Starting phenix.real_space_refine on Wed Mar 4 14:23:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wqz_21874/03_2026/6wqz_21874.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wqz_21874/03_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_21874/03_2026/6wqz_21874.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wqz_21874/03_2026/6wqz_21874.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wqz_21874/03_2026/6wqz_21874.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wqz_21874/03_2026/6wqz_21874.map" } 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-dev-5986/lib/python3.9/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: 3.21, per 1000 atoms: 0.23 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: 1.34 Conformation dependent library (CDL) restraints added in 404.2 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: 0.28 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: 1.89 Time building geometry restraints manager: 1.77 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: 8236 29.46 - 58.93: 565 58.93 - 88.39: 65 88.39 - 117.85: 101 117.85 - 147.31: 9 Dihedral angle restraints: 8976 sinusoidal: 3939 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 8973 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.580 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 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 : 23.320 147.314 5702 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 covalent geometry : bond 0.01598 (14512) covalent geometry : angle 1.44305 (19733) hydrogen bonds : bond 0.14715 ( 900) hydrogen bonds : angle 6.28016 ( 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 : 0.489 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: 0.5623 time to fit residues: 196.7590 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 : 0.478 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4376 r_free = 0.4376 target = 0.217865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167162 restraints weight = 15313.744| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 1.81 r_work: 0.3743 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2690 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= 0.147 Angle : 0.693 8.161 19733 Z= 0.342 Chirality : 0.045 0.420 2273 Planarity : 0.005 0.052 2414 Dihedral : 15.397 168.178 2630 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 4.58 % Allowed : 19.10 % Favored : 76.32 % 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: -0.10 (0.21), residues: 1590 helix: 0.96 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -2.29 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 231 TYR 0.021 0.002 TYR C 471 PHE 0.019 0.001 PHE B 432 TRP 0.014 0.002 TRP C 257 HIS 0.006 0.001 HIS A 38 Details of bonding type rmsd covalent geometry : bond 0.00305 (14512) covalent geometry : angle 0.69323 (19733) hydrogen bonds : bond 0.04735 ( 900) hydrogen bonds : angle 4.37115 ( 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 283 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 218 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.3446 (OUTLIER) cc_final: 0.3191 (tt) REVERT: C 62 MET cc_start: 0.8506 (ttp) cc_final: 0.8227 (ttm) REVERT: C 181 GLN cc_start: 0.7890 (mm110) cc_final: 0.7494 (mm-40) REVERT: C 225 LYS cc_start: 0.7866 (mtpp) cc_final: 0.7649 (mtpt) REVERT: C 233 ARG cc_start: 0.7683 (tpp-160) cc_final: 0.7290 (mtm-85) REVERT: C 424 PHE cc_start: 0.7875 (m-80) cc_final: 0.7595 (m-80) REVERT: C 497 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7156 (tpp80) REVERT: C 524 MET cc_start: 0.6682 (mtt) cc_final: 0.5961 (mtt) REVERT: C 558 MET cc_start: 0.4164 (OUTLIER) cc_final: 0.3440 (tpt) REVERT: B 62 MET cc_start: 0.8521 (ttm) cc_final: 0.8215 (ttm) REVERT: B 69 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7300 (mt-10) REVERT: B 205 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.6139 (tt0) REVERT: B 249 TYR cc_start: 0.8779 (t80) cc_final: 0.8557 (t80) REVERT: B 250 ASN cc_start: 0.8574 (m-40) cc_final: 0.8315 (m110) REVERT: B 290 ILE cc_start: 0.8009 (tt) cc_final: 0.7414 (mt) REVERT: B 354 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7999 (mt) REVERT: B 379 ASN cc_start: 0.8109 (m-40) cc_final: 0.7840 (m110) REVERT: B 497 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6879 (tpp80) REVERT: B 558 MET cc_start: 0.4209 (OUTLIER) cc_final: 0.3481 (tpt) REVERT: A 90 ASP cc_start: 0.5847 (OUTLIER) cc_final: 0.5251 (p0) REVERT: A 149 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7673 (ttmm) REVERT: A 225 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7464 (mtpt) REVERT: A 267 TRP cc_start: 0.7235 (p90) cc_final: 0.7011 (p90) REVERT: A 354 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 376 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7196 (mt) REVERT: A 453 GLN cc_start: 0.7266 (OUTLIER) cc_final: 0.6948 (pt0) REVERT: A 484 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 558 MET cc_start: 0.4794 (OUTLIER) cc_final: 0.4034 (tpt) outliers start: 65 outliers final: 21 residues processed: 264 average time/residue: 0.5491 time to fit residues: 159.4761 Evaluate