Starting phenix.real_space_refine on Sat Jul 4 02:19:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fhn_31587/07_2026/7fhn_31587.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8728 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 6 9.91 5 S 44 5.16 5 C 7102 2.51 5 N 1630 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 10648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.17, per 1000 atoms: 0.20 Number of scatterers: 10648 At special positions: 0 Unit cell: (108.498, 119.652, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 6 19.99 S 44 16.00 O 1866 8.00 N 1630 7.00 C 7102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 101 " distance=2.03 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: 0.71 Conformation dependent library (CDL) restraints added in 301.1 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 80.0% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.601A pdb=" N ASP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.536A pdb=" N ILE A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 56 through 69 removed outlier: 4.180A pdb=" N SER A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.582A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.652A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.759A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.874A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.681A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 335 removed outlier: 3.660A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 297 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ASN A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.639A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 4.065A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 390 through 396 removed outlier: 4.057A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.666A pdb=" N TYR A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.517A pdb=" N ARG A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.618A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.582A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 493 Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.900A pdb=" N THR A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 541 Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 548 through 587 removed outlier: 3.622A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix Processing helix chain 'A' and resid 601 through 606 removed outlier: 3.712A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 627 removed outlier: 3.565A pdb=" N GLY A 619 " --> pdb=" O ASP A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.857A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 659 removed outlier: 3.937A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.972A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.624A pdb=" N ASP C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.695A pdb=" N LEU C 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 69 removed outlier: 4.040A pdb=" N SER C 60 " --> pdb=" O SER C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.506A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 144 through 149 removed outlier: 3.582A pdb=" N TRP C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.681A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.658A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.606A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 335 removed outlier: 4.381A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 Processing helix chain 'C' and resid 365 through 376 removed outlier: 4.182A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 390 through 396 removed outlier: 4.140A pdb=" N ALA C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.606A pdb=" N TYR C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 removed outlier: 3.526A pdb=" N ARG C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.710A pdb=" N TYR C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.706A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 4.637A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 516 removed outlier: 3.596A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 543 removed outlier: 3.576A pdb=" N ILE C 530 " --> pdb=" O ASN C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 547 Processing helix chain 'C' and resid 548 through 565 Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.711A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 628 removed outlier: 3.594A pdb=" N GLY C 619 " --> pdb=" O ASP C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.918A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 660 removed outlier: 3.919A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 removed outlier: 3.572A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU C 683 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 Processing sheet with id=AA2, first strand: chain 'C' and resid 341 through 342 707 hydrogen bonds defined for protein. 