Starting phenix.real_space_refine on Thu Jul 2 17:44:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oj8_12939/07_2026/7oj8_12939.cif" } resolution = 3.4 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= 0.002 sd= 0.057 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 P 6 5.49 5 S 59 5.16 5 C 5958 2.51 5 N 1484 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9148 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4475 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 20, 'TRANS': 554} Chain breaks: 3 Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 575, 4475 Classifications: {'peptide': 575} Link IDs: {'PTRANS': 20, 'TRANS': 554} Chain breaks: 3 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 87 Unusual residues: {'ATP': 1, 'CLR': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 111 Unusual residues: {'ATP': 1, 'CLR': 2, 'FY5': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.00, per 1000 atoms: 0.22 Number of scatterers: 9148 At special positions: 0 Unit cell: (78.66, 90.896, 129.352, 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 59 16.00 P 6 15.00 O 1641 8.00 N 1484 7.00 C 5958 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 230.2 milliseconds 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2128 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 61.9% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 85 through 94 removed outlier: 3.789A pdb=" N LEU A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.506A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 168 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.756A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 232 removed outlier: 3.607A pdb=" N ALA A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 4.059A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 280 removed outlier: 4.212A pdb=" N LEU A 274 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY A 275 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 327 through 337 removed outlier: 3.730A pdb=" N LYS A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 removed outlier: 3.661A pdb=" N SER A 353 " --> pdb=" O LEU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 Processing helix chain 'A' and resid 391 through 413 removed outlier: 3.844A pdb=" N SER A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 440 Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 451 through 461 Processing helix chain 'A' and resid 465 through 477 Processing helix chain 'A' and resid 479 through 497 Proline residue: A 485 - end of helix removed outlier: 4.785A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.577A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 551 removed outlier: 3.644A pdb=" N ALA A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.529A pdb=" N SER A 566 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP A 567 " --> pdb=" O TRP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 removed outlier: 3.560A pdb=" N ASN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.718A pdb=" N THR A 598 " --> pdb=" O LEU A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 617 removed outlier: 3.655A pdb=" N TYR A 613 " --> pdb=" O THR A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 650 Processing helix chain 'B' and resid 85 through 94 removed outlier: 3.790A pdb=" N LEU B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 148 removed outlier: 3.506A pdb=" N LEU B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.757A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 232 removed outlier: 3.608A pdb=" N ALA B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 253 removed outlier: 4.059A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 280 removed outlier: 4.214A pdb=" N LEU B 274 " --> pdb=" O ALA B 270 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 275 " --> pdb=" O GLN B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 299 Processing helix chain 'B' and resid 327 through 337 removed outlier: 3.730A pdb=" N LYS B 331 " --> pdb=" O PRO B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 removed outlier: 3.661A pdb=" N SER B 353 " --> pdb=" O LEU B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 391 Processing helix chain 'B' and resid 391 through 413 removed outlier: 3.844A pdb=" N SER B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLN B 398 " --> pdb=" O ALA B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 440 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 451 through 461 Processing helix chain 'B' and resid 465 through 477 Processing helix chain 'B' and resid 479 through 497 Proline residue: B 485 - end of