side-chains 215 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 180 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE 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 497 ARG 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 112 LEU 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: 6.9990 chunk 67 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 84 optimal weight: 0.0370 chunk 85 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 114 optimal weight: 0.0770 overall best weight: 1.1820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 ASN B 52 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN B 181 GLN B 288 ASN ** B 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 564 ASN ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 57 ASN A 278 GLN A 288 ASN A 379 ASN ** A 529 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.218959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.172106 restraints weight = 15481.561| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.91 r_work: 0.3749 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14512 Z= 0.140 Angle : 0.623 6.291 19733 Z= 0.314 Chirality : 0.040 0.176 2273 Planarity : 0.005 0.050 2414 Dihedral : 13.225 135.009 2621 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.44 % Allowed : 19.87 % Favored : 75.69 % 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: 0.64 (0.21), residues: 1590 helix: 1.50 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : -1.96 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 231 TYR 0.013 0.002 TYR C 316 PHE 0.018 0.001 PHE A 432 TRP 0.014 0.002 TRP B 180 HIS 0.006 0.001 HIS B 38 Details of bonding type rmsd covalent geometry : bond 0.00305 (14512) covalent geometry : angle 0.62341 (19733) hydrogen bonds : bond 0.04551 ( 900) hydrogen bonds : angle 4.20654 ( 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 256 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 193 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.3549 (OUTLIER) cc_final: 0.2794 (tt) REVERT: C 62 MET cc_start: 0.8517 (ttp) cc_final: 0.8150 (ttm) REVERT: C 193 GLU cc_start: 0.7331 (mp0) cc_final: 0.7005 (mt-10) REVERT: C 225 LYS cc_start: 0.7978 (mtpp) cc_final: 0.7717 (mtpt) REVERT: C 233 ARG cc_start: 0.7575 (tpp-160) cc_final: 0.7142 (mtm-85) REVERT: C 290 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7607 (mt) REVERT: C 477 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7906 (tt) REVERT: C 489 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7094 (mt) REVERT: C 497 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7130 (tpp80) REVERT: C 506 ARG cc_start: 0.8407 (ttp-110) cc_final: 0.7982 (ttp-110) REVERT: C 524 MET cc_start: 0.6508 (mtt) cc_final: 0.6221 (mtt) REVERT: C 558 MET cc_start: 0.4216 (OUTLIER) cc_final: 0.2953 (tmt) REVERT: B 69 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7564 (mt-10) REVERT: B 181 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7712 (mm-40) REVERT: B 222 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7655 (tp) REVERT: B 224 ASN cc_start: 0.7605 (t0) cc_final: 0.7141 (t0) REVERT: B 249 TYR cc_start: 0.8743 (t80) cc_final: 0.8460 (t80) REVERT: B 290 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7580 (mt) REVERT: B 354 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7955 (mt) REVERT: B 445 ILE cc_start: 0.7559 (OUTLIER) cc_final: 0.7300 (tp) REVERT: B 453 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.6836 (pt0) REVERT: B 558 MET cc_start: 0.4511 (OUTLIER) cc_final: 0.3454 (tmt) REVERT: A 63 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8515 (tt) REVERT: A 149 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7611 (ttmm) REVERT: A 205 GLU cc_start: 0.6860 (tt0) cc_final: 0.6633 (mt-10) REVERT: A 225 LYS cc_start: 0.7863 (mtpp) cc_final: 0.7511 (mtpt) REVERT: A 354 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8103 (mt) REVERT: A 375 LEU cc_start: 0.7424 (mp) cc_final: 0.7181 (mt) REVERT: A 445 ILE cc_start: 0.7346 (OUTLIER) cc_final: 0.7094 (tp) REVERT: A 489 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7170 (mt) REVERT: A 518 THR cc_start: 0.8103 (p) cc_final: 0.7887 (m) REVERT: A 558 MET cc_start: 0.4567 (OUTLIER) cc_final: 0.3689 (tpt) outliers start: 63 outliers final: 17 residues processed: 231 average time/residue: 0.5415 time to fit residues: 137.9824 Evaluate side-chains 203 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE 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 412 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 489 ILE Chi-restraints excluded: chain C residue 497 ARG Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain B residue 60 THR 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 149 LYS Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 445 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 48 optimal weight: 8.9990 chunk 158 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 116 optimal weight: 6.9990 chunk 151 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 HIS ** C 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 288 ASN B 529 HIS ** B 