Starting phenix.real_space_refine on Fri Feb 6 08:57:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gsp_51553/02_2026/9gsp_51553_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gsp_51553/02_2026/9gsp_51553.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gsp_51553/02_2026/9gsp_51553_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gsp_51553/02_2026/9gsp_51553_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gsp_51553/02_2026/9gsp_51553.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gsp_51553/02_2026/9gsp_51553.map" } resolution = 3.68 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= 0.002 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 7530 2.51 5 N 2034 2.21 5 O 2385 1.98 5 H 11235 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23235 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 7622 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "B" Number of atoms: 7622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 7622 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "C" Number of atoms: 7622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 7622 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.39, per 1000 atoms: 0.19 Number of scatterers: 23235 At special positions: 0 Unit cell: (90.335, 95.41, 148.19, 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) S 51 16.00 O 2385 8.00 N 2034 7.00 C 7530 6.00 H 11235 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 136 " distance=2.02 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 475 " distance=2.02 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 136 " distance=2.02 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 475 " distance=2.02 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 136 " distance=2.02 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS C 475 " distance=2.02 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 601 " - " ASN A 11 " " NAG A 602 " - " ASN A 23 " " NAG A 603 " - " ASN A 162 " " NAG A 604 " - " ASN A 481 " " NAG B 601 " - " ASN B 162 " " NAG B 602 " - " ASN B 23 " " NAG B 603 " - " ASN B 481 " " NAG B 604 " - " ASN B 11 " " NAG C 601 " - " ASN C 11 " " NAG C 602 " - " ASN C 162 " " NAG C 603 " - " ASN C 23 " " NAG C 604 " - " ASN C 481 " " NAG D 1 " - " ASN A 87 " " NAG E 1 " - " ASN A 276 " " NAG F 1 " - " ASN B 87 " " NAG G 1 " - " ASN B 276 " " NAG H 1 " - " ASN C 276 " " NAG I 1 " - " ASN C 87 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 722.0 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2718 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 33 sheets defined 24.8% alpha, 18.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 97 through 105 removed outlier: 3.687A pdb=" N GLU A 103 " --> pdb=" O GLU A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 193 Processing helix chain 'A' and resid 364 through 385 removed outlier: 3.706A pdb=" N ILE A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 451 removed outlier: 3.644A pdb=" N ASP A 436 " --> pdb=" O GLU A 432 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ASP A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.559A pdb=" N TYR A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU A 491 " --> pdb=" O PRO A 487 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N GLU A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LEU A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 97 through 105 removed outlier: 3.585A pdb=" N GLU B 103 " --> pdb=" O GLU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 193 Processing helix chain 'B' and resid 364 through 385 removed outlier: 3.767A pdb=" N ILE B 383 " --> pdb=" O VAL B 379 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 451 removed outlier: 3.591A pdb=" N ASP B 436 " --> pdb=" O GLU B 432 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASP B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 485 through 498 removed outlier: 4.355A pdb=" N TYR B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 491 " --> pdb=" O PRO B 487 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 492 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LEU B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 97 through 105 Processing helix chain 'C' and resid 184 through 193 Processing helix chain 'C' and resid 364 through 385 removed outlier: 3.628A pdb=" N ILE C 383 " --> pdb=" O VAL C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 451 removed outlier: 3.664A pdb=" N ASP C 436 " --> pdb=" O GLU C 432 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 485 through 