helix removed outlier: 4.785A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 528 removed outlier: 3.577A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 551 removed outlier: 3.644A pdb=" N ALA B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE B 551 " --> pdb=" O PHE B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 571 removed outlier: 3.528A pdb=" N SER B 566 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP B 567 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 586 removed outlier: 3.560A pdb=" N ASN B 584 " --> pdb=" O ALA B 580 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 removed outlier: 3.718A pdb=" N THR B 598 " --> pdb=" O LEU B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 617 removed outlier: 3.656A pdb=" N TYR B 613 " --> pdb=" O THR B 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 650 Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 40 removed outlier: 3.997A pdb=" N HIS A 40 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 105 " --> pdb=" O HIS A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 78 removed outlier: 3.523A pdb=" N ILE A 238 " --> pdb=" O GLY A 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 240 " --> pdb=" O ASN A 76 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY A 122 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 259 removed outlier: 6.587A pdb=" N LEU A 256 " --> pdb=" O HIS A 267 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N HIS A 267 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU A 258 " --> pdb=" O MET A 265 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 40 removed outlier: 3.997A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 78 removed outlier: 3.522A pdb=" N ILE B 238 " --> pdb=" O GLY B 74 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE B 240 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLY B 122 " --> pdb=" O PHE B 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 255 through 259 removed outlier: 6.587A pdb=" N LEU B 256 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N HIS B 267 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N LEU B 258 " --> pdb=" O MET B 265 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1440 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1413 1.31 - 1.44: 2494 1.44 - 1.57: 5327 1.57 - 1.70: 27 1.70 - 1.83: 94 Bond restraints: 9355 Sorted by residual: bond pdb=" C5 ATP B1501 " pdb=" N7 ATP B1501 " ideal model delta sigma weight residual 1.387 1.521 -0.134 1.00e-02 1.00e+04 1.79e+02 bond pdb=" C5 ATP A1501 " pdb=" N7 ATP A1501 " ideal model delta sigma weight residual 1.387 1.520 -0.133 1.00e-02 1.00e+04 1.76e+02 bond pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " ideal model delta sigma weight residual 1.374 1.265 0.109 1.00e-02 1.00e+04 1.18e+02 bond pdb=" C4 ATP B1501 " pdb=" N9 ATP B1501 " ideal model delta sigma weight residual 1.374 1.266 0.108 1.00e-02 1.00e+04 1.16e+02 bond pdb=" C6 ATP A1501 " pdb=" N6 ATP A1501 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.10e+02 ... (remaining 9350 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 12598 4.66 - 9.32: 78 9.32 - 13.98: 18 13.98 - 18.63: 7 18.63 - 23.29: 2 Bond angle restraints: 12703 Sorted by residual: angle pdb=" PB ATP B1501 " pdb=" O3B ATP B1501 " pdb=" PG ATP B1501 " ideal model delta sigma weight residual 139.87 116.58 23.29 1.00e+00 1.00e+00 5.43e+02 angle pdb=" PB ATP A1501 " pdb=" O3B ATP A1501 " pdb=" PG ATP A1501 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.42e+02 angle pdb=" PA ATP B1501 " pdb=" O3A ATP B1501 " pdb=" PB ATP B1501 " ideal model delta sigma weight residual 136.83 118.24 18.59 1.00e+00 1.00e+00 3.45e+02 angle pdb=" PA ATP A1501 " pdb=" O3A ATP A1501 " pdb=" PB ATP A1501 " ideal model delta sigma weight residual 136.83 118.28 18.55 1.00e+00 1.00e+00 3.44e+02 angle pdb=" C4 ATP A1501 " pdb=" N9 ATP A1501 " pdb=" C8 ATP A1501 " ideal model delta sigma weight residual 105.72 121.87 -16.15 1.00e+00 1.00e+00 2.61e+02 ... (remaining 12698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 5063 17.71 - 35.42: 339 35.42 - 53.13: 55 53.13 - 70.84: 10 70.84 - 88.55: 8 Dihedral angle restraints: 5475 sinusoidal: 2161 harmonic: 3314 Sorted by residual: dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual -86.00 -139.87 53.87 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual -86.00 -139.85 53.85 1 1.00e+01 1.00e-02 3.94e+01 dihedral pdb=" CA LEU A 64 " pdb=" C LEU A 64 " pdb=" N SER A 65 " pdb=" CA SER A 65 " ideal model delta harmonic sigma weight residual 180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 5472 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1253 