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN A 529 HIS ** 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 = 0.4344 r_free = 0.4344 target = 0.215462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.168205 restraints weight = 15220.607| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.01 r_work: 0.3714 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14512 Z= 0.164 Angle : 0.649 6.778 19733 Z= 0.327 Chirality : 0.042 0.194 2273 Planarity : 0.005 0.056 2414 Dihedral : 12.254 109.245 2615 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.93 % Allowed : 21.63 % Favored : 73.43 % 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: 0.75 (0.21), residues: 1590 helix: 1.62 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -1.99 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 231 TYR 0.014 0.002 TYR C 316 PHE 0.016 0.001 PHE C 432 TRP 0.015 0.002 TRP A 180 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00377 (14512) covalent geometry : angle 0.64896 (19733) hydrogen bonds : bond 0.04838 ( 900) hydrogen bonds : angle 4.24418 ( 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 253 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 183 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 MET cc_start: 0.8492 (ttp) cc_final: 0.8064 (ttm) REVERT: C 193 GLU cc_start: 0.7331 (mp0) cc_final: 0.6963 (mt-10) REVERT: C 225 LYS cc_start: 0.7842 (mtpp) cc_final: 0.7566 (mtpt) REVERT: C 233 ARG cc_start: 0.7721 (tpp-160) cc_final: 0.7010 (mtm-85) REVERT: C 290 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7457 (mt) REVERT: C 375 LEU cc_start: 0.7441 (mp) cc_final: 0.7152 (mt) REVERT: C 489 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7273 (mt) REVERT: C 506 ARG cc_start: 0.8392 (ttp-110) cc_final: 0.8023 (ttp-110) REVERT: C 524 MET cc_start: 0.6607 (mtt) cc_final: 0.6283 (mtt) REVERT: C 558 MET cc_start: 0.4167 (OUTLIER) cc_final: 0.2944 (tmt) REVERT: B 40 ILE cc_start: 0.3757 (OUTLIER) cc_final: 0.3101 (tt) REVERT: B 69 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7439 (mt-10) REVERT: B 71 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7879 (mtp) REVERT: B 186 ARG cc_start: 0.7388 (tpt-90) cc_final: 0.7182 (tpt-90) REVERT: B 222 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7560 (tp) REVERT: B 249 TYR cc_start: 0.8688 (t80) cc_final: 0.8409 (t80) REVERT: B 290 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7533 (mt) REVERT: B 327 LEU cc_start: 0.8192 (mt) cc_final: 0.7780 (mm) REVERT: B 354 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7913 (mt) REVERT: B 445 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7343 (tp) REVERT: B 470 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.6880 (tm-30) REVERT: B 558 MET cc_start: 0.4358 (OUTLIER) cc_final: 0.3519 (tmt) REVERT: A 63 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8325 (tp) REVERT: A 225 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7461 (mtpt) REVERT: A 290 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7564 (mt) REVERT: A 345 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7921 (tm-30) REVERT: A 375 LEU cc_start: 0.7492 (mp) cc_final: 0.7219 (mt) REVERT: A 436 GLN cc_start: 0.7342 (mm-40) cc_final: 0.6817 (mt0) REVERT: A 489 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7193 (mt) REVERT: A 518 THR cc_start: 0.8103 (p) cc_final: 0.7886 (m) REVERT: A 558 MET cc_start: 0.4086 (OUTLIER) cc_final: 0.3219 (tpt) outliers start: 70 outliers final: 17 residues processed: 231 average time/residue: 0.4874 time to fit residues: 125.3111 Evaluate side-chains 201 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 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 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 71 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 222 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 470 GLN Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ARG Chi-restraints excluded: chain B residue 550 ASP 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 264 LEU Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 299 LEU 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: 0.8980 chunk 7 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4397 r_free = 0.4397 target = 0.219915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.178856 restraints weight = 15105.136| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.67 r_work: 0.3647 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14512 Z= 0.147 Angle : 0.614 6.513 19733 Z= 0.312 Chirality : 0.041 0.198 2273 Planarity : 0.005 0.050 2414 Dihedral : 11.239 85.134 2609 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 4.51 % Allowed : 22.69 % Favored : 72.