498 removed outlier: 4.187A pdb=" N TYR C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU C 491 " --> pdb=" O PRO C 487 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU C 492 " --> pdb=" O LYS C 488 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU C 495 " --> pdb=" O GLU C 491 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363 removed outlier: 3.597A pdb=" N CYS A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44 removed outlier: 5.962A pdb=" N LEU A 41 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 275 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 removed outlier: 6.632A pdb=" N LEU A 50 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.944A pdb=" N SER A 110 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 258 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 133 through 138 removed outlier: 7.008A pdb=" N ALA A 135 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N ALA A 141 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 148 through 149 Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 166 Processing sheet with id=AB2, first strand: chain 'A' and resid 279 through 280 removed outlier: 3.720A pdb=" N ILE A 300 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 360 through 363 removed outlier: 3.503A pdb=" N GLY B 6 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 34 removed outlier: 3.564A pdb=" N GLU B 34 " --> pdb=" O PHE B 292 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44 removed outlier: 5.989A pdb=" N LEU B 41 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS B 275 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.691A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 110 through 114 removed outlier: 4.062A pdb=" N SER B 110 " --> pdb=" O GLU B 258 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 258 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU B 172 " --> pdb=" O MET B 257 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 133 through 138 removed outlier: 7.044A pdb=" N ALA B 135 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 10.931A pdb=" N ALA B 141 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 148 through 149 Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 166 Processing sheet with id=AC4, first strand: chain 'B' and resid 279 through 280 Processing sheet with id=AC5, first strand: chain 'C' and resid 360 through 363 removed outlier: 3.615A pdb=" N CYS C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 15 through 18 removed outlier: 6.108A pdb=" N THR C 18 " --> pdb=" O LYS C 22 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS C 22 " --> pdb=" O THR C 18 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AC8, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.563A pdb=" N GLU C 34 " --> pdb=" O PHE C 292 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 44 removed outlier: 5.942A pdb=" N LEU C 41 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N CYS C 275 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 51 removed outlier: 6.637A pdb=" N LEU C 50 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.946A pdb=" N SER C 110 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 133 through 138 removed outlier: 6.890A pdb=" N ALA C 135 " --> pdb=" O ALA C 141 " (cutoff:3.500A) removed outlier: 10.878A pdb=" N ALA C 141 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 148 through 150 Processing sheet with id=AD5, first strand: chain 'C' and resid 164 through 166 Processing sheet with id=AD6, first strand: chain 'C' and resid 279 through 280 removed outlier: 3.506A pdb=" N ILE C 300 " --> pdb=" O GLN C 280 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1191 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: 5.62 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 11211 1.02 - 1.22: 28 1.22 - 1.42: 5223 1.42 - 1.61: 6980 1.61 - 1.81: 66 Bond restraints: 23508 Sorted by residual: bond pdb=" CB TRP A 231 " pdb=" CG TRP A 231 " ideal model delta sigma weight residual 1.498 1.441 0.057 3.10e-02 1.04e+03 3.41e+00 bond pdb=" N ASP B 1 " pdb=" CA ASP B 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.24e+00 bond pdb=" N ASP C 1 " pdb=" CA ASP C 1 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.14e+00 bond pdb=" N ASP A 1 " pdb=" CA ASP A 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" CB GLU B 34 " pdb=" CG GLU B 34 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 2.95e+00 ... (remaining 23503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 40040 1.61 - 3.23: 1942 3.23 - 4.84: 189 