0.073 - 0.147: 187 0.147 - 0.220: 24 0.220 - 0.294: 10 0.294 - 0.367: 4 Chirality restraints: 1478 Sorted by residual: chirality pdb=" C17 CLR B1503 " pdb=" C13 CLR B1503 " pdb=" C16 CLR B1503 " pdb=" C20 CLR B1503 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C17 CLR A1503 " pdb=" C13 CLR A1503 " pdb=" C16 CLR A1503 " pdb=" C20 CLR A1503 " both_signs ideal model delta sigma weight residual False 2.55 2.90 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" C17 CLR B1504 " pdb=" C13 CLR B1504 " pdb=" C16 CLR B1504 " pdb=" C20 CLR B1504 " both_signs ideal model delta sigma weight residual False 2.55 2.89 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 1475 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 65 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C SER B 65 " 0.033 2.00e-02 2.50e+03 pdb=" O SER B 65 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN B 66 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 65 " 0.010 2.00e-02 2.50e+03 1.88e-02 3.55e+00 pdb=" C SER A 65 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 65 " 0.012 2.00e-02 2.50e+03 pdb=" N ASN A 66 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 98 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.39e+00 pdb=" N PRO B 99 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 99 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 99 " -0.026 5.00e-02 4.00e+02 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 153 2.67 - 3.23: 9428 3.23 - 3.79: 13773 3.79 - 4.34: 18285 4.34 - 4.90: 30462 Nonbonded interactions: 72101 Sorted by model distance: nonbonded pdb=" OH TYR B 494 " pdb=" O LYS B 500 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR A 494 " pdb=" O LYS A 500 " model vdw 2.114 3.040 nonbonded pdb=" OD1 ASP A 91 " pdb=" OH TYR A 123 " model vdw 2.249 3.040 nonbonded pdb=" OD1 ASP B 91 " pdb=" OH TYR B 123 " model vdw 2.249 3.040 nonbonded pdb=" OE1 GLN A 393 " pdb=" OG SER B 535 " model vdw 2.395 3.040 ... (remaining 72096 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' and (resid 34 through 1501 or resid 1503)) selection = (chain 'B' and (resid 34 through 1501 or resid 1503)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.360 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.010 0.190 9358 Z= 0.594 Angle : 1.145 23.292 12709 Z= 0.731 Chirality : 0.059 0.367 1478 Planarity : 0.004 0.046 1544 Dihedral : 12.411 88.547 3338 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.29 % Favored : 94.18 % Rotamer: Outliers : 0.41 % Allowed : 4.38 % Favored : 95.21 % 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: -1.11 (0.24), residues: 1134 helix: 0.23 (0.19), residues: 672 sheet: -1.55 (0.49), residues: 98 loop : -2.24 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 184 TYR 0.016 0.002 TYR B 342 PHE 0.017 0.002 PHE B 507 TRP 0.018 0.002 TRP B 624 HIS 0.004 0.001 HIS A 283 Details of bonding type rmsd/Z covalent geometry : bond 0.01030 / 0.59 ( 9355) covalent geometry : angle 1.14493 / 0.73 (12703) SS BOND : bond 0.00830 / 0.47 ( 3) SS BOND : angle 1.59043 / 0.94 ( 6) hydrogen bonds : bond 0.15723 / 11.10 ( 494) hydrogen bonds : angle 5.64620 / 4.02 ( 1440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 261 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 LYS cc_start: 0.8462 (mttt) cc_final: 0.8236 (mttp) REVERT: A 263 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7325 (mmt90) REVERT: A 265 MET cc_start: 0.7120 (mmt) cc_final: 0.6722 (mmp) REVERT: A 521 SER cc_start: 0.9032 (m) cc_final: 0.8795 (p) REVERT: A 523 MET cc_start: 0.8433 (ttp) cc_final: 0.7930 (ttt) REVERT: B 483 MET cc_start: 0.8109 (tmm) cc_final: 0.7846 (ttm) REVERT: B 514 MET cc_start: 0.8531 (mtt) cc_final: 0.8330 (mtm) outliers start: 4 outliers final: 0 residues processed: 265 average time/residue: 0.0923 time to fit residues: 33.4983 Evaluate side-chains 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 243 HIS A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN B 222 ASN B 299 ASN B 338 ASN B 376 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.125671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108196 restraints weight = 16912.212| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.95 r_work: 0.3422 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9358 Z= 0.145 Angle : 0.652 15.280 12709 Z= 0.332 Chirality : 0.044 0.260 1478 Planarity : 0.004 0.051 1544 Dihedral : 5.878 52.927 1274 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.06 % Favored : 95.77 % Rotamer: Outliers : 3.16 % Allowed : 11.41 % Favored : 85.44 % 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: 0.33 (0.26), residues: 