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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 (0.22), residues: 1590 helix: 1.94 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -2.01 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 231 TYR 0.013 0.002 TYR C 316 PHE 0.014 0.001 PHE C 432 TRP 0.016 0.002 TRP A 158 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00329 (14512) covalent geometry : angle 0.61372 (19733) hydrogen bonds : bond 0.04560 ( 900) hydrogen bonds : angle 4.18933 ( 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 243 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 179 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.2921 (OUTLIER) cc_final: 0.2144 (tt) REVERT: C 62 MET cc_start: 0.8461 (ttp) cc_final: 0.7964 (ttm) REVERT: C 193 GLU cc_start: 0.7390 (mp0) cc_final: 0.7038 (mt-10) REVERT: C 225 LYS cc_start: 0.7886 (mtpp) cc_final: 0.7599 (mtpt) REVERT: C 233 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7039 (mtm-85) REVERT: C 290 ILE cc_start: 0.8060 (OUTLIER) cc_final: 0.7444 (mt) REVERT: C 375 LEU cc_start: 0.7586 (mp) cc_final: 0.7283 (mt) REVERT: C 399 GLU cc_start: 0.5120 (OUTLIER) cc_final: 0.4619 (mt-10) REVERT: C 489 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7223 (mt) REVERT: C 506 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.8104 (ttp-110) REVERT: C 524 MET cc_start: 0.6531 (mtt) cc_final: 0.6297 (mtt) REVERT: C 558 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.2941 (tmt) REVERT: B 40 ILE cc_start: 0.3468 (OUTLIER) cc_final: 0.3247 (pp) REVERT: B 71 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7820 (mtp) REVERT: B 186 ARG cc_start: 0.7448 (tpt-90) cc_final: 0.7244 (tpt-90) REVERT: B 191 GLN cc_start: 0.6483 (OUTLIER) cc_final: 0.6088 (pp30) REVERT: B 205 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5983 (tt0) REVERT: B 222 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7565 (tp) REVERT: B 249 TYR cc_start: 0.8681 (t80) cc_final: 0.8386 (t80) REVERT: B 290 ILE cc_start: 0.8037 (tt) cc_final: 0.7527 (mt) REVERT: B 327 LEU cc_start: 0.8138 (mt) cc_final: 0.7825 (mm) REVERT: B 354 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7914 (mt) REVERT: B 399 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.4789 (mt-10) REVERT: B 445 ILE cc_start: 0.7564 (OUTLIER) cc_final: 0.7280 (tp) REVERT: B 453 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6704 (pt0) REVERT: B 470 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.6647 (tm-30) REVERT: B 558 MET cc_start: 0.4512 (OUTLIER) cc_final: 0.3628 (tmt) REVERT: A 63 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8384 (tp) REVERT: A 193 GLU cc_start: 0.6959 (mp0) cc_final: 0.6318 (mt-10) REVERT: A 225 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7472 (mtpt) REVERT: A 233 ARG cc_start: 0.7391 (tpp-160) cc_final: 0.7035 (mpp-170) REVERT: A 264 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.5792 (tt) REVERT: A 290 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7534 (mt) REVERT: A 373 LEU cc_start: 0.8603 (tp) cc_final: 0.8378 (tt) REVERT: A 375 LEU cc_start: 0.7555 (mp) cc_final: 0.7305 (mt) REVERT: A 399 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.5037 (mt-10) REVERT: A 432 PHE cc_start: 0.7532 (t80) cc_final: 0.6865 (t80) REVERT: A 489 ILE cc_start: 0.7671 (OUTLIER) cc_final: 0.7219 (mt) REVERT: A 558 MET cc_start: 0.4052 (OUTLIER) cc_final: 0.3219 (tpt) outliers start: 64 outliers final: 20 residues processed: 225 average time/residue: 0.5067 time to fit residues: 126.4925 Evaluate side-chains 212 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE 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 399 GLU 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 558 MET Chi-restraints excluded: chain B residue 40 ILE Chi-restraints excluded: chain B residue 71 MET Chi-restraints excluded: chain B residue 191 GLN 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 299 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 445 ILE Chi-restraints excluded: chain B residue 448 MET 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 40 ILE 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 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 399 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: 5.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 145 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.219384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.178337 restraints weight = 15024.721| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.67 r_work: 0.3640 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14512 Z= 0.156 Angle : 0.624 6.717 19733 Z= 0.317 Chirality : 0.041 0.210 2273 Planarity : 0.005 0.050 2414 Dihedral : 11.158 84.718 2609 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 4.30 % Allowed : 23.33 % Favored : 72.37 % 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: 0.97 (0.22), residues: 1590 helix: 1.80 (0.16), residues: 1071 sheet: None (None), residues: 0 loop : -1.95 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 186 TYR 0.014 0.002 TYR C 316 PHE 0.014 0.001 PHE A 432 TRP 0.020 0.002 TRP C 158 HIS 0.006 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00356 (14512) covalent geometry : angle 0.62396 (19733) hydrogen bonds : bond 0.04701 ( 900) hydrogen bonds : angle 4.22315 ( 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 229 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 168 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.2921 (OUTLIER) cc_final: 0.2064 (tt) REVERT: C 