Starting phenix.real_space_refine on Fri Jul 3 10:48:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.cif" model { file = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fhk_31585/07_2026/7fhk_31585.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3394 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 44 5.16 5 C 7346 2.51 5 N 1710 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.28, per 1000 atoms: 0.21 Number of scatterers: 11058 At special positions: 0 Unit cell: (88.218, 120.666, 116.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 44 16.00 O 1954 8.00 N 1710 7.00 C 7346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 310.4 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.520A pdb=" N ALA A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 88 removed outlier: 3.525A pdb=" N TRP A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE A 86 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.766A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 143 through 150 removed outlier: 3.616A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 197 removed outlier: 3.598A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.295A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.503A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.769A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.937A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.719A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.857A pdb=" N LYS A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 4.231A pdb=" N GLY A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.772A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 390 " --> pdb=" O ASP A 386 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 429 Processing helix chain 'A' and resid 429 through 456 removed outlier: 3.964A pdb=" N GLY A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.058A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLY A 472 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 4.209A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 Processing helix chain 'A' and resid 528 through 538 removed outlier: 4.377A pdb=" N TYR A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 Processing helix chain 'A' and resid 551 through 565 Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 587 Processing helix chain 'A' and resid 595 through 601 removed outlier: 4.047A pdb=" N PHE A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLU A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR A 601 " --> pdb=" O LYS A 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 595 through 601' Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.786A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.957A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.957A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 686 removed outlier: 3.601A pdb=" N LEU A 681 " --> pdb=" O THR A 677 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 48 through 54 Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.517A pdb=" N ALA C 61 " --> pdb=" O PHE C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 88 removed outlier: 3.511A pdb=" N TRP C 74 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ASN C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N PHE C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.749A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 143 through 150 removed outlier: 3.552A pdb=" N THR C 149 " --> pdb=" O ARG C 145 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.775A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.930A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 250 through 264 Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.944A pdb=" N VAL C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.208A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 290 " --> pdb=" O VAL C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 335 Processing helix chain 'C' and resid 343 through 358 Processing helix chain 'C' and resid 364 through 376 removed outlier: 3.505A pdb=" N PHE C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 411 through 416 Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 429 through 456 removed outlier: 4.204A pdb=" N GLY C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.479A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 