1134 helix: 1.20 (0.20), residues: 680 sheet: -0.02 (0.61), residues: 64 loop : -1.50 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 163 TYR 0.021 0.002 TYR A 413 PHE 0.020 0.001 PHE B 39 TRP 0.015 0.002 TRP B 624 HIS 0.011 0.001 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 ( 9355) covalent geometry : angle 0.65174 / 0.33 (12703) SS BOND : bond 0.00296 / 0.17 ( 3) SS BOND : angle 1.09072 / 0.58 ( 6) hydrogen bonds : bond 0.05307 / 3.59 ( 494) hydrogen bonds : angle 4.03048 / 2.90 ( 1440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7848 (tttp) cc_final: 0.7543 (ttmm) REVERT: A 97 LYS cc_start: 0.8585 (mttt) cc_final: 0.8300 (mttp) REVERT: A 222 ASN cc_start: 0.8059 (OUTLIER) cc_final: 0.7805 (m-40) REVERT: A 242 ILE cc_start: 0.8512 (tp) cc_final: 0.8212 (pt) REVERT: A 243 HIS cc_start: 0.7770 (t70) cc_final: 0.7488 (t-90) REVERT: A 263 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7737 (mmt90) REVERT: A 265 MET cc_start: 0.7532 (mmt) cc_final: 0.7321 (mmp) REVERT: A 393 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7958 (pt0) REVERT: A 496 MET cc_start: 0.8103 (ttm) cc_final: 0.7903 (ttm) REVERT: A 515 MET cc_start: 0.8942 (mmm) cc_final: 0.8603 (mmm) REVERT: A 521 SER cc_start: 0.9035 (m) cc_final: 0.8772 (p) REVERT: B 71 MET cc_start: 0.7226 (mmt) cc_final: 0.7017 (mmt) REVERT: B 187 SER cc_start: 0.8033 (m) cc_final: 0.7724 (p) REVERT: B 190 GLU cc_start: 0.7298 (mp0) cc_final: 0.6898 (mp0) REVERT: B 261 SER cc_start: 0.8744 (m) cc_final: 0.8515 (t) REVERT: B 299 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7145 (m110) REVERT: B 483 MET cc_start: 0.8449 (tmm) cc_final: 0.8177 (ttm) outliers start: 31 outliers final: 14 residues processed: 193 average time/residue: 0.0776 time to fit residues: 21.2389 Evaluate side-chains 153 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 299 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 622 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 83 optimal weight: 0.0270 chunk 62 optimal weight: 0.2980 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 GLN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 GLN B 457 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.126154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.109129 restraints weight = 16836.754| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.89 r_work: 0.3411 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9358 Z= 0.138 Angle : 0.598 13.087 12709 Z= 0.306 Chirality : 0.042 0.190 1478 Planarity : 0.004 0.041 1544 Dihedral : 5.573 52.241 1274 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.75 % Allowed : 14.26 % Favored : 82.99 % 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: 0.68 (0.26), residues: 1134 helix: 1.46 (0.20), residues: 680 sheet: 0.12 (0.57), residues: 62 loop : -1.31 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 96 TYR 0.017 0.001 TYR A 413 PHE 0.009 0.001 PHE A 293 TRP 0.014 0.002 TRP B 379 HIS 0.006 0.001 HIS B 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 9355) covalent geometry : angle 0.59844 / 0.31 (12703) SS BOND : bond 0.00226 / 0.14 ( 3) SS BOND : angle 0.65203 / 0.33 ( 6) hydrogen bonds : bond 0.04806 / 3.25 ( 494) hydrogen bonds : angle 3.85024 / 2.77 ( 1440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7842 (tttp) cc_final: 0.7559 (ttmm) REVERT: A 76 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: A 97 LYS cc_start: 0.8554 (mttt) cc_final: 0.8247 (mttp) REVERT: A 207 LEU cc_start: 0.8762 (mt) cc_final: 0.8467 (mt) REVERT: A 222 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7769 (m-40) REVERT: A 242 ILE cc_start: 0.8542 (tp) cc_final: 0.8183 (pt) REVERT: A 243 HIS cc_start: 0.7869 (t70) cc_final: 0.7510 (t-90) REVERT: A 263 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7750 (mmt90) REVERT: A 496 MET cc_start: 0.8078 (ttm) cc_final: 0.7781 (ttp) REVERT: A 515 MET cc_start: 0.8915 (mmm) cc_final: 0.8593 (mmm) REVERT: B 187 SER cc_start: 0.8036 (m) cc_final: 0.7729 (p) REVERT: B 190 GLU cc_start: 0.7324 (mp0) cc_final: 0.6970 (mp0) REVERT: B 261 SER cc_start: 0.8722 (m) cc_final: 0.8502 (t) REVERT: B 293 PHE cc_start: 0.7556 (t80) cc_final: 0.6599 (t80) REVERT: B 477 ASP cc_start: 0.8291 (t70) cc_final: 0.7893 (m-30) outliers start: 27 outliers final: 20 residues processed: 172 average time/residue: 0.0880 time to fit residues: 21.9758 Evaluate side-chains 161 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 54 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 76 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 350 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.117985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100536 