2091 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: 1.33 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3189 1.34 - 1.46: 2356 1.46 - 1.57: 5317 1.57 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10934 Sorted by residual: bond pdb=" CA ILE C 562 " pdb=" CB ILE C 562 " ideal model delta sigma weight residual 1.539 1.548 -0.009 5.40e-03 3.43e+04 2.54e+00 bond pdb=" CG LEU A 312 " pdb=" CD2 LEU A 312 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.19e+00 bond pdb=" C LEU A 109 " pdb=" N GLY A 110 " ideal model delta sigma weight residual 1.319 1.333 -0.014 1.34e-02 5.57e+03 1.10e+00 bond pdb=" CG LEU C 109 " pdb=" CD1 LEU C 109 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.03e+00 bond pdb=" CG LEU A 115 " pdb=" CD1 LEU A 115 " ideal model delta sigma weight residual 1.521 1.488 0.033 3.30e-02 9.18e+02 9.81e-01 ... (remaining 10929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 14456 1.59 - 3.18: 323 3.18 - 4.77: 64 4.77 - 6.36: 24 6.36 - 7.95: 9 Bond angle restraints: 14876 Sorted by residual: angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 110.66 118.61 -7.95 2.18e+00 2.10e-01 1.33e+01 angle pdb=" C PHE C 351 " pdb=" N GLU C 352 " pdb=" CA GLU C 352 " ideal model delta sigma weight residual 121.18 114.41 6.77 1.98e+00 2.55e-01 1.17e+01 angle pdb=" C VAL A 628 " pdb=" CA VAL A 628 " pdb=" CB VAL A 628 " ideal model delta sigma weight residual 110.93 107.24 3.69 1.10e+00 8.26e-01 1.13e+01 angle pdb=" N GLU C 352 " pdb=" CA GLU C 352 " pdb=" CB GLU C 352 " ideal model delta sigma weight residual 110.39 116.10 -5.71 1.75e+00 3.27e-01 1.06e+01 angle pdb=" C ILE C 542 " pdb=" CA ILE C 542 " pdb=" CB ILE C 542 " ideal model delta sigma weight residual 112.04 107.83 4.21 1.31e+00 5.83e-01 1.03e+01 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5660 17.18 - 34.35: 536 34.35 - 51.53: 90 51.53 - 68.71: 16 68.71 - 85.89: 10 Dihedral angle restraints: 6312 sinusoidal: 2484 harmonic: 3828 Sorted by residual: dihedral pdb=" CB CYS A 93 " pdb=" SG CYS A 93 " pdb=" SG CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sinusoidal sigma weight residual 93.00 137.62 -44.62 1 1.00e+01 1.00e-02 2.77e+01 dihedral pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " pdb=" SG CYS C 101 " pdb=" CB CYS C 101 " ideal model delta sinusoidal sigma weight residual 93.00 137.40 -44.40 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1067 0.034 - 0.068: 493 0.068 - 0.102: 91 0.102 - 0.136: 28 0.136 - 0.169: 7 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA LYS C 462 " pdb=" N LYS C 462 " pdb=" C LYS C 462 " pdb=" CB LYS C 462 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA LYS C 98 " pdb=" N LYS C 98 " pdb=" C LYS C 98 " pdb=" CB LYS C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA LYS A 462 " pdb=" N LYS A 462 " pdb=" C LYS A 462 " pdb=" CB LYS A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 ... (remaining 1683 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 293 " 0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C VAL C 293 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL C 293 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR C 294 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 562 " 0.029 5.00e-02 4.00e+02 4.40e-02 3.09e+00 pdb=" N PRO A 563 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 501 " -0.014 2.00e-02 2.50e+03 1.29e-02 2.93e+00 pdb=" CG PHE C 501 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 501 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 PHE C 501 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 501 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 501 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 501 " -0.001 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 134 2.67 - 3.22: 10864 3.22 - 3.78: 17133 3.78 - 4.34: 21992 4.34 - 4.90: 36140 Nonbonded interactions: 86263 Sorted by model distance: nonbonded pdb=" O TRP C 647 " pdb=" OG1 THR C 650 " model vdw 2.107 3.040 nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.127 3.040 nonbonded pdb=" O TRP