4.083A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.554A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 removed outlier: 4.296A pdb=" N TYR C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 533 " --> pdb=" O TRP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 547 Processing helix chain 'C' and resid 551 through 587 Proline residue: C 563 - end of helix Proline residue: C 567 - end of helix Processing helix chain 'C' and resid 595 through 601 removed outlier: 4.065A pdb=" N PHE C 599 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLU C 600 " --> pdb=" O LYS C 596 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 601 " --> pdb=" O LYS C 597 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 595 through 601' Processing helix chain 'C' and resid 601 through 607 removed outlier: 3.645A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 Processing helix chain 'C' and resid 615 through 628 Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.890A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 659 removed outlier: 4.129A pdb=" N THR C 650 " --> pdb=" O TRP C 646 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR C 651 " --> pdb=" O TRP C 647 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 686 Processing helix chain 'D' and resid 7 through 17 769 hydrogen bonds defined for protein. 2259 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: 1.71 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3351 1.34 - 1.46: 2092 1.46 - 1.57: 5835 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 11350 Sorted by residual: bond pdb=" C LYS A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.23e-02 6.61e+03 1.65e+00 bond pdb=" CG LEU C 440 " pdb=" CD1 LEU C 440 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 bond pdb=" CB GLU C 468 " pdb=" CG GLU C 468 " ideal model delta sigma weight residual 1.520 1.487 0.033 3.00e-02 1.11e+03 1.23e+00 bond pdb=" N PHE A 57 " pdb=" CA PHE A 57 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.07e+00 bond pdb=" N PHE C 57 " pdb=" CA PHE C 57 " ideal model delta sigma weight residual 1.457 1.471 -0.013 1.29e-02 6.01e+03 1.04e+00 ... (remaining 11345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 14967 1.43 - 2.85: 360 2.85 - 4.28: 81 4.28 - 5.71: 29 5.71 - 7.13: 3 Bond angle restraints: 15440 Sorted by residual: angle pdb=" C THR C 246 " pdb=" N VAL C 247 " pdb=" CA VAL C 247 " ideal model delta sigma weight residual 123.16 120.08 3.08 1.06e+00 8.90e-01 8.43e+00 angle pdb=" C THR A 246 " pdb=" N VAL A 247 " pdb=" CA VAL A 247 " ideal model delta sigma weight residual 123.16 120.11 3.05 1.06e+00 8.90e-01 8.29e+00 angle pdb=" N VAL C 286 " pdb=" CA VAL C 286 " pdb=" C VAL C 286 " ideal model delta sigma weight residual 113.00 109.55 3.45 1.30e+00 5.92e-01 7.04e+00 angle pdb=" N GLN C 393 " pdb=" CA GLN C 393 " pdb=" CB GLN C 393 " ideal model delta sigma weight residual 110.12 113.99 -3.87 1.47e+00 4.63e-01 6.93e+00 angle pdb=" CA LYS C 385 " pdb=" CB LYS C 385 " pdb=" CG LYS C 385 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 ... (remaining 15435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 6027 17.42 - 34.84: 455 34.84 - 52.25: 70 52.25 - 69.67: 6 69.67 - 87.09: 8 Dihedral angle restraints: 6566 sinusoidal: 2570 harmonic: 3996 Sorted by residual: dihedral pdb=" CA SER A 56 " pdb=" C SER A 56 " pdb=" N PHE A 57 " pdb=" CA PHE A 57 " ideal model delta harmonic sigma weight residual 180.00 163.15 16.85 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA SER C 56 " pdb=" C SER C 56 " pdb=" N PHE C 57 " pdb=" CA PHE C 57 " ideal model delta harmonic sigma weight residual 180.00 163.20 16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 163.31 16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 6563 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1276 0.038 - 0.077: 381 0.077 - 0.115: 76 0.115 - 0.153: 14 0.153 - 0.192: 1 Chirality restraints: 1748 Sorted by residual: chirality pdb=" CA LYS C 98 " pdb=" N LYS C 98 " pdb=" C LYS C 98 " pdb=" CB LYS C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.19e-01 chirality pdb=" CA VAL C 404 " pdb=" N VAL C 404 " pdb=" C VAL C 404 " pdb=" CB VAL C 404 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 1745 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 