restraints weight = 17631.059| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.08 r_work: 0.3272 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9358 Z= 0.238 Angle : 0.677 16.958 12709 Z= 0.351 Chirality : 0.045 0.147 1478 Planarity : 0.004 0.053 1544 Dihedral : 5.678 52.668 1274 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.18 % Allowed : 14.26 % Favored : 81.57 % 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: 0.32 (0.25), residues: 1134 helix: 1.19 (0.20), residues: 684 sheet: -0.21 (0.55), residues: 62 loop : -1.48 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 96 TYR 0.017 0.002 TYR B 413 PHE 0.019 0.002 PHE B 495 TRP 0.013 0.002 TRP B 624 HIS 0.006 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.24 ( 9355) covalent geometry : angle 0.67683 / 0.35 (12703) SS BOND : bond 0.00361 / 0.21 ( 3) SS BOND : angle 0.70258 / 0.34 ( 6) hydrogen bonds : bond 0.05582 / 3.77 ( 494) hydrogen bonds : angle 4.10974 / 2.96 ( 1440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 146 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7720 (tttp) cc_final: 0.7466 (ttmm) REVERT: A 97 LYS cc_start: 0.8612 (mttt) cc_final: 0.8225 (mttp) REVERT: A 222 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7306 (m-40) REVERT: A 243 HIS cc_start: 0.8007 (t70) cc_final: 0.7789 (t-90) REVERT: A 263 ARG cc_start: 0.8044 (mmm-85) cc_final: 0.7675 (mmt90) REVERT: A 296 ASP cc_start: 0.7336 (m-30) cc_final: 0.7072 (m-30) REVERT: A 343 LYS cc_start: 0.7739 (mptt) cc_final: 0.7467 (mppt) REVERT: A 496 MET cc_start: 0.8377 (ttm) cc_final: 0.8022 (ttm) REVERT: B 187 SER cc_start: 0.8232 (m) cc_final: 0.7861 (t) REVERT: B 190 GLU cc_start: 0.7399 (mp0) cc_final: 0.7149 (mp0) REVERT: B 214 THR cc_start: 0.8077 (m) cc_final: 0.7768 (t) REVERT: B 261 SER cc_start: 0.8677 (m) cc_final: 0.8473 (t) REVERT: B 385 PHE cc_start: 0.6885 (OUTLIER) cc_final: 0.6333 (t80) REVERT: B 511 PHE cc_start: 0.7912 (t80) cc_final: 0.6763 (m-10) REVERT: B 515 MET cc_start: 0.8623 (mmm) cc_final: 0.8052 (mpp) outliers start: 41 outliers final: 31 residues processed: 171 average time/residue: 0.0854 time to fit residues: 21.3921 Evaluate side-chains 156 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 476 SER Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 489 PHE Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 244 GLN ** B 590 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.117071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099589 restraints weight = 17428.589| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 3.04 r_work: 0.3247 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9358 Z= 0.226 Angle : 0.670 12.674 12709 Z= 0.349 Chirality : 0.044 0.152 1478 Planarity : 0.004 0.040 1544 Dihedral : 5.931 59.501 1274 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.07 % Allowed : 16.80 % Favored : 79.12 % 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: 0.48 (0.26), residues: 1134 helix: 1.31 (0.20), residues: 666 sheet: -0.30 (0.50), residues: 82 loop : -1.28 (0.35), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 163 TYR 0.018 0.002 TYR B 413 PHE 0.018 0.002 PHE B 495 TRP 0.013 0.002 TRP B 379 HIS 0.005 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 ( 9355) covalent geometry : angle 0.66952 / 0.35 (12703) SS BOND : bond 0.00303 / 0.18 ( 3) SS BOND : angle 0.66479 / 0.32 ( 6) hydrogen bonds : bond 0.05505 / 3.73 ( 494) hydrogen bonds : angle 4.12238 / 2.97 ( 1440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7776 (tttp) cc_final: 0.7533 (ttmm) REVERT: A 97 LYS cc_start: 0.8522 (mttt) cc_final: 0.8304 (mttp) REVERT: A 222 ASN cc_start: 0.7833 (OUTLIER) cc_final: 0.7403 (m-40) REVERT: A 243 HIS cc_start: 0.7941 (t70) cc_final: 0.7732 (t-90) REVERT: A 263 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7102 (mpp-170) REVERT: A 296 ASP cc_start: 0.7390 (m-30) cc_final: 0.7018 (m-30) REVERT: A 438 CYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8940 (t) REVERT: A 496 MET cc_start: 0.8354 (ttm) cc_final: 0.8098 (ttm) REVERT: A 515 MET cc_start: 0.9036 (mmm) cc_final: 0.8707 (mmm) REVERT: B 172 LYS cc_start: 0.8300 (mtmm) cc_final: 0.7947 (mmtm) REVERT: B 187 SER cc_start: 0.8363 (m) cc_final: 0.7988 (t) REVERT: B 190 GLU cc_start: 0.7486 (mp0) cc_final: 0.7249 (mp0) REVERT: B 385 PHE cc_start: 0.7158 (OUTLIER) cc_final: 0.6556 (t80) REVERT: B 477 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7764 (m-30) outliers start: 40 outliers final: 26 residues processed: 157 average time/residue: 0.0835 time to fit residues: 19.1394 Evaluate side-chains 150 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 