A 647 " pdb=" OG1 THR A 650 " model vdw 2.139 3.040 nonbonded pdb=" ND2 ASN C 339 " pdb="CA CA C1002 " model vdw 2.144 2.590 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.158 3.040 ... (remaining 86258 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.670 Find NCS groups from input model: 0.160 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:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10936 Z= 0.172 Angle : 0.648 7.952 14880 Z= 0.345 Chirality : 0.040 0.169 1686 Planarity : 0.004 0.044 1832 Dihedral : 13.868 85.886 3834 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.23), residues: 1282 helix: 1.62 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.31 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 104 TYR 0.020 0.002 TYR C 294 PHE 0.029 0.002 PHE C 501 TRP 0.013 0.001 TRP A 271 HIS 0.001 0.000 HIS A 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (10934) covalent geometry : angle 0.64774 / 0.34 (14876) SS BOND : bond 0.00107 / 0.06 ( 2) SS BOND : angle 0.99979 / 0.47 ( 4) hydrogen bonds : bond 0.14508 / 9.44 ( 707) hydrogen bonds : angle 5.54490 / 3.89 ( 2091) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 239 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7845 (mm-30) cc_final: 0.6677 (tm-30) REVERT: A 171 PHE cc_start: 0.7973 (t80) cc_final: 0.7772 (t80) REVERT: A 320 ASP cc_start: 0.8325 (m-30) cc_final: 0.8023 (t0) REVERT: A 392 CYS cc_start: 0.6846 (m) cc_final: 0.6530 (m) REVERT: A 670 PHE cc_start: 0.8228 (m-80) cc_final: 0.8022 (m-80) REVERT: C 111 GLU cc_start: 0.7733 (mm-30) cc_final: 0.6777 (tm-30) outliers start: 1 outliers final: 0 residues processed: 239 average time/residue: 0.0754 time to fit residues: 27.3389 Evaluate side-chains 172 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 0.0020 chunk 35 optimal weight: 1.9990 overall best weight: 1.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 54 GLN C 117 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 HIS C 443 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.151029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.115237 restraints weight = 18483.242| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.41 r_work: 0.3382 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10936 Z= 0.173 Angle : 0.636 7.897 14880 Z= 0.325 Chirality : 0.041 0.196 1686 Planarity : 0.004 0.044 1832 Dihedral : 4.116 21.700 1406 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.39 % Allowed : 9.71 % Favored : 88.91 % 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: 1.87 (0.23), residues: 1282 helix: 1.85 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -0.40 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 537 TYR 0.017 0.002 TYR C 294 PHE 0.022 0.002 PHE A 499 TRP 0.013 0.001 TRP C 271 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10934) covalent geometry : angle 0.63545 / 0.33 (14876) SS BOND : bond 0.00303 / 0.19 ( 2) SS BOND : angle 1.23518 / 0.58 ( 4) hydrogen bonds : bond 0.04768 / 3.16 ( 707) hydrogen bonds : angle 4.36797 / 3.12 ( 2091) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.7902 (mm-30) cc_final: 0.6861 (tm-30) REVERT: A 320 ASP cc_start: 0.8437 (m-30) cc_final: 0.8108 (t0) REVERT: A 322 MET cc_start: 0.7795 (ppp) cc_final: 0.7568 (ppp) REVERT: C 111 GLU cc_start: 0.7966 (mm-30) cc_final: 0.6791 (tm-30) REVERT: C 478 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8612 (tm-30) outliers start: 16 outliers final: 12 residues processed: 206 average time/residue: 0.0726 time to fit residues: 22.6011 Evaluate side-chains 186 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 411 PHE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 ASN ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.152945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.117895 restraints weight = 18558.527| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.53 r_work: 0.3413 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10936 Z= 0.128 Angle : 0.583 7.106 14880 Z= 0.296 Chirality : 0.040 0.185 1686 Planarity : 0.003 0.046 1832 Dihedral : 3.990 20.296 1406 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.73 % Allowed : 13.60 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.24), residues: 1282 helix: 1.91 (0.17), residues: 946 sheet: None (None), residues: 0 loop : -0.24 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 537 TYR 0.014 0.001 TYR C 491 PHE 0.027 0.001 PHE A 444 TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS C 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (10934) covalent