62 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8005 (ttm) REVERT: C 83 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7160 (mp) REVERT: C 193 GLU cc_start: 0.7309 (mp0) cc_final: 0.6970 (mt-10) REVERT: C 225 LYS cc_start: 0.7914 (mtpp) cc_final: 0.7612 (mtpt) REVERT: C 233 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.7103 (mtm-85) REVERT: C 290 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7469 (mt) REVERT: C 375 LEU cc_start: 0.7612 (mp) cc_final: 0.7319 (mt) REVERT: C 489 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7245 (mt) REVERT: C 497 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7258 (tpp80) REVERT: C 506 ARG cc_start: 0.8480 (ttp-110) cc_final: 0.8172 (ttp-110) REVERT: C 558 MET cc_start: 0.4203 (OUTLIER) cc_final: 0.3016 (tmt) REVERT: B 40 ILE cc_start: 0.3500 (OUTLIER) cc_final: 0.3283 (pp) REVERT: B 71 MET cc_start: 0.8078 (OUTLIER) cc_final: 0.7872 (mtp) REVERT: B 191 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6268 (pp30) REVERT: B 205 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6053 (tt0) REVERT: B 222 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7577 (tp) REVERT: B 249 TYR cc_start: 0.8691 (t80) cc_final: 0.8389 (t80) REVERT: B 290 ILE cc_start: 0.8098 (OUTLIER) cc_final: 0.7585 (mt) REVERT: B 327 LEU cc_start: 0.8016 (mt) cc_final: 0.7667 (mm) REVERT: B 354 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7819 (mt) REVERT: B 445 ILE cc_start: 0.7608 (OUTLIER) cc_final: 0.7317 (tp) REVERT: B 558 MET cc_start: 0.4523 (OUTLIER) cc_final: 0.3639 (tmt) REVERT: A 52 ASN cc_start: 0.7828 (t0) cc_final: 0.7578 (t0) REVERT: A 63 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8393 (tp) REVERT: A 225 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7576 (mtpt) REVERT: A 233 ARG cc_start: 0.7448 (tpp-160) cc_final: 0.7067 (mpp-170) REVERT: A 264 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.5905 (tt) REVERT: A 290 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7593 (mt) REVERT: A 375 LEU cc_start: 0.7557 (mp) cc_final: 0.7302 (mt) REVERT: A 489 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7239 (mt) REVERT: A 558 MET cc_start: 0.4088 (OUTLIER) cc_final: 0.3201 (tpt) outliers start: 61 outliers final: 20 residues processed: 213 average time/residue: 0.5109 time to fit residues: 120.8664 Evaluate side-chains 205 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 262 LEU Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 303 LEU 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 71 MET Chi-restraints excluded: chain B residue 191 GLN 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 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 60 THR Chi-restraints excluded: chain A residue 63 LEU 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 455 ASN Chi-restraints excluded: chain A residue 489 ILE 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: 0.4980 chunk 161 optimal weight: 6.9990 chunk 162 optimal weight: 30.0000 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 288 ASN B 531 HIS ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 145 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.211000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.159290 restraints weight = 15242.984| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.03 r_work: 0.3553 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14512 Z= 0.240 Angle : 0.737 7.897 19733 Z= 0.372 Chirality : 0.047 0.304 2273 Planarity : 0.006 0.058 2414 Dihedral : 11.655 87.750 2609 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.93 % Allowed : 23.19 % Favored : 71.88 % 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: 0.47 (0.21), residues: 1590 helix: 1.49 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -2.18 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 186 TYR 0.016 0.003 TYR C 152 PHE 0.022 0.002 PHE B 469 TRP 0.023 0.003 TRP C 158 HIS 0.008 0.002 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00573 (14512) covalent geometry : angle 0.73686 (19733) hydrogen bonds : bond 0.05698 ( 900) hydrogen bonds : angle 4.50905 ( 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 234 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 164 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.3204 (OUTLIER) cc_final: 0.2382 (tt) REVERT: C 62 MET cc_start: 0.8515 (ttp) cc_final: 0.8117 (ttm) REVERT: C 233 ARG cc_start: 0.7793 (tpp-160) cc_final: 0.7178 (mtm-85) REVERT: C 264 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6188 (pp) REVERT: C 290 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7519 (mt) REVERT: C 375 LEU cc_start: 0.7777 (mp) cc_final: 0.7523 (mt) REVERT: C 489 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7391 (mt) REVERT: C 524 MET cc_start: 0.6752 (mtt) cc_final: 0.6346 (mtt) REVERT: C 558 MET cc_start: 0.4289 (OUTLIER) cc_final: 0.2994 (tmt) REVERT: B 40 ILE cc_start: 0.4081 (OUTLIER) cc_final: 0.3485 (tt) REVERT: B 71 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7944 (mtp) REVERT: B 191 GLN cc_start: 0.6727 (pp30) cc_final: 0.6298 (pp30) REVERT: B 205 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6411 (mt-10) REVERT: B 249 TYR cc_start: 0.8724 (t80) cc_final: 0.8423 (t80) REVERT: B 290 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7692 (mt) REVERT: B 354 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7945 (mt) REVERT: B 375 LEU cc_start: 0.7810 (mp) cc_final: 0.7537 (mt) REVERT: B 470 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: B 558 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3710 (tmt) REVERT: A 63 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8453 (tp) REVERT: A 225 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7710 (mtpt) REVERT: A 233 ARG cc_start: 0.7543 (tpp-160) cc_final: 0.7246 (mpp-170) REVERT: A 290 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7733 (mt) REVERT: A 345 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: A 391 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.5473 (mp) REVERT: A 489 ILE cc_start: 0.8211 (OUTLIER) cc_final: 0.7582 (mt) REVERT: A 558 MET cc_start: 0.4240 (OUTLIER) cc_final: 0.3320 (tpt) outliers start: 70 outliers final: 24 residues processed: 213 average time/residue: 0.4684 time to fit residues: 111.5583 Evaluate side-chains 197 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE 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 445 ILE Chi-restraints excluded: chain C residue 474 VAL 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 71 MET 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 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 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 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 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: 3.9990 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 194 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 = 0.4398 r_free = 0.4398 target = 0.220294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.178818 restraints weight = 15086.864| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.65 r_work: 0.3657 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4484 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= 0.126 Angle : 0.591 7.044 19733 Z= 0.302 Chirality : 0.039 0.199 2273 Planarity : 0.005 0.048 2414 Dihedral : 10.827 89.227 2609 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.89 % Allowed : 25.23 % Favored : 71.88 % 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: 1.14 (0.22), residues: 1590 helix: 2.03 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.98 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 330 TYR 0.015 0.001 TYR C 152 PHE 0.013 0.001 PHE B 432 TRP 0.023 0.002 TRP A 158 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00267 (14512) covalent geometry : angle 0.59110 (19733) hydrogen bonds : bond 0.04237 ( 900) hydrogen bonds : angle 4.18726 ( 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 223 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 182 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.2430 (OUTLIER) cc_final: 0.2216 (pp) REVERT: C 62 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.7981 (ttm) REVERT: C 225 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7662 (mtpt) REVERT: C 233 ARG cc_start: 0.7506 (tpp-160) cc_final: 0.7166 (mtm-85) REVERT: C 264 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5844 (tt) REVERT: C 375 LEU cc_start: 0.7463 (mp) cc_final: 0.7179 (mt) REVERT: C 462 ARG cc_start: 0.7785 (tmm160) cc_final: 0.7260 (tmt-80) REVERT: C 489 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7189 (mt) REVERT: C 520 SER cc_start: 0.8690 (t) cc_final: 0.8387 (t) REVERT: C 524 MET cc_start: 0.6732 (mtt) cc_final: 0.6437 (mtt) REVERT: C 558 MET cc_start: 0.4122 (OUTLIER) cc_final: 0.2933 (tmt) REVERT: B 40 ILE cc_start: 0.3511 (OUTLIER) cc_final: 0.3298 (pp) REVERT: B 62 MET cc_start: 0.8418 (ttm) cc_final: 0.7927 (ttm) REVERT: B 191 GLN cc_start: 0.6602 (pp30) cc_final: 0.6221 (pp30) REVERT: B 205 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5928 (tt0) REVERT: B 224 ASN cc_start: 0.7456 (t0) cc_final: 0.7126 (t0) REVERT: B 225 LYS cc_start: 0.8056 (mtpp) cc_final: 0.7785 (mtpt) REVERT: B 249 TYR cc_start: 0.8674 (t80) cc_final: 0.8368 (t80) REVERT: B 290 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7551 (mt) REVERT: B 327 LEU cc_start: 0.7812 (mt) cc_final: 0.7364 (mm) REVERT: B 354 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7848 (mt) REVERT: B 445 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.7179 (tp) REVERT: B 558 MET cc_start: 0.4519 (OUTLIER) cc_final: 0.3630 (tmt) REVERT: A 186 ARG cc_start: 0.7819 (tpt90) cc_final: 0.6880 (tpt-90) REVERT: A 225 LYS cc_start: 0.7887 (mtpp) cc_final: 0.7475 (mtpt) REVERT: A 264 LEU cc_start: 0.6651 (OUTLIER) cc_final: 0.6109 (tt) REVERT: A 290 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7574 (mt) REVERT: A 432 PHE cc_start: 0.7499 (t80) cc_final: 0.6565 (t80) REVERT: A 489 ILE cc_start: 0.7628 (OUTLIER) cc_final: 0.7168 (mt) REVERT: A 558 MET cc_start: 0.4180 (OUTLIER) cc_final: 0.3418 (tpt) outliers start: 41 outliers final: 11 residues processed: 211 average time/residue: 0.4845 time to fit residues: 