120 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 438 CYS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 477 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 104 optimal weight: 0.0980 chunk 13 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 398 GLN B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.117689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.100783 restraints weight = 17550.633| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.12 r_work: 0.3299 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9358 Z= 0.120 Angle : 0.583 14.866 12709 Z= 0.294 Chirality : 0.040 0.155 1478 Planarity : 0.004 0.036 1544 Dihedral : 5.644 58.714 1274 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.77 % Allowed : 16.60 % Favored : 79.63 % 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: 1.05 (0.26), residues: 1134 helix: 1.74 (0.20), residues: 660 sheet: 0.29 (0.57), residues: 62 loop : -0.96 (0.34), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.012 0.001 TYR A 459 PHE 0.018 0.001 PHE A 277 TRP 0.016 0.001 TRP B 379 HIS 0.002 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 9355) covalent geometry : angle 0.58264 / 0.29 (12703) SS BOND : bond 0.00142 / 0.09 ( 3) SS BOND : angle 0.48454 / 0.24 ( 6) hydrogen bonds : bond 0.04476 / 3.04 ( 494) hydrogen bonds : angle 3.76385 / 2.71 ( 1440) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7879 (tttp) cc_final: 0.7641 (ttmm) REVERT: A 207 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8272 (mt) REVERT: A 222 ASN cc_start: 0.7858 (OUTLIER) cc_final: 0.7415 (m110) REVERT: A 243 HIS cc_start: 0.7975 (t70) cc_final: 0.7767 (t-90) REVERT: A 263 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7799 (mmt90) REVERT: A 343 LYS cc_start: 0.7832 (mptt) cc_final: 0.7460 (mppt) REVERT: A 496 MET cc_start: 0.8014 (ttm) cc_final: 0.7511 (ttp) REVERT: B 172 LYS cc_start: 0.8304 (mtmm) cc_final: 0.7954 (mmtm) REVERT: B 187 SER cc_start: 0.8321 (m) cc_final: 0.7956 (t) REVERT: B 328 LEU cc_start: 0.7865 (tp) cc_final: 0.7526 (mp) REVERT: B 371 THR cc_start: 0.6579 (OUTLIER) cc_final: 0.6331 (p) REVERT: B 477 ASP cc_start: 0.8094 (OUTLIER) cc_final: 0.7868 (m-30) REVERT: B 511 PHE cc_start: 0.7877 (t80) cc_final: 0.6815 (m-10) REVERT: B 515 MET cc_start: 0.8483 (mmm) cc_final: 0.7942 (mpp) outliers start: 37 outliers final: 21 residues processed: 167 average time/residue: 0.0820 time to fit residues: 20.3229 Evaluate side-chains 147 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 198 MET Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 477 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 20 optimal weight: 0.0060 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 ASN B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.100948 restraints weight = 17587.419| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 2.96 r_work: 0.3286 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9358 Z= 0.190 Angle : 0.622 13.106 12709 Z= 0.321 Chirality : 0.042 0.147 1478 Planarity : 0.004 0.039 1544 Dihedral : 5.699 59.227 1274 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.18 % Allowed : 17.31 % Favored : 78.51 % 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: 0.83 (0.26), residues: 1134 helix: 1.51 (0.20), residues: 670 sheet: 0.33 (0.52), residues: 82 loop : -1.14 (0.36), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.014 0.002 TYR B 413 PHE 0.018 0.001 PHE A 277 TRP 0.012 0.001 TRP B 379 HIS 0.004 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.19 ( 9355) covalent geometry : angle 0.62240 / 0.32 (12703) SS BOND : bond 0.00232 / 0.14 ( 3) SS BOND : angle 0.51716 / 0.25 ( 6) hydrogen bonds : bond 0.04936 / 3.36 ( 494) hydrogen bonds : angle 3.93073 / 2.83 ( 1440) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7958 (tttp) cc_final: 0.7735 (ttmm) REVERT: A 207 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 222 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7637 (m-40) REVERT: A 243 HIS cc_start: 0.7903 (t70) cc_final: 0.7684 (t-90) REVERT: A 263 ARG cc_start: 0.8228 (mmm-85) cc_final: 0.7908 (mmt90) REVERT: A 343 LYS cc_start: 0.7836 (mptt) cc_final: 0.7567 (mppt) REVERT: A 496 MET cc_start: 0.8124 (ttm) cc_final: 0.7734 (ttp) REVERT: A 515 MET cc_start: 0.8969 (mmm) cc_final: 0.8640 (mmm) REVERT: B 172 LYS cc_start: 0.8319 (mtmm) cc_final: 0.7978 (mmtm) REVERT: B 328 LEU cc_start: 0.7741 (tp) cc_final: 0.7440 (mp) REVERT: B 385 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6590 (t80) outliers start: 41 outliers final: 30 residues processed: 154 average time/residue: 0.0863 time to fit residues: 19.4131 Evaluate