4.84 - 6.45: 22 6.45 - 8.06: 5 Bond angle restraints: 42198 Sorted by residual: angle pdb=" N ASN A 23 " pdb=" CA ASN A 23 " pdb=" CB ASN A 23 " ideal model delta sigma weight residual 112.63 106.53 6.10 1.61e+00 3.86e-01 1.44e+01 angle pdb=" N ASN B 23 " pdb=" CA ASN B 23 " pdb=" CB ASN B 23 " ideal model delta sigma weight residual 112.41 107.37 5.04 1.55e+00 4.16e-01 1.06e+01 angle pdb=" N HIS A 399 " pdb=" CA HIS A 399 " pdb=" C HIS A 399 " ideal model delta sigma weight residual 111.11 115.00 -3.89 1.20e+00 6.94e-01 1.05e+01 angle pdb=" N HIS B 399 " pdb=" CA HIS B 399 " pdb=" C HIS B 399 " ideal model delta sigma weight residual 111.11 114.97 -3.86 1.20e+00 6.94e-01 1.03e+01 angle pdb=" N ASN C 23 " pdb=" CA ASN C 23 " pdb=" CB ASN C 23 " ideal model delta sigma weight residual 112.41 107.68 4.73 1.55e+00 4.16e-01 9.31e+00 ... (remaining 42193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.93: 10523 20.93 - 41.87: 629 41.87 - 62.80: 303 62.80 - 83.74: 60 83.74 - 104.67: 16 Dihedral angle restraints: 11531 sinusoidal: 6458 harmonic: 5073 Sorted by residual: dihedral pdb=" CA CYS C 303 " pdb=" C CYS C 303 " pdb=" N PRO C 304 " pdb=" CA PRO C 304 " ideal model delta harmonic sigma weight residual 180.00 150.28 29.72 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA CYS A 303 " pdb=" C CYS A 303 " pdb=" N PRO A 304 " pdb=" CA PRO A 304 " ideal model delta harmonic sigma weight residual 180.00 150.69 29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA CYS B 303 " pdb=" C CYS B 303 " pdb=" N PRO B 304 " pdb=" CA PRO B 304 " ideal model delta harmonic sigma weight residual 180.00 150.92 29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 11528 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.229: 1867 0.229 - 0.459: 5 0.459 - 0.688: 0 0.688 - 0.918: 0 0.918 - 1.147: 3 Chirality restraints: 1875 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B 87 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.25 -1.15 2.00e-01 2.50e+01 3.29e+01 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 87 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.27 -1.13 2.00e-01 2.50e+01 3.21e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 87 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.29 -1.11 2.00e-01 2.50e+01 3.08e+01 ... (remaining 1872 not shown) Planarity restraints: 3537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 23 " 0.025 2.00e-02 2.50e+03 5.48e-02 3.76e+01 pdb=" CG ASN B 23 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASN B 23 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 23 " 0.091 2.00e-02 2.50e+03 pdb="HD22 ASN B 23 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 253 " -0.031 2.00e-02 2.50e+03 5.97e-02 3.56e+01 pdb=" N ALA B 254 " 0.103 2.00e-02 2.50e+03 pdb=" CA ALA B 254 " -0.026 2.00e-02 2.50e+03 pdb=" H ALA B 254 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 253 " -0.030 2.00e-02 2.50e+03 5.87e-02 3.44e+01 pdb=" N ALA C 254 " 0.101 2.00e-02 2.50e+03 pdb=" CA ALA C 254 " -0.026 2.00e-02 2.50e+03 pdb=" H ALA C 254 " -0.045 2.00e-02 2.50e+03 ... (remaining 3534 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 8443 2.36 - 2.92: 51896 2.92 - 3.48: 56784 3.48 - 4.04: 79219 4.04 - 4.60: 117822 Nonbonded interactions: 314164 Sorted by model distance: nonbonded pdb=" H PHE C 114 " pdb=" HD1 PHE C 114 " model vdw 1.801 2.100 nonbonded pdb=" H PHE B 114 " pdb=" HD1 PHE B 114 " model vdw 1.806 2.100 nonbonded pdb=" H PHE A 114 " pdb=" HD1 PHE A 114 " model vdw 1.817 2.100 nonbonded pdb=" HG1 THR C 82 " pdb=" O ASN C 84 " model vdw 1.852 2.450 nonbonded pdb=" HG1 THR B 82 " pdb=" O ASN B 84 " model vdw 1.853 2.450 ... (remaining 314159 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' selection = chain 'F' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 1.050 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: 0.150 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.520 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 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 : 0.008 0.057 12306 Z= 0.342 Angle : 1.004 15.674 16734 Z= 0.545 Chirality : 0.074 1.147 1875 Planarity : 0.008 0.085 2121 Dihedral : 15.783 104.670 4923 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.64 % Allowed : 4.45 % Favored : 93.91 % 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: -2.26 (0.18), residues: 1452 helix: -1.59 (0.23), residues: 327 sheet: -0.95 (0.28), residues: 273 loop : -1.67 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.003 ARG B 223 TYR 0.032 0.008 TYR A 253 PHE 0.032 0.004 PHE