651 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.69e+00 pdb=" C TYR C 651 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR C 651 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE C 652 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 531 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.35e+00 pdb=" C ARG C 531 " 0.027 2.00e-02 2.50e+03 pdb=" O ARG C 531 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR C 532 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 607 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" C ASP C 607 " -0.022 2.00e-02 2.50e+03 pdb=" O ASP C 607 " 0.008 2.00e-02 2.50e+03 pdb=" N TYR C 608 " 0.007 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1579 2.75 - 3.29: 11731 3.29 - 3.82: 18218 3.82 - 4.36: 20059 4.36 - 4.90: 35187 Nonbonded interactions: 86774 Sorted by model distance: nonbonded pdb=" OH TYR C 216 " pdb=" O VAL C 657 " model vdw 2.210 3.040 nonbonded pdb=" O PHE C 426 " pdb=" OG SER C 429 " model vdw 2.225 3.040 nonbonded pdb=" O TYR A 107 " pdb=" ND2 ASN A 614 " model vdw 2.231 3.120 nonbonded pdb=" OE2 GLU C 478 " pdb=" NH2 ARG C 537 " model vdw 2.252 3.120 nonbonded pdb=" O TYR C 107 " pdb=" ND2 ASN C 614 " model vdw 2.253 3.120 ... (remaining 86769 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.050 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.004 0.037 11350 Z= 0.158 Angle : 0.596 7.132 15440 Z= 0.335 Chirality : 0.038 0.192 1748 Planarity : 0.003 0.031 1914 Dihedral : 12.525 87.090 3982 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.23), residues: 1318 helix: 1.18 (0.16), residues: 972 sheet: None (None), residues: 0 loop : -0.01 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.017 0.002 TYR C 256 PHE 0.019 0.001 PHE C 248 TRP 0.016 0.001 TRP C 492 HIS 0.005 0.002 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (11350) covalent geometry : angle 0.59645 / 0.34 (15440) hydrogen bonds : bond 0.20223 / 13.28 ( 769) hydrogen bonds : angle 6.29209 / 4.46 ( 2259) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.306 Fit side-chains REVERT: A 149 THR cc_start: 0.8234 (m) cc_final: 0.7903 (p) REVERT: A 321 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 406 SER cc_start: 0.7673 (t) cc_final: 0.6224 (t) REVERT: A 620 MET cc_start: 0.8906 (mmm) cc_final: 0.8676 (mmt) REVERT: A 637 GLU cc_start: 0.7542 (tm-30) cc_final: 0.6692 (tm-30) REVERT: C 149 THR cc_start: 0.8179 (m) cc_final: 0.7867 (p) REVERT: C 321 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7654 (tm-30) REVERT: C 406 SER cc_start: 0.7776 (t) cc_final: 0.7461 (t) REVERT: C 629 MET cc_start: 0.8850 (mmm) cc_final: 0.8537 (mmm) REVERT: C 637 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6847 (tm-30) REVERT: C 641 ASP cc_start: 0.7434 (m-30) cc_final: 0.7143 (m-30) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.0742 time to fit residues: 20.9403 Evaluate side-chains 128 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.126741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.095761 restraints weight = 18381.438| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.41 r_work: 0.3052 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11350 Z= 0.138 Angle : 0.568 7.306 15440 Z= 0.300 Chirality : 0.038 0.182 1748 Planarity : 0.004 0.054 1914 Dihedral : 4.089 17.136 1468 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.84 % Allowed : 6.90 % Favored : 92.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.24), residues: 1318 helix: 1.96 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -0.03 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 424 TYR 0.017 0.002 TYR A 305 PHE 0.026 0.001 PHE C 408 TRP 0.021 0.001 TRP C 492 HIS 0.002 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.14 (11350) covalent geometry : angle 0.56806 / 0.30 (15440) hydrogen bonds : bond 0.05404 / 3.38 ( 769) hydrogen bonds : angle 4.18240 / 2.97 ( 2259) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.366 Fit side-chains REVERT: A 52 LEU cc_start: 0.8946 (mm) cc_final: 0.8739 (mm) REVERT: A 154 LEU cc_start: 0.8993 (mt) cc_final: 0.8770 (mt) REVERT: A 443 ASN cc_start: 0.9110 (t0) cc_final: 0.8832 (t0) REVERT: A 538 MET cc_start: 0.8714 (mtm) cc_final: 0.8453 (mtm) REVERT: A 566 MET cc_start: 0.8481 (tpp) cc_final: 0.8191 (mmm) REVERT: C 154 LEU cc_start: 0.9013 (mt) cc_final: 