114.1687 Evaluate side-chains 194 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 264 LEU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 474 VAL 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 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 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 111 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 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: 4.9990 chunk 132 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 138 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.220960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.181684 restraints weight = 15031.168| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.56 r_work: 0.3674 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.4580 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 : 0.608 8.245 19733 Z= 0.309 Chirality : 0.040 0.211 2273 Planarity : 0.004 0.045 2414 Dihedral : 10.343 83.974 2609 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.68 % Allowed : 26.00 % Favored : 71.32 % 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: 1.17 (0.22), residues: 1590 helix: 2.05 (0.16), residues: 1053 sheet: None (None), residues: 0 loop : -1.96 (0.25), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 330 TYR 0.014 0.002 TYR C 152 PHE 0.013 0.001 PHE B 432 TRP 0.023 0.002 TRP A 158 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00297 (14512) covalent geometry : angle 0.60839 (19733) hydrogen bonds : bond 0.04362 ( 900) hydrogen bonds : angle 4.18213 ( 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: 38 poor density : 171 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.2701 (OUTLIER) cc_final: 0.2265 (pp) REVERT: C 62 MET cc_start: 0.8586 (ttp) cc_final: 0.8023 (ttm) REVERT: C 222 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7633 (mp) REVERT: C 225 LYS cc_start: 0.8029 (mtpp) cc_final: 0.7735 (mtpt) REVERT: C 264 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.5836 (tt) REVERT: C 290 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7535 (mt) REVERT: C 375 LEU cc_start: 0.7520 (mp) cc_final: 0.7212 (mt) REVERT: C 478 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 489 ILE cc_start: 0.7571 (OUTLIER) cc_final: 0.7158 (mt) REVERT: C 497 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7248 (tpp80) REVERT: C 520 SER cc_start: 0.8682 (t) cc_final: 0.8364 (t) REVERT: C 524 MET cc_start: 0.6744 (mtt) cc_final: 0.6370 (mtt) REVERT: C 558 MET cc_start: 0.4077 (OUTLIER) cc_final: 0.2886 (tmt) REVERT: B 40 ILE cc_start: 0.3596 (OUTLIER) cc_final: 0.3340 (pp) REVERT: B 62 MET cc_start: 0.8451 (ttm) cc_final: 0.7981 (ttm) REVERT: B 69 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7653 (mt-10) REVERT: B 191 GLN cc_start: 0.6589 (pp30) cc_final: 0.6197 (pp30) REVERT: B 205 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.6125 (tt0) REVERT: B 224 ASN cc_start: 0.7547 (t0) cc_final: 0.7183 (t0) REVERT: B 225 LYS cc_start: 0.8101 (mtpp) cc_final: 0.7842 (mtpt) REVERT: B 249 TYR cc_start: 0.8718 (t80) cc_final: 0.8403 (t80) REVERT: B 290 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (mt) REVERT: B 327 LEU cc_start: 0.7909 (mt) cc_final: 0.7493 (mm) REVERT: B 354 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7837 (mt) REVERT: B 375 LEU cc_start: 0.7519 (mp) cc_final: 0.7282 (mt) REVERT: B 445 ILE cc_start: 0.7556 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 558 MET cc_start: 0.4412 (OUTLIER) cc_final: 0.3550 (tmt) REVERT: A 186 ARG cc_start: 0.7839 (tpt90) cc_final: 0.6829 (tpt-90) REVERT: A 225 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7581 (mtpt) REVERT: A 264 LEU cc_start: 0.6517 (OUTLIER) cc_final: 0.5882 (tt) REVERT: A 290 ILE cc_start: 0.8071 (OUTLIER) cc_final: 0.7635 (mt) REVERT: A 489 ILE cc_start: 0.7613 (OUTLIER) cc_final: 0.7103 (mt) REVERT: A 558 MET cc_start: 0.4060 (OUTLIER) cc_final: 0.3094 (tpt) outliers start: 38 outliers final: 14 residues processed: 197 average time/residue: 0.5093 time to fit residues: 111.3399 Evaluate side-chains 197 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 239 GLU 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 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 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 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 111 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 412 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 4.9990 chunk 105 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 164 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 121 optimal weight: 0.0570 chunk 67 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 507 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.222232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.184420 restraints weight = 15008.777| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 2.20 r_work: 0.3700 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.4697 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= 0.128 Angle : 0.592 7.918 19733 Z= 0.302 Chirality : 0.039 0.207 2273 Planarity : 0.004 0.044 2414 Dihedral : 9.698 78.967 2609 