0.31 (19733) hydrogen bonds : bond 0.04315 / 2.86 ( 900) hydrogen bonds : angle 4.14238 / 2.96 ( 2619) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8605 (ttp) cc_final: 0.7988 (ttm) REVERT: C 225 LYS cc_start: 0.7996 (mtpp) cc_final: 0.7673 (mtpt) REVERT: C 264 LEU cc_start: 0.6459 (OUTLIER) cc_final: 0.5745 (tt) REVERT: C 290 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7525 (mt) REVERT: C 375 LEU cc_start: 0.7468 (mp) cc_final: 0.7158 (mt) REVERT: C 489 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7162 (mt) REVERT: C 497 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7258 (tpp80) REVERT: C 520 SER cc_start: 0.8687 (t) cc_final: 0.8413 (m) REVERT: C 524 MET cc_start: 0.6748 (mtt) cc_final: 0.6371 (mtt) REVERT: C 558 MET cc_start: 0.4066 (OUTLIER) cc_final: 0.2856 (tmt) REVERT: B 40 ILE cc_start: 0.3098 (OUTLIER) cc_final: 0.2822 (pp) REVERT: B 62 MET cc_start: 0.8394 (ttm) cc_final: 0.8052 (ttp) REVERT: B 69 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7590 (mt-10) REVERT: B 191 GLN cc_start: 0.7264 (tm-30) cc_final: 0.6636 (pp30) REVERT: B 205 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6076 (tt0) REVERT: B 222 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7520 (tp) REVERT: B 233 ARG cc_start: 0.7731 (mmm160) cc_final: 0.6931 (mtm180) REVERT: B 290 ILE cc_start: 0.8054 (OUTLIER) cc_final: 0.7592 (mt) REVERT: B 327 LEU cc_start: 0.7876 (mt) cc_final: 0.7558 (mm) REVERT: B 354 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7876 (mt) REVERT: B 375 LEU cc_start: 0.7408 (mp) cc_final: 0.7154 (mt) REVERT: B 445 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7227 (tp) REVERT: B 453 GLN cc_start: 0.6908 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: B 558 MET cc_start: 0.4341 (OUTLIER) cc_final: 0.3483 (tmt) REVERT: A 186 ARG cc_start: 0.7798 (tpt90) cc_final: 0.6796 (tpt-90) REVERT: A 224 ASN cc_start: 0.7723 (t0) cc_final: 0.7516 (t0) REVERT: A 225 LYS cc_start: 0.8009 (mtpp) cc_final: 0.7592 (mtpt) REVERT: A 264 LEU cc_start: 0.6575 (OUTLIER) cc_final: 0.5909 (tt) REVERT: A 290 ILE cc_start: 0.8014 (OUTLIER) cc_final: 0.7653 (mt) REVERT: A 372 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 470 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6898 (tm-30) REVERT: A 489 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7046 (mt) REVERT: A 558 MET cc_start: 0.4264 (OUTLIER) cc_final: 0.3302 (tpt) outliers start: 38 outliers final: 15 residues processed: 194 average time/residue: 0.4615 time to fit residues: 100.1969 Evaluate side-chains 199 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 470 GLN Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 484 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 453 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 558 MET Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 470 GLN Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 558 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 152 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 27 optimal weight: 0.0010 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.215990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.164306 restraints weight = 15164.975| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.05 r_work: 0.3668 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14512 Z= 0.138 Angle : 0.630 8.452 19733 Z= 0.314 Chirality : 0.042 0.215 2273 Planarity : 0.004 0.042 2414 Dihedral : 8.339 57.014 1973 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.82 % Allowed : 25.65 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.22 (0.22), residues: 1590 helix: 2.09 (0.16), residues: 1050 sheet: None (None), residues: 0 loop : -1.92 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 330 TYR 0.015 0.001 TYR C 152 PHE 0.024 0.001 PHE A 432 TRP 0.024 0.002 TRP B 158 HIS 0.012 0.001 HIS C 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (14512) covalent geometry : angle 0.63008 / 0.31 (19733) hydrogen bonds : bond 0.04342 / 2.87 ( 900) hydrogen bonds : angle 4.14048 / 2.95 ( 2619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4639.74 seconds wall clock time: 79 minutes 55.55 seconds (4795.55 seconds total)