A 114 TRP 0.025 0.005 TRP C 348 HIS 0.008 0.002 HIS B 37 Details of bonding type rmsd covalent geometry : bond 0.00751 (12273) covalent geometry : angle 0.93845 (16641) SS BOND : bond 0.01197 ( 6) SS BOND : angle 1.10340 ( 12) hydrogen bonds : bond 0.20303 ( 422) hydrogen bonds : angle 8.74308 ( 1191) link_BETA1-4 : bond 0.00855 ( 9) link_BETA1-4 : angle 3.40907 ( 27) link_NAG-ASN : bond 0.00511 ( 18) link_NAG-ASN : angle 5.90813 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 SER cc_start: 0.7759 (m) cc_final: 0.7323 (p) REVERT: A 338 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6652 (tm-30) REVERT: B 22 LYS cc_start: 0.7144 (mttt) cc_final: 0.6877 (mptt) REVERT: B 275 CYS cc_start: 0.6629 (t) cc_final: 0.6425 (p) REVERT: B 338 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6853 (tm-30) REVERT: B 465 PHE cc_start: 0.7592 (m-80) cc_final: 0.7230 (m-80) REVERT: C 235 GLU cc_start: 0.8018 (pt0) cc_final: 0.7596 (pm20) REVERT: C 338 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6563 (tm-30) outliers start: 21 outliers final: 13 residues processed: 248 average time/residue: 0.2975 time to fit residues: 100.8351 Evaluate side-chains 163 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 HIS B 399 HIS B 455 ASN C 8 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.169028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.140559 restraints weight = 44527.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146152 restraints weight = 20843.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.149619 restraints weight = 12385.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.151592 restraints weight = 8663.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.153144 restraints weight = 6895.517| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12306 Z= 0.145 Angle : 0.732 8.006 16734 Z= 0.387 Chirality : 0.050 0.578 1875 Planarity : 0.004 0.031 2121 Dihedral : 10.971 62.833 2163 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.11 % Allowed : 9.68 % Favored : 88.21 % 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: -1.36 (0.18), residues: 1452 helix: -0.44 (0.26), residues: 333 sheet: -0.29 (0.33), residues: 201 loop : -1.25 (0.17), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 319 TYR 0.016 0.002 TYR C 98 PHE 0.033 0.002 PHE C 114 TRP 0.009 0.001 TRP B 177 HIS 0.009 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00307 (12273) covalent geometry : angle 0.70246 (16641) SS BOND : bond 0.00769 ( 6) SS BOND : angle 1.32338 ( 12) hydrogen bonds : bond 0.05709 ( 422) hydrogen bonds : angle 5.94469 ( 1191) link_BETA1-4 : bond 0.00715 ( 9) link_BETA1-4 : angle 2.34352 ( 27) link_NAG-ASN : bond 0.00380 ( 18) link_NAG-ASN : angle 3.32412 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.7143 (tpt) cc_final: 0.6862 (tpt) REVERT: B 430 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7173 (mt-10) REVERT: C 476 MET cc_start: 0.7298 (tpt) cc_final: 0.7034 (tpt) outliers start: 27 outliers final: 23 residues processed: 207 average time/residue: 0.2773 time to fit residues: 80.3677 Evaluate side-chains 173 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS B 228 ASN B 399 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 ASN C 455 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.165122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.136185 restraints weight = 45346.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141716 restraints weight = 21584.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.145124 restraints weight = 13038.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.147240 restraints weight = 9232.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148315 restraints weight = 7324.079| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12306 Z= 0.208 Angle : 0.714 8.800 16734 Z= 0.377 Chirality : 0.051 0.668 1875 Planarity : 0.004 0.049 2121 Dihedral : 9.567 59.940 2159 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.81 % Allowed : 11.48 % Favored : 85.71 % 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: -1.55 (0.19), residues: 1452 helix: -0.26 (0.26), residues: 339 sheet: -1.31 (0.32), residues: 252 loop : -1.24 (0.17), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.014 0.002 TYR A 437 PHE 0.032 0.003 PHE B 114 TRP 0.010 0.002 TRP C 348 HIS 0.035 0.002 HIS C 8 Details of bonding type rmsd covalent geometry : bond 0.00450 (12273) covalent geometry : angle 0.68386 (16641) SS BOND : bond 0.00664 ( 6) SS BOND : angle 0.60348 ( 12) hydrogen bonds : bond 0.05646 ( 422) hydrogen bonds : angle 5.71635 ( 1191) link_BETA1-4 : bond 0.00608 ( 9) link_BETA1-4 : angle 2.28702 ( 27) link_NAG-ASN : bond 0.00252 ( 18) link_NAG-ASN : angle 3.36257 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.7213 (tpt) cc_final: 0.6879 (tpt) REVERT: B 138 HIS cc_start: 0.6441 (OUTLIER) cc_final: 0.6198 (t-170) REVERT: B 430 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7268 (mt-10) REVERT: C 8 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6408 (p90) outliers start: 36 outliers final: 25 residues processed: 180 average time/residue: 0.2607 time to fit residues: 66.5046 Evaluate side-chains 168 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 420 THR Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 63 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 0.9980 chunk 102 optimal weight: 0.0040 chunk 92 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS B 399 HIS ** C 163 GLN ** 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 = 0.4187 r_free = 0.4187 target = 0.165473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.136795 restraints weight = 44737.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.142377 restraints weight = 20852.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145857 restraints weight = 12420.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147999 restraints weight = 8670.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149357 restraints weight = 6807.526| |-----------------------------------------------------------------------------| r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12306 Z= 0.142 Angle : 0.646 7.108 16734 Z= 0.343 Chirality : 0.048 0.557 1875 Planarity : 0.004 0.042 2121 Dihedral : 8.639 59.050 2159 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.42 % Allowed : 12.26 % Favored : 85.32 % 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: -1.32 (0.20), residues: 1452 helix: -0.15 (0.26), residues: 339 sheet: -0.78 (0.31), residues: 279 loop : -1.21 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 497 TYR 0.012 0.002 TYR B 206 PHE 0.030 0.002 PHE A 114 TRP 0.007 0.001 TRP C 348 HIS 0.034 0.002 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00303 (12273) covalent geometry : angle 0.62021 (16641) SS BOND : bond 0.00322 ( 6) SS BOND : angle 0.26408 ( 12) hydrogen bonds : bond 0.04929 ( 422) hydrogen bonds : angle 5.47496 ( 1191) link_BETA1-4 : bond 0.00588 ( 9) link_BETA1-4 : angle 2.11389 ( 27) link_NAG-ASN : bond 0.00292 ( 18) link_NAG-ASN : angle 2.91423 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.7141 (tpt) cc_final: 0.6816 (tpt) REVERT: B 430 GLU cc_start: 0.7359 (mt-10) cc_final: 0.7146 (mt-10) outliers start: 31 outliers final: 23 residues processed: 181 average time/residue: 0.2739 time to fit residues: 69.4165 Evaluate side-chains 170 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 420 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 21 optimal weight: 0.4980 chunk 48 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.165396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.136771 restraints weight = 44518.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.142357 restraints weight = 20785.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145809 restraints weight = 12369.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.147979 restraints weight = 8679.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.149299 restraints weight = 6810.083| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12306 Z= 0.150 Angle : 0.627 7.104 16734 Z= 0.332 Chirality : 0.047 0.566 1875 Planarity : 0.004 0.044 2121 Dihedral : 7.869 53.140 2153 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.73 % Allowed : 13.11 % Favored : 84.15 % 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: -1.26 (0.20), residues: 1452 helix: -0.03 (0.27), residues: 339 sheet: -0.79 (0.32), residues: 279 loop : -1.19 (0.18), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 319 TYR 0.012 0.002 TYR A 437 PHE 0.022 0.002 PHE B 114 TRP 0.006 0.001 TRP C 76 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00323 (12273) covalent geometry : angle 0.60080 (16641) SS BOND : bond 0.00340 ( 6) SS BOND : angle 0.20344 ( 12) hydrogen bonds : bond 0.04776 ( 422) hydrogen bonds : angle 5.37286 ( 1191) link_BETA1-4 : bond 0.00500 ( 9) link_BETA1-4 : angle 1.92908 ( 27) link_NAG-ASN : bond 0.00275 ( 18) link_NAG-ASN : angle 2.93368 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.7236 (tpt) cc_final: 0.6871 (tpt) REVERT: B 111 PHE cc_start: 0.7734 (t80) cc_final: 0.7457 (t80) outliers start: 35 outliers final: 29 residues processed: 184 average time/residue: 0.2291 time to fit residues: 60.1598 Evaluate side-chains 177 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 365 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 399 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.162275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.133039 restraints weight = 45165.