geometry : angle 0.58322 / 0.30 (14876) SS BOND : bond 0.00160 / 0.09 ( 2) SS BOND : angle 0.90710 / 0.44 ( 4) hydrogen bonds : bond 0.04137 / 2.74 ( 707) hydrogen bonds : angle 4.12504 / 2.96 ( 2091) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8003 (mm-30) cc_final: 0.6940 (tm-30) REVERT: A 320 ASP cc_start: 0.8478 (m-30) cc_final: 0.8168 (t0) REVERT: A 322 MET cc_start: 0.7960 (ppp) cc_final: 0.7730 (ppp) REVERT: C 111 GLU cc_start: 0.7974 (mm-30) cc_final: 0.6866 (tm-30) REVERT: C 322 MET cc_start: 0.7437 (tmm) cc_final: 0.7199 (tmm) REVERT: C 478 GLU cc_start: 0.8938 (tm-30) cc_final: 0.8725 (tm-30) outliers start: 20 outliers final: 13 residues processed: 221 average time/residue: 0.0731 time to fit residues: 24.7059 Evaluate side-chains 193 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 59 optimal weight: 0.0770 chunk 81 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.150865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.115714 restraints weight = 18712.770| |-----------------------------------------------------------------------------| r_work (start): 0.3614 rms_B_bonded: 2.60 r_work: 0.3376 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10936 Z= 0.153 Angle : 0.586 7.143 14880 Z= 0.301 Chirality : 0.041 0.202 1686 Planarity : 0.004 0.054 1832 Dihedral : 3.971 19.600 1406 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.08 % Allowed : 14.99 % Favored : 82.93 % 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: 2.00 (0.24), residues: 1282 helix: 1.89 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.015 0.002 TYR C 491 PHE 0.020 0.001 PHE A 499 TRP 0.014 0.001 TRP A 271 HIS 0.002 0.001 HIS A 410 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (10934) covalent geometry : angle 0.58612 / 0.30 (14876) SS BOND : bond 0.00072 / 0.04 ( 2) SS BOND : angle 1.01607 / 0.50 ( 4) hydrogen bonds : bond 0.04163 / 2.76 ( 707) hydrogen bonds : angle 4.11118 / 2.94 ( 2091) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 GLU cc_start: 0.8063 (mm-30) cc_final: 0.6932 (tm-30) REVERT: A 237 MET cc_start: 0.7666 (ttt) cc_final: 0.7457 (ttm) REVERT: A 320 ASP cc_start: 0.8463 (m-30) cc_final: 0.8143 (t0) REVERT: A 322 MET cc_start: 0.8024 (ppp) cc_final: 0.7732 (ppp) REVERT: C 111 GLU cc_start: 0.8044 (mm-30) cc_final: 0.6760 (tm-30) REVERT: C 322 MET cc_start: 0.7469 (tmm) cc_final: 0.7197 (tmm) outliers start: 24 outliers final: 17 residues processed: 203 average time/residue: 0.0707 time to fit residues: 21.9297 Evaluate side-chains 191 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 0.6980 chunk 119 optimal weight: 0.0070 chunk 75 optimal weight: 0.2980 chunk 127 optimal weight: 1.9990 chunk 23 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 99 optimal weight: 0.2980 overall best weight: 0.1496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.155633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.121434 restraints weight = 18333.238| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.67 r_work: 0.3461 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10936 Z= 0.116 Angle : 0.564 8.270 14880 Z= 0.286 Chirality : 0.039 0.202 1686 Planarity : 0.003 0.047 1832 Dihedral : 3.808 18.040 1406 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.56 % Allowed : 16.90 % Favored : 81.54 % 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: 2.12 (0.24), residues: 1282 helix: 1.97 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.17 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 493 TYR 0.012 0.001 TYR A 216 PHE 0.027 0.001 PHE C 351 TRP 0.012 0.001 TRP A 464 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (10934) covalent geometry : angle 0.56437 / 0.29 (14876) SS BOND : bond 0.00427 / 0.24 ( 2) SS BOND : angle 0.79799 / 0.42 ( 4) hydrogen bonds : bond 0.03650 / 2.41 ( 707) hydrogen bonds : angle 3.95229 / 2.84 ( 2091) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 220 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8019 (mmmm) REVERT: A 111 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7098 (tm-30) REVERT: A 319 MET cc_start: 0.6617 (tpp) cc_final: 0.6372 (tpt) REVERT: A 320 ASP cc_start: 0.8415 (m-30) cc_final: 0.8092 (t0) REVERT: A 327 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.7215 (mt) REVERT: A 633 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: A 678 GLU cc_start: 0.7526 (pp20) cc_final: 0.7166 (tm-30) REVERT: C 111 GLU cc_start: 0.8033 (mm-30) cc_final: 0.6845 (tm-30) REVERT: C 322 MET cc_start: 0.7458 (tmm) cc_final: 