side-chains 154 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 283 HIS A 350 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.118540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.101408 restraints weight = 17426.881| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.98 r_work: 0.3276 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9358 Z= 0.173 Angle : 0.616 12.400 12709 Z= 0.314 Chirality : 0.042 0.147 1478 Planarity : 0.004 0.040 1544 Dihedral : 5.706 58.997 1274 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 3.77 % Allowed : 18.53 % Favored : 77.70 % 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: 0.88 (0.26), residues: 1134 helix: 1.57 (0.20), residues: 670 sheet: 0.41 (0.53), residues: 82 loop : -1.16 (0.36), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 96 TYR 0.014 0.002 TYR B 413 PHE 0.017 0.001 PHE A 277 TRP 0.013 0.001 TRP B 379 HIS 0.018 0.001 HIS A 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 9355) covalent geometry : angle 0.61566 / 0.31 (12703) SS BOND : bond 0.00215 / 0.13 ( 3) SS BOND : angle 0.52369 / 0.26 ( 6) hydrogen bonds : bond 0.04859 / 3.32 ( 494) hydrogen bonds : angle 3.88165 / 2.79 ( 1440) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 129 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7917 (tttp) cc_final: 0.7704 (ttmm) REVERT: A 243 HIS cc_start: 0.7935 (t70) cc_final: 0.7723 (t-90) REVERT: A 263 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7833 (mmt90) REVERT: A 343 LYS cc_start: 0.7832 (mptt) cc_final: 0.7545 (mppt) REVERT: A 515 MET cc_start: 0.9000 (mmm) cc_final: 0.8683 (mmm) REVERT: A 541 MET cc_start: 0.8434 (mmm) cc_final: 0.8126 (mtp) REVERT: B 172 LYS cc_start: 0.8327 (mtmm) cc_final: 0.8007 (mmtm) REVERT: B 328 LEU cc_start: 0.7809 (tp) cc_final: 0.7481 (mp) REVERT: B 385 PHE cc_start: 0.7360 (OUTLIER) cc_final: 0.6724 (t80) REVERT: B 418 ASN cc_start: 0.8011 (p0) cc_final: 0.7768 (p0) REVERT: B 548 MET cc_start: 0.9218 (ttm) cc_final: 0.8973 (ttp) outliers start: 37 outliers final: 29 residues processed: 158 average time/residue: 0.0833 time to fit residues: 19.1843 Evaluate side-chains 147 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 438 CYS Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 overall best weight: 0.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 283 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 590 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.118396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.101513 restraints weight = 17665.575| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 3.11 r_work: 0.3301 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9358 Z= 0.119 Angle : 0.583 12.579 12709 Z= 0.292 Chirality : 0.039 0.147 1478 Planarity : 0.004 0.036 1544 Dihedral : 5.423 56.813 1274 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.16 % Allowed : 19.76 % Favored : 77.09 % 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 (0.26), residues: 1134 helix: 1.86 (0.20), residues: 670 sheet: 0.89 (0.60), residues: 62 loop : -0.97 (0.34), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.011 0.001 TYR A 282 PHE 0.013 0.001 PHE A 277 TRP 0.016 0.002 TRP B 379 HIS 0.003 0.001 HIS B 267 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 9355) covalent geometry : angle 0.58295 / 0.29 (12703) SS BOND : bond 0.00108 / 0.06 ( 3) SS BOND : angle 0.48118 / 0.25 ( 6) hydrogen bonds : bond 0.04140 / 2.83 ( 494) hydrogen bonds : angle 3.68000 / 2.65 ( 1440) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7871 (tttp) cc_final: 0.7640 (ttmm) REVERT: A 207 LEU cc_start: 0.8532 (mt) cc_final: 0.8325 (mt) REVERT: A 243 HIS cc_start: 0.7928 (t70) cc_final: 0.7704 (t-90) REVERT: A 263 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7764 (mmt90) REVERT: A 343 LYS cc_start: 0.7860 (mptt) cc_final: 0.7574 (mppt) REVERT: A 515 MET cc_start: 0.9007 (mmm) cc_final: 0.8697 (mmm) REVERT: A 541 MET cc_start: 0.8402 (mmm) cc_final: 0.7995 (mtp) REVERT: B 172 LYS cc_start: 0.8343 (mtmm) cc_final: 0.8029 (mmtm) REVERT: B 243 HIS cc_start: 0.7199 (t-90) cc_final: 0.6942 (m170) REVERT: B 328 LEU cc_start: 0.7735 (tp) cc_final: 0.7386 (mp) REVERT: B 371 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6485 (p) REVERT: B 385 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6727 (t80) REVERT: B 418 ASN cc_start: 0.7952 (p0) cc_final: 0.7692 (p0) REVERT: B 548 MET cc_start: 0.9218 (ttm) cc_final: 0.8945 (ttp) outliers start: 31 outliers final: 24 residues processed: 155 average time/residue: 0.0783 time to fit residues: 17.7866 Evaluate side-chains 144 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 514 