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.138533 restraints weight = 21557.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.141960 restraints weight = 13041.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.144133 restraints weight = 9254.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.145508 restraints weight = 7324.205| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12306 Z= 0.241 Angle : 0.685 8.875 16734 Z= 0.363 Chirality : 0.050 0.652 1875 Planarity : 0.005 0.045 2121 Dihedral : 8.009 58.424 2152 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 3.67 % Allowed : 12.96 % Favored : 83.37 % 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: -1.70 (0.20), residues: 1452 helix: -0.10 (0.27), residues: 339 sheet: -1.47 (0.33), residues: 249 loop : -1.46 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.016 0.002 TYR B 206 PHE 0.018 0.002 PHE A 117 TRP 0.011 0.002 TRP C 76 HIS 0.008 0.001 HIS A 8 Details of bonding type rmsd covalent geometry : bond 0.00528 (12273) covalent geometry : angle 0.65720 (16641) SS BOND : bond 0.00571 ( 6) SS BOND : angle 0.39195 ( 12) hydrogen bonds : bond 0.05116 ( 422) hydrogen bonds : angle 5.49851 ( 1191) link_BETA1-4 : bond 0.00493 ( 9) link_BETA1-4 : angle 1.86212 ( 27) link_NAG-ASN : bond 0.00205 ( 18) link_NAG-ASN : angle 3.23583 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 476 MET cc_start: 0.7216 (tpt) cc_final: 0.6867 (tpt) REVERT: B 111 PHE cc_start: 0.7830 (t80) cc_final: 0.7595 (t80) REVERT: B 318 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.7140 (mp) outliers start: 47 outliers final: 39 residues processed: 184 average time/residue: 0.2434 time to fit residues: 64.5287 Evaluate side-chains 178 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 408 ASN Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 365 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 130 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 137 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 140 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS B 8 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.165811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.136711 restraints weight = 44584.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.142383 restraints weight = 20940.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145903 restraints weight = 12500.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148086 restraints weight = 8778.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149371 restraints weight = 6904.382| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12306 Z= 0.128 Angle : 0.613 6.547 16734 Z= 0.324 Chirality : 0.047 0.533 1875 Planarity : 0.004 0.046 2121 Dihedral : 7.694 53.445 2152 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.20 % Allowed : 13.58 % Favored : 83.22 % 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: -1.43 (0.20), residues: 1452 helix: 0.13 (0.27), residues: 339 sheet: -1.17 (0.34), residues: 249 loop : -1.34 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.011 0.001 TYR B 98 PHE 0.040 0.002 PHE B 117 TRP 0.008 0.001 TRP C 123 HIS 0.007 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00272 (12273) covalent geometry : angle 0.58920 (16641) SS BOND : bond 0.00247 ( 6) SS BOND : angle 0.20693 ( 12) hydrogen bonds : bond 0.04510 ( 422) hydrogen bonds : angle 5.26363 ( 1191) link_BETA1-4 : bond 0.00491 ( 9) link_BETA1-4 : angle 1.76953 ( 27) link_NAG-ASN : bond 0.00293 ( 18) link_NAG-ASN : angle 2.77977 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 194 ASN cc_start: 0.7715 (m-40) cc_final: 0.7359 (p0) REVERT: B 111 PHE cc_start: 0.7715 (t80) cc_final: 0.7468 (t80) REVERT: B 318 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7152 (mp) outliers start: 41 outliers final: 33 residues processed: 176 average time/residue: 0.2429 time to fit residues: 60.4808 Evaluate side-chains 176 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 0.1980 chunk 69 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.163755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134567 restraints weight = 44938.