0.7198 (tmm) REVERT: C 464 TRP cc_start: 0.8019 (m100) cc_final: 0.7777 (m100) REVERT: C 505 TRP cc_start: 0.8425 (OUTLIER) cc_final: 0.7906 (m100) outliers start: 18 outliers final: 7 residues processed: 229 average time/residue: 0.0701 time to fit residues: 24.6299 Evaluate side-chains 200 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.118870 restraints weight = 18499.704| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 2.71 r_work: 0.3422 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10936 Z= 0.131 Angle : 0.582 7.257 14880 Z= 0.294 Chirality : 0.041 0.203 1686 Planarity : 0.003 0.045 1832 Dihedral : 3.798 17.575 1406 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.56 % Allowed : 18.46 % Favored : 79.98 % 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: 2.10 (0.24), residues: 1282 helix: 1.96 (0.16), residues: 946 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.012 0.001 TYR C 288 PHE 0.023 0.001 PHE C 351 TRP 0.014 0.001 TRP A 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (10934) covalent geometry : angle 0.58226 / 0.29 (14876) SS BOND : bond 0.00174 / 0.10 ( 2) SS BOND : angle 1.00187 / 0.52 ( 4) hydrogen bonds : bond 0.03772 / 2.49 ( 707) hydrogen bonds : angle 4.00027 / 2.87 ( 2091) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: A 98 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7994 (mmmm) REVERT: A 111 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7088 (tm-30) REVERT: A 320 ASP cc_start: 0.8491 (m-30) cc_final: 0.8141 (t0) REVERT: A 322 MET cc_start: 0.8068 (ppp) cc_final: 0.7717 (ppp) REVERT: A 633 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 678 GLU cc_start: 0.7553 (pp20) cc_final: 0.7200 (tm-30) REVERT: C 50 GLU cc_start: 0.8264 (pm20) cc_final: 0.7958 (mp0) REVERT: C 111 GLU cc_start: 0.8045 (mm-30) cc_final: 0.6794 (tm-30) REVERT: C 322 MET cc_start: 0.7425 (tmm) cc_final: 0.7102 (tmm) REVERT: C 464 TRP cc_start: 0.8070 (m100) cc_final: 0.7825 (m100) REVERT: C 505 TRP cc_start: 0.8399 (OUTLIER) cc_final: 0.7842 (m100) outliers start: 18 outliers final: 12 residues processed: 197 average time/residue: 0.0655 time to fit residues: 20.1020 Evaluate side-chains 197 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.152903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.118434 restraints weight = 18516.785| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.71 r_work: 0.3414 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10936 Z= 0.133 Angle : 0.583 10.269 14880 Z= 0.293 Chirality : 0.041 0.274 1686 Planarity : 0.003 0.044 1832 Dihedral : 3.803 17.051 1406 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.56 % Allowed : 19.76 % Favored : 78.68 % 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: 2.10 (0.24), residues: 1282 helix: 1.96 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.013 0.001 TYR C 294 PHE 0.029 0.001 PHE A 229 TRP 0.014 0.001 TRP C 271 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (10934) covalent geometry : angle 0.58327 / 0.29 (14876) SS BOND : bond 0.00174 / 0.10 ( 2) SS BOND : angle 0.92869 / 0.48 ( 4) hydrogen bonds : bond 0.03803 / 2.52 ( 707) hydrogen bonds : angle 3.99580 / 2.86 ( 2091) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.318 Fit side-chains REVERT: A 98 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7947 (mmmm) REVERT: A 111 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7071 (tm-30) REVERT: A 319 MET cc_start: 0.6634 (tpp) cc_final: 0.6368 (tpt) REVERT: A 320 ASP cc_start: 0.8480 (m-30) cc_final: 0.8131 (t0) REVERT: A 505 TRP cc_start: 0.8359 (OUTLIER) cc_final: 0.7726 (m100) REVERT: A 633 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: A 678 GLU cc_start: 0.7512 (pp20) cc_final: 0.7153 (tm-30) REVERT: C 111 GLU cc_start: 0.7934 (mm-30) cc_final: 0.6789 (tm-30) REVERT: C 322 MET cc_start: 0.7487 (tmm) cc_final: 0.7163 (tmm) REVERT: C 453 LEU cc_start: 0.8661 (mm) cc_final: 0.8189 (tp) REVERT: C 505 TRP cc_start: 0.8326 (OUTLIER) cc_final: 0.7738 (m100) REVERT: C 579 TYR cc_start: 0.9050 (m-80) cc_final: 0.8834 (m-80) outliers start: 18 outliers final: 9 residues processed: 199 average time/residue: 0.0686 time to fit residues: 21.3664 Evaluate side-chains 198 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 185 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.152006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.117305 restraints weight = 18435.054| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.61 r_work: 0.3399 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10936 