0.8791 (mt) REVERT: C 321 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 515 PHE cc_start: 0.7420 (t80) cc_final: 0.6952 (t80) REVERT: C 564 SER cc_start: 0.9159 (t) cc_final: 0.8848 (p) REVERT: C 637 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 641 ASP cc_start: 0.8253 (m-30) cc_final: 0.8019 (m-30) outliers start: 10 outliers final: 9 residues processed: 152 average time/residue: 0.0679 time to fit residues: 16.7045 Evaluate side-chains 135 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 327 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 31 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.093993 restraints weight = 18567.544| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.39 r_work: 0.3017 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11350 Z= 0.142 Angle : 0.549 7.831 15440 Z= 0.287 Chirality : 0.038 0.178 1748 Planarity : 0.004 0.049 1914 Dihedral : 3.980 15.549 1468 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.18 % Allowed : 8.75 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.24), residues: 1318 helix: 2.10 (0.16), residues: 1012 sheet: None (None), residues: 0 loop : -0.02 (0.40), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 424 TYR 0.021 0.002 TYR C 357 PHE 0.023 0.001 PHE A 368 TRP 0.011 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (11350) covalent geometry : angle 0.54875 / 0.29 (15440) hydrogen bonds : bond 0.04970 / 3.10 ( 769) hydrogen bonds : angle 3.94389 / 2.80 ( 2259) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.361 Fit side-chains REVERT: A 52 LEU cc_start: 0.8884 (mm) cc_final: 0.8672 (mm) REVERT: A 154 LEU cc_start: 0.9014 (mt) cc_final: 0.8776 (mt) REVERT: A 321 GLN cc_start: 0.8083 (tm-30) cc_final: 0.7832 (tm-30) REVERT: A 443 ASN cc_start: 0.9162 (t0) cc_final: 0.8854 (t0) REVERT: A 566 MET cc_start: 0.8487 (tpp) cc_final: 0.8248 (mmm) REVERT: C 52 LEU cc_start: 0.8911 (mm) cc_final: 0.8686 (mm) REVERT: C 321 GLN cc_start: 0.8088 (tm-30) cc_final: 0.7773 (tm-30) REVERT: C 564 SER cc_start: 0.9199 (t) cc_final: 0.8789 (p) REVERT: C 637 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7576 (tm-30) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.0764 time to fit residues: 17.4284 Evaluate side-chains 130 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 9.9990 chunk 55 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095400 restraints weight = 18529.895| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 2.41 r_work: 0.3025 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11350 Z= 0.123 Angle : 0.529 8.649 15440 Z= 0.274 Chirality : 0.037 0.169 1748 Planarity : 0.003 0.041 1914 Dihedral : 3.925 15.586 1468 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.18 % Allowed : 10.94 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.41 (0.24), residues: 1318 helix: 2.11 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.11 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 424 TYR 0.023 0.001 TYR C 415 PHE 0.022 0.001 PHE A 368 TRP 0.011 0.001 TRP A 492 HIS 0.003 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11350) covalent geometry : angle 0.52905 / 0.27 (15440) hydrogen bonds : bond 0.04491 / 2.78 ( 769) hydrogen bonds : angle 3.80531 / 2.71 ( 2259) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 321 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7815 (tm-30) REVERT: A 415 TYR cc_start: 0.7194 (t80) cc_final: 0.6504 (m-80) REVERT: A 443 ASN cc_start: 0.9178 (t0) cc_final: 0.8877 (t0) REVERT: A 566 MET cc_start: 0.8458 (tpp) cc_final: 0.8251 (mmm) REVERT: C 52 LEU cc_start: 0.8875 (mm) cc_final: 0.8665 (mm) REVERT: C 321 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7792 (tm-30) REVERT: C 564 SER cc_start: 0.9220 (t) cc_final: 0.8819 (p) REVERT: C 629 MET cc_start: 0.9101 (mmm) cc_final: 0.8882 (mmm) REVERT: C 637 GLU cc_start: 0.8269 (tm-30) cc_final: 0.7858 (tm-30) outliers start: 14 outliers final: 9 residues processed: 145 average time/residue: 0.0767 time to fit residues: 17.5239 Evaluate side-chains 135 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 474 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 92 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095616 restraints weight = 18390.122| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.39 r_work: 0.3039 