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.140120 restraints weight = 21206.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.143604 restraints weight = 12776.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145796 restraints weight = 9017.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147215 restraints weight = 7128.609| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12306 Z= 0.190 Angle : 0.642 7.877 16734 Z= 0.338 Chirality : 0.048 0.589 1875 Planarity : 0.004 0.046 2121 Dihedral : 7.735 55.922 2152 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 3.59 % Allowed : 12.96 % Favored : 83.45 % 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: -1.58 (0.20), residues: 1452 helix: 0.13 (0.27), residues: 339 sheet: -1.40 (0.33), residues: 249 loop : -1.45 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.013 0.002 TYR A 437 PHE 0.051 0.003 PHE B 117 TRP 0.010 0.001 TRP C 76 HIS 0.005 0.001 HIS C 399 Details of bonding type rmsd covalent geometry : bond 0.00417 (12273) covalent geometry : angle 0.61669 (16641) SS BOND : bond 0.00442 ( 6) SS BOND : angle 0.26857 ( 12) hydrogen bonds : bond 0.04749 ( 422) hydrogen bonds : angle 5.32616 ( 1191) link_BETA1-4 : bond 0.00427 ( 9) link_BETA1-4 : angle 1.77715 ( 27) link_NAG-ASN : bond 0.00185 ( 18) link_NAG-ASN : angle 2.97780 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 142 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7805 (m-10) cc_final: 0.7539 (m-10) REVERT: B 111 PHE cc_start: 0.7769 (t80) cc_final: 0.7493 (t80) REVERT: B 318 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7244 (mp) outliers start: 46 outliers final: 42 residues processed: 177 average time/residue: 0.2265 time to fit residues: 57.7537 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 136 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 67 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 ASN Chi-restraints excluded: chain C residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 0.3980 chunk 80 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS C 163 GLN C 399 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.166006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.136768 restraints weight = 44699.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.142443 restraints weight = 21045.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.145943 restraints weight = 12591.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.148174 restraints weight = 8878.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.149522 restraints weight = 6969.682| |-----------------------------------------------------------------------------| r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12306 Z= 0.126 Angle : 0.602 6.388 16734 Z= 0.317 Chirality : 0.046 0.519 1875 Planarity : 0.004 0.046 2121 Dihedral : 7.564 56.697 2152 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.28 % Allowed : 13.35 % Favored : 83.37 % 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: -1.43 (0.20), residues: 1452 helix: 0.23 (0.27), residues: 339 sheet: -1.23 (0.33), residues: 249 loop : -1.37 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.015 0.001 TYR C 446 PHE 0.044 0.002 PHE B 117 TRP 0.007 0.001 TRP A 60 HIS 0.006 0.001 HIS C 399 Details of bonding type rmsd covalent geometry : bond 0.00272 (12273) covalent geometry : angle 0.57889 (16641) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.21176 ( 12) hydrogen bonds : bond 0.04365 ( 422) hydrogen bonds : angle 5.17440 ( 1191) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.75479 ( 27) link_NAG-ASN : bond 0.00261 ( 18) link_NAG-ASN : angle 2.72739 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 146 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 PHE cc_start: 0.7729 (m-10) cc_final: 0.7480 (m-10) REVERT: B 111 PHE cc_start: 0.7728 (t80) cc_final: 0.7500 (t80) REVERT: B 349 TYR cc_start: 0.8210 (OUTLIER) cc_final: 0.7719 (m-10) outliers start: 42 outliers final: 35 residues processed: 177 average time/residue: 0.2392 time to fit residues: 60.7692 Evaluate side-chains 179 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 94 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS C 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.164137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.134869 restraints weight = 44895.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140405 restraints weight = 21256.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.143881 restraints weight = 12804.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146036 restraints weight = 9074.