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.89 % Allowed : 25.79 % Favored : 71.32 % 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: 1.29 (0.22), residues: 1590 helix: 2.13 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.85 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 330 TYR 0.013 0.001 TYR C 152 PHE 0.022 0.001 PHE A 432 TRP 0.022 0.002 TRP A 158 HIS 0.004 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00275 (14512) covalent geometry : angle 0.59198 (19733) hydrogen bonds : bond 0.04178 ( 900) hydrogen bonds : angle 4.13574 ( 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 216 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 ILE cc_start: 0.2086 (OUTLIER) cc_final: 0.1801 (pp) REVERT: C 62 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8007 (ttm) REVERT: C 222 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7618 (mp) REVERT: C 225 LYS cc_start: 0.8003 (mtpp) cc_final: 0.7699 (mtpt) REVERT: C 264 LEU cc_start: 0.6518 (OUTLIER) cc_final: 0.5861 (tt) REVERT: C 290 ILE cc_start: 0.8081 (OUTLIER) cc_final: 0.7554 (mt) REVERT: C 375 LEU cc_start: 0.7509 (mp) cc_final: 0.7215 (mt) REVERT: C 478 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8288 (mt-10) REVERT: C 489 ILE cc_start: 0.7554 (OUTLIER) cc_final: 0.7126 (mt) REVERT: C 497 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7261 (tpp80) REVERT: C 520 SER cc_start: 0.8656 (t) cc_final: 0.8450 (m) REVERT: C 558 MET cc_start: 0.4147 (OUTLIER) cc_final: 0.2957 (tmt) REVERT: B 40 ILE cc_start: 0.3329 (OUTLIER) cc_final: 0.3045 (pp) REVERT: B 62 MET cc_start: 0.8317 (ttm) cc_final: 0.8016 (ttp) REVERT: B 63 LEU cc_start: 0.8731 (tt) cc_final: 0.8502 (tp) REVERT: B 69 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7636 (mt-10) REVERT: B 205 GLU cc_start: 0.6334 (OUTLIER) cc_final: 0.5971 (tt0) REVERT: B 224 ASN cc_start: 0.7530 (t0) cc_final: 0.7152 (t0) REVERT: B 225 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7796 (mtpt) REVERT: B 249 TYR cc_start: 0.8707 (t80) cc_final: 0.8386 (t80) REVERT: B 290 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7610 (mt) REVERT: B 327 LEU cc_start: 0.7848 (mt) cc_final: 0.7458 (mm) REVERT: B 354 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7864 (mt) REVERT: B 375 LEU cc_start: 0.7397 (mp) cc_final: 0.7131 (mt) REVERT: B 445 ILE cc_start: 0.7525 (OUTLIER) cc_final: 0.7229 (tp) REVERT: B 524 MET cc_start: 0.6082 (mtt) cc_final: 0.5873 (mpp) REVERT: B 558 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.3582 (tmt) REVERT: A 186 ARG cc_start: 0.7828 (tpt90) cc_final: 0.6862 (tpt-90) REVERT: A 225 LYS cc_start: 0.7926 (mtpp) cc_final: 0.7547 (mtpt) REVERT: A 264 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.5935 (tt) REVERT: A 290 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7655 (mt) REVERT: A 489 ILE cc_start: 0.7592 (OUTLIER) cc_final: 0.7039 (mt) REVERT: A 507 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6933 (m110) REVERT: A 558 MET cc_start: 0.4268 (OUTLIER) cc_final: 0.3355 (tpt) outliers start: 41 outliers final: 13 residues processed: 202 average time/residue: 0.5219 time to fit residues: 116.8702 Evaluate side-chains 197 residues out of total 1425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 ILE Chi-restraints excluded: chain C residue 62 MET Chi-restraints excluded: chain C residue 222 LEU 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 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 262 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 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 177 TYR 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 412 THR Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 507 ASN 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: 6.9990 chunk 131 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 42 optimal weight: 0.0770 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 ASN ** C 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.222116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.181742 restraints weight = 14963.571| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.65 r_work: 0.3709 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14512 Z= 0.168 Angle : 0.806 59.197 19733 Z= 0.457 Chirality : 0.043 0.597 2273 Planarity : 0.004 0.042 2414 Dihedral : 9.725 78.943 2609 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.17 % Favored : 92.77 % Rotamer: Outliers : 2.40 % Allowed : 26.50 % Favored : 71.11 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: 1.28 (0.22), residues: 1590 helix: 2.12 (0.16), residues: 1047 sheet: None (None), residues: 0 loop : -1.85 (0.25), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 330 TYR 0.013 0.002 TYR C 152 PHE 0.022 0.001 PHE A 432 TRP 0.020 0.002 TRP A 158 HIS 0.005 0.001 HIS C 348 Details of bonding type rmsd covalent geometry : bond 0.00366 (14512) covalent geometry : angle 0.80604 (19733) hydrogen bonds : bond 0.04442 ( 900) hydrogen bonds : angle 4.14995 ( 2619) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5054.10 seconds wall clock time: 86 minutes 39.10 seconds (5199.10 seconds total)