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11350 Z= 0.119 Angle : 0.522 8.979 15440 Z= 0.269 Chirality : 0.036 0.161 1748 Planarity : 0.003 0.044 1914 Dihedral : 3.871 15.238 1468 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.09 % Allowed : 12.37 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.52 (0.24), residues: 1318 helix: 2.20 (0.16), residues: 1014 sheet: None (None), residues: 0 loop : -0.12 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 424 TYR 0.018 0.001 TYR C 415 PHE 0.022 0.001 PHE A 368 TRP 0.012 0.001 TRP A 492 HIS 0.002 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (11350) covalent geometry : angle 0.52181 / 0.27 (15440) hydrogen bonds : bond 0.04261 / 2.63 ( 769) hydrogen bonds : angle 3.72607 / 2.65 ( 2259) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 144 time to evaluate : 0.435 Fit side-chains REVERT: A 321 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7823 (tm-30) REVERT: A 351 PHE cc_start: 0.8202 (t80) cc_final: 0.7993 (t80) REVERT: A 443 ASN cc_start: 0.9208 (t0) cc_final: 0.8975 (t0) REVERT: A 637 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7498 (tm-30) REVERT: C 321 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7804 (tm-30) REVERT: C 351 PHE cc_start: 0.8273 (t80) cc_final: 0.7974 (t80) REVERT: C 564 SER cc_start: 0.9229 (t) cc_final: 0.8826 (p) REVERT: C 629 MET cc_start: 0.9112 (mmm) cc_final: 0.8875 (mmm) REVERT: C 637 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7522 (tm-30) outliers start: 13 outliers final: 11 residues processed: 154 average time/residue: 0.0794 time to fit residues: 19.3030 Evaluate side-chains 141 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 82 optimal weight: 10.0000 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.0670 chunk 12 optimal weight: 0.0370 chunk 65 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.128582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.097681 restraints weight = 18651.910| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.42 r_work: 0.3074 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11350 Z= 0.109 Angle : 0.521 9.694 15440 Z= 0.267 Chirality : 0.036 0.154 1748 Planarity : 0.004 0.046 1914 Dihedral : 3.806 15.444 1468 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.18 % Allowed : 14.23 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.73 (0.24), residues: 1318 helix: 2.31 (0.17), residues: 996 sheet: None (None), residues: 0 loop : 0.27 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 424 TYR 0.026 0.001 TYR C 415 PHE 0.021 0.001 PHE A 368 TRP 0.013 0.001 TRP A 492 HIS 0.003 0.001 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11350) covalent geometry : angle 0.52099 / 0.27 (15440) hydrogen bonds : bond 0.03839 / 2.37 ( 769) hydrogen bonds : angle 3.63401 / 2.59 ( 2259) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 321 GLN cc_start: 0.7956 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 324 ARG cc_start: 0.8248 (tpp80) cc_final: 0.7981 (tpp80) REVERT: A 351 PHE cc_start: 0.8148 (t80) cc_final: 0.7934 (t80) REVERT: A 443 ASN cc_start: 0.9149 (t0) cc_final: 0.8857 (t0) REVERT: A 456 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7317 (tt0) REVERT: A 637 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7253 (tm-30) REVERT: C 321 GLN cc_start: 0.7978 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 351 PHE cc_start: 0.8143 (t80) cc_final: 0.7844 (t80) REVERT: C 564 SER cc_start: 0.9154 (t) cc_final: 0.8765 (p) REVERT: C 629 MET cc_start: 0.8994 (mmm) cc_final: 0.8710 (mmm) REVERT: C 637 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7623 (tm-30) outliers start: 14 outliers final: 11 residues processed: 159 average time/residue: 0.0730 time to fit residues: 18.1210 Evaluate side-chains 147 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 133 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.123244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.092293 restraints weight = 18565.922| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.37 r_work: 0.2982 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11350 Z= 0.181 Angle : 0.584 9.749 15440 Z= 0.303 Chirality : 0.039 0.259 1748 Planarity : 0.004 0.080 1914 Dihedral : 3.913 14.080 1468 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.52 % Allowed : 14.73 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.33 (0.24), residues: 1318 helix: 2.09 (0.17), residues: 1006 sheet: None (None), residues: 0 loop : -0.22 (0.37), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 424 TYR 0.020 0.002 TYR C 256 PHE 0.022 0.001 PHE A 368 TRP 0.015 0.001 TRP A 271 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (11350) covalent geometry : angle 0.58378 / 0.30 (15440) hydrogen bonds : bond 0.04838 / 3.00 ( 769) hydrogen bonds : angle 3.86499 / 2.73 ( 2259) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.457 Fit side-chains REVERT: A 321 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7773 (tm-30) REVERT: A 324 ARG cc_start: 0.8478 (tpp80) cc_final: 0.8218 (tpp80) REVERT: A 351 PHE cc_start: 0.8267 (t80) cc_final: 0.8045 (t80) REVERT: C 321 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7805 (tm-30) REVERT: C 351 PHE cc_start: 0.8328 (t80) cc_final: 0.8089 (t80) REVERT: C 456 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7174 (tt0) REVERT: C 515 PHE cc_start: 0.6970 (t80) cc_final: 0.6737 (t80) REVERT: C 620 MET cc_start: 0.9051 (mmm) cc_final: 0.8672 (mmt) REVERT: C 629 MET cc_start: 0.9157 (mmm) cc_final: 0.8922 (mmm) REVERT: C 637 GLU cc_start: 0.8407 (tm-30) cc_final: 0.7961 (tm-30) outliers start: 18 outliers final: 14 residues processed: 148 average time/residue: 0.0833 time to fit residues: 19.2464 Evaluate side-chains 141 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 474 ILE Chi-restraints excluded: chain C residue 541 LEU Chi-restraints excluded: chain C residue 636 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 89 optimal weight: 0.1980 chunk 80 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.123917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093147 restraints weight = 18617.977| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.38 r_work: 0.3000 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11350 Z= 0.149 Angle : 0.558 9.588 15440 Z= 0.288 Chirality : 0.038 0.259 1748 Planarity : 0.004 0.056 1914 Dihedral : 3.916 14.779 1468 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.09 % Allowed : 15.57 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.24), residues: 1318 helix: 2.06 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.26 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 424 TYR 0.017 0.002 TYR C 256 PHE 0.022 0.001 PHE A 368 TRP 0.011 0.001 TRP A 271 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (11350) covalent geometry : angle 0.55798 / 0.29 (15440) hydrogen bonds : bond 0.04556 / 2.82 ( 769) hydrogen bonds : angle 3.80527 / 2.69 ( 2259) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.295 Fit side-chains REVERT: A 321 GLN cc_start: 0.8080 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 324 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8200 (tpp80) REVERT: A 456 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7289 (tt0) REVERT: A 682 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7839 (tt0) REVERT: C 321 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7802 (tm-30) REVERT: C 351 PHE cc_start: 0.8284 (t80) cc_final: 0.7979 (t80) REVERT: C 456 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7244 (tt0) REVERT: C 515 PHE cc_start: 0.7102 (t80) cc_final: 0.6823 (t80) REVERT: C 629 MET cc_start: 0.9125 (mmm) cc_final: 0.8908 (mmm) REVERT: C 637 GLU cc_start: 0.8372 (tm-30) cc_final: 0.7918 (tm-30) outliers start: 13 outliers final: 10 residues processed: 144 average time/residue: 0.0774 time to fit residues: 17.4888 Evaluate side-chains 140 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 130 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 4 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093938 restraints weight = 18518.168| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.38 r_work: 0.3014 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11350 Z= 0.133 Angle : 0.556 10.067 15440 Z= 0.283 Chirality : 0.037 0.245 1748 Planarity : 0.004 0.051 1914 Dihedral : 3.875 14.296 1468 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.93 % Allowed : 15.91 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.35 (0.24), residues: 1318 helix: 2.10 (0.17), residues: 1016 sheet: None (None), residues: 0 loop : -0.28 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 424 TYR 0.016 0.001 TYR C 256 PHE 0.021 0.001 