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147292 restraints weight = 7194.196| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12306 Z= 0.181 Angle : 0.634 7.529 16734 Z= 0.334 Chirality : 0.048 0.570 1875 Planarity : 0.004 0.045 2121 Dihedral : 7.617 55.362 2152 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.36 % Allowed : 13.11 % Favored : 83.53 % 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: -1.57 (0.20), residues: 1452 helix: 0.20 (0.27), residues: 339 sheet: -1.46 (0.33), residues: 249 loop : -1.45 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 403 TYR 0.014 0.002 TYR B 98 PHE 0.048 0.002 PHE B 117 TRP 0.009 0.001 TRP C 76 HIS 0.006 0.001 HIS C 399 Details of bonding type rmsd covalent geometry : bond 0.00399 (12273) covalent geometry : angle 0.60948 (16641) SS BOND : bond 0.00409 ( 6) SS BOND : angle 0.27224 ( 12) hydrogen bonds : bond 0.04614 ( 422) hydrogen bonds : angle 5.26178 ( 1191) link_BETA1-4 : bond 0.00419 ( 9) link_BETA1-4 : angle 1.75203 ( 27) link_NAG-ASN : bond 0.00175 ( 18) link_NAG-ASN : angle 2.92313 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 143 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 ARG cc_start: 0.7417 (tmm-80) cc_final: 0.7062 (ttp-110) REVERT: A 117 PHE cc_start: 0.7793 (m-10) cc_final: 0.7587 (m-10) REVERT: B 111 PHE cc_start: 0.7707 (t80) cc_final: 0.7437 (t80) REVERT: B 349 TYR cc_start: 0.8247 (OUTLIER) cc_final: 0.7752 (m-10) outliers start: 43 outliers final: 39 residues processed: 175 average time/residue: 0.2315 time to fit residues: 58.3904 Evaluate side-chains 181 residues out of total 1281 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 28 HIS Chi-restraints excluded: chain A residue 55 CYS Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 138 HIS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 279 CYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 28 HIS Chi-restraints excluded: chain B residue 34 GLU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 55 CYS Chi-restraints excluded: chain B residue 67 CYS Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 138 HIS Chi-restraints excluded: chain B residue 185 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 279 CYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 349 TYR Chi-restraints excluded: chain C residue 8 HIS Chi-restraints excluded: chain C residue 28 HIS Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 67 CYS Chi-restraints excluded: chain C residue 106 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 138 HIS Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 279 CYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 365 LEU Chi-restraints excluded: chain C residue 408 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 128 optimal weight: 4.9990 chunk 63 optimal weight: 0.6980 chunk 126 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 HIS B 399 HIS C 399 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.165732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.136613 restraints weight = 44401.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.142240 restraints weight = 20940.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.145726 restraints weight = 12535.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147748 restraints weight = 8835.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.149320 restraints weight = 7029.774| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12306 Z= 0.135 Angle : 0.600 6.344 16734 Z= 0.316 Chirality : 0.046 0.515 1875 Planarity : 0.004 0.044 2121 Dihedral : 7.406 55.291 2152 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.12 % Allowed : 13.43 % Favored : 83.45 % 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: -1.46 (0.20), residues: 1452 helix: 0.28 (0.28), residues: 339 sheet: -1.37 (0.33), residues: 249 loop : -1.39 (0.18), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 403 TYR 0.012 0.001 TYR C 446 PHE 0.053 0.002 PHE B 117 TRP 0.006 0.001 TRP A 60 HIS 0.006 0.001 HIS C 399 Details of bonding type rmsd covalent geometry : bond 0.00293 (12273) covalent geometry : angle 0.57678 (16641) SS BOND : bond 0.00229 ( 6) SS BOND : angle 0.25324 ( 12) hydrogen bonds : bond 0.04319 ( 422) hydrogen bonds : angle 5.15177 ( 1191) link_BETA1-4 : bond 0.00441 ( 9) link_BETA1-4 : angle 1.74684 ( 27) link_NAG-ASN : bond 0.00244 ( 18) link_NAG-ASN : angle 2.71794 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3469.93 seconds wall clock time: 60 minutes 8.05 seconds (3608.05 seconds total)