MET Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 24 optimal weight: 2.9990 chunk 78 optimal weight: 0.0570 chunk 69 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 70 optimal weight: 0.0670 chunk 49 optimal weight: 0.7980 overall best weight: 0.9838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 222 ASN A 283 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.117749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.100845 restraints weight = 17560.591| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 3.13 r_work: 0.3296 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9358 Z= 0.130 Angle : 0.606 11.557 12709 Z= 0.304 Chirality : 0.040 0.197 1478 Planarity : 0.004 0.037 1544 Dihedral : 5.383 56.538 1274 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.95 % Allowed : 19.86 % Favored : 77.19 % 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: 1.13 (0.26), residues: 1134 helix: 1.76 (0.20), residues: 682 sheet: 1.02 (0.60), residues: 62 loop : -1.17 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.011 0.001 TYR A 413 PHE 0.023 0.001 PHE B 39 TRP 0.014 0.001 TRP B 379 HIS 0.007 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 ( 9355) covalent geometry : angle 0.60620 / 0.30 (12703) SS BOND : bond 0.00137 / 0.08 ( 3) SS BOND : angle 0.48638 / 0.25 ( 6) hydrogen bonds : bond 0.04202 / 2.89 ( 494) hydrogen bonds : angle 3.69854 / 2.66 ( 1440) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2268 Ramachandran restraints generated. 1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 LYS cc_start: 0.7822 (tttp) cc_final: 0.7587 (ttmm) REVERT: A 207 LEU cc_start: 0.8504 (mt) cc_final: 0.8289 (mt) REVERT: A 243 HIS cc_start: 0.7942 (t70) cc_final: 0.7712 (t-90) REVERT: A 263 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7774 (mmt90) REVERT: A 515 MET cc_start: 0.8992 (mmm) cc_final: 0.8671 (mmm) REVERT: A 541 MET cc_start: 0.8393 (mmm) cc_final: 0.7867 (mmt) REVERT: B 172 LYS cc_start: 0.8338 (mtmm) cc_final: 0.8029 (mmtm) REVERT: B 328 LEU cc_start: 0.7744 (tp) cc_final: 0.7421 (mp) REVERT: B 371 THR cc_start: 0.6790 (OUTLIER) cc_final: 0.6539 (p) REVERT: B 385 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6759 (t80) REVERT: B 418 ASN cc_start: 0.7979 (p0) cc_final: 0.7710 (p0) REVERT: B 548 MET cc_start: 0.9217 (ttm) cc_final: 0.8917 (ttt) outliers start: 29 outliers final: 24 residues processed: 147 average time/residue: 0.0876 time to fit residues: 18.7982 Evaluate side-chains 145 residues out of total 982 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 284 CYS Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 489 PHE Chi-restraints excluded: chain A residue 533 VAL Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 569 GLN Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 605 TYR Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 352 LEU Chi-restraints excluded: chain B residue 367 ILE Chi-restraints excluded: chain B residue 371 THR Chi-restraints excluded: chain B residue 385 PHE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 443 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 458 GLU Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 556 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 14 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 59 optimal weight: 0.0370 chunk 56 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS ** A 457 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.117524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.100707 restraints weight = 17434.490| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.10 r_work: 0.3294 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 9358 Z= 0.183 Angle : 0.893 59.191 12709 Z= 0.515 Chirality : 0.042 0.437 1478 Planarity : 0.004 0.053 1544 Dihedral : 5.405 56.612 1274 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.95 % Allowed : 19.45 % Favored : 77.60 % Cbeta Deviations : 0.09 % 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: 1.08 (0.26), residues: 1134 helix: 1.72 (0.20), residues: 682 sheet: 1.04 (0.60), residues: 62 loop : -1.16 (0.34), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 96 TYR 0.011 0.001 TYR A 413 PHE 0.019 0.001 PHE A 277 TRP 0.013 0.001 TRP B 379 HIS 0.003 0.001 HIS B 243 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 ( 9355) covalent geometry : angle 0.89282 / 0.52 (12703) SS BOND : bond 0.00150 / 0.09 ( 3) SS BOND : angle 0.48013 / 0.25 ( 6) hydrogen bonds : bond 0.04235 / 2.91 ( 494) hydrogen bonds : angle 3.71619 / 2.66 ( 1440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.69 seconds wall clock time: 31 minutes 40.67 seconds (1900.67 seconds total)