PHE A 368 TRP 0.010 0.001 TRP A 271 HIS 0.003 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11350) covalent geometry : angle 0.55585 / 0.28 (15440) hydrogen bonds : bond 0.04335 / 2.68 ( 769) hydrogen bonds : angle 3.73386 / 2.64 ( 2259) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.419 Fit side-chains REVERT: A 321 GLN cc_start: 0.8077 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 324 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8150 (tpp80) REVERT: A 456 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7278 (tt0) REVERT: A 682 GLU cc_start: 0.8569 (mm-30) cc_final: 0.7808 (tt0) REVERT: C 321 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7798 (tm-30) REVERT: C 351 PHE cc_start: 0.8247 (t80) cc_final: 0.7948 (t80) REVERT: C 443 ASN cc_start: 0.9190 (t0) cc_final: 0.8963 (t0) REVERT: C 456 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7249 (tt0) REVERT: C 538 MET cc_start: 0.7210 (mtp) cc_final: 0.6877 (mtp) REVERT: C 629 MET cc_start: 0.9141 (mmm) cc_final: 0.8910 (mmm) REVERT: C 637 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7895 (tm-30) outliers start: 11 outliers final: 11 residues processed: 141 average time/residue: 0.0785 time to fit residues: 17.4047 Evaluate side-chains 139 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 0.0670 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.095814 restraints weight = 18632.764| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 2.39 r_work: 0.3036 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11350 Z= 0.118 Angle : 0.547 10.237 15440 Z= 0.278 Chirality : 0.037 0.244 1748 Planarity : 0.004 0.045 1914 Dihedral : 3.822 14.390 1468 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.93 % Allowed : 16.33 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.24), residues: 1318 helix: 2.27 (0.17), residues: 996 sheet: None (None), residues: 0 loop : 0.21 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 424 TYR 0.014 0.001 TYR C 256 PHE 0.021 0.001 PHE A 368 TRP 0.010 0.001 TRP A 505 HIS 0.002 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (11350) covalent geometry : angle 0.54661 / 0.28 (15440) hydrogen bonds : bond 0.04032 / 2.49 ( 769) hydrogen bonds : angle 3.66614 / 2.60 ( 2259) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.450 Fit side-chains REVERT: A 321 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7806 (tm-30) REVERT: A 324 ARG cc_start: 0.8391 (tpp80) cc_final: 0.8136 (tpp80) REVERT: A 456 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7283 (tt0) REVERT: C 321 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7803 (tm-30) REVERT: C 351 PHE cc_start: 0.8218 (t80) cc_final: 0.7916 (t80) REVERT: C 443 ASN cc_start: 0.9201 (t0) cc_final: 0.8948 (t0) REVERT: C 538 MET cc_start: 0.7137 (mtp) cc_final: 0.6888 (mtp) REVERT: C 637 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7849 (tm-30) outliers start: 11 outliers final: 10 residues processed: 144 average time/residue: 0.0851 time to fit residues: 19.2604 Evaluate side-chains 135 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 470 VAL Chi-restraints excluded: chain C residue 541 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 131 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.127631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.096275 restraints weight = 18476.377| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.43 r_work: 0.3049 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11350 Z= 0.120 Angle : 0.554 10.221 15440 Z= 0.280 Chirality : 0.037 0.240 1748 Planarity : 0.004 0.042 1914 Dihedral : 3.795 14.386 1468 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.93 % Allowed : 16.41 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.67 (0.24), residues: 1318 helix: 2.28 (0.17), residues: 996 sheet: None (None), residues: 0 loop : 0.16 (0.39), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 424 TYR 0.018 0.001 TYR C 357 PHE 0.022 0.001 PHE A 368 TRP 0.013 0.001 TRP A 505 HIS 0.003 0.001 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (11350) covalent geometry : angle 0.55409 / 0.28 (15440) hydrogen bonds : bond 0.03996 / 2.48 ( 769) hydrogen bonds : angle 3.64035 / 2.59 ( 2259) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2375.64 seconds wall clock time: 41 minutes 27.69 seconds (2487.69 seconds total)