Z= 0.144 Angle : 0.617 14.871 14880 Z= 0.306 Chirality : 0.042 0.291 1686 Planarity : 0.003 0.044 1832 Dihedral : 3.823 16.840 1406 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.65 % Allowed : 19.84 % 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: 2.07 (0.23), residues: 1282 helix: 1.95 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.27 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 537 TYR 0.014 0.001 TYR C 294 PHE 0.024 0.001 PHE A 229 TRP 0.015 0.001 TRP A 271 HIS 0.001 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (10934) covalent geometry : angle 0.61731 / 0.31 (14876) SS BOND : bond 0.00139 / 0.08 ( 2) SS BOND : angle 0.91227 / 0.46 ( 4) hydrogen bonds : bond 0.03895 / 2.58 ( 707) hydrogen bonds : angle 4.01651 / 2.88 ( 2091) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.310 Fit side-chains REVERT: A 50 GLU cc_start: 0.8684 (mp0) cc_final: 0.8474 (mp0) REVERT: A 98 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7966 (mmmm) REVERT: A 111 GLU cc_start: 0.8019 (mm-30) cc_final: 0.6948 (tm-30) REVERT: A 319 MET cc_start: 0.6771 (tpp) cc_final: 0.6506 (tpt) REVERT: A 320 ASP cc_start: 0.8433 (m-30) cc_final: 0.8096 (t0) REVERT: A 633 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: A 678 GLU cc_start: 0.7449 (pp20) cc_final: 0.7098 (tm-30) REVERT: C 111 GLU cc_start: 0.7923 (mm-30) cc_final: 0.6770 (tm-30) REVERT: C 322 MET cc_start: 0.7528 (tmm) cc_final: 0.7206 (tmm) REVERT: C 453 LEU cc_start: 0.8661 (mm) cc_final: 0.8158 (tp) REVERT: C 505 TRP cc_start: 0.8316 (OUTLIER) cc_final: 0.7762 (m100) REVERT: C 579 TYR cc_start: 0.9057 (m-80) cc_final: 0.8748 (m-80) outliers start: 19 outliers final: 14 residues processed: 195 average time/residue: 0.0685 time to fit residues: 20.9520 Evaluate side-chains 195 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.152311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.117677 restraints weight = 18479.144| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.64 r_work: 0.3408 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10936 Z= 0.138 Angle : 0.643 20.310 14880 Z= 0.313 Chirality : 0.042 0.310 1686 Planarity : 0.003 0.044 1832 Dihedral : 3.824 16.269 1406 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.73 % Allowed : 20.02 % Favored : 78.25 % 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: 2.09 (0.23), residues: 1282 helix: 1.96 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 537 TYR 0.013 0.001 TYR C 294 PHE 0.024 0.001 PHE A 195 TRP 0.013 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10934) covalent geometry : angle 0.64265 / 0.31 (14876) SS BOND : bond 0.00114 / 0.06 ( 2) SS BOND : angle 0.69669 / 0.35 ( 4) hydrogen bonds : bond 0.03845 / 2.54 ( 707) hydrogen bonds : angle 4.00125 / 2.87 ( 2091) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.383 Fit side-chains REVERT: A 50 GLU cc_start: 0.8718 (mp0) cc_final: 0.8505 (mp0) REVERT: A 98 LYS cc_start: 0.8414 (OUTLIER) cc_final: 0.7985 (mmmm) REVERT: A 111 GLU cc_start: 0.8009 (mm-30) cc_final: 0.6942 (tm-30) REVERT: A 319 MET cc_start: 0.6817 (tpp) cc_final: 0.6535 (tpt) REVERT: A 320 ASP cc_start: 0.8453 (m-30) cc_final: 0.8118 (t0) REVERT: A 505 TRP cc_start: 0.8249 (OUTLIER) cc_final: 0.7619 (m100) REVERT: A 633 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: A 678 GLU cc_start: 0.7414 (pp20) cc_final: 0.7053 (tm-30) REVERT: C 111 GLU cc_start: 0.7937 (mm-30) cc_final: 0.6796 (tm-30) REVERT: C 322 MET cc_start: 0.7649 (tmm) cc_final: 0.7330 (tmm) REVERT: C 453 LEU cc_start: 0.8485 (mm) cc_final: 0.8060 (tp) REVERT: C 486 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: C 505 TRP cc_start: 0.8265 (OUTLIER) cc_final: 0.7760 (m100) REVERT: C 579 TYR cc_start: 0.9038 (m-80) cc_final: 0.8777 (m-80) REVERT: C 633 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.7846 (pm20) outliers start: 20 outliers final: 12 residues processed: 201 average time/residue: 0.0761 time to fit residues: 23.8776 Evaluate side-chains 200 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain C residue 172 LEU Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 0.0570 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.153466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119364 restraints weight = 18303.705| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.54 r_work: 0.3433 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10936 Z= 0.124 Angle : 0.603 12.137 14880 Z= 0.300 Chirality : 0.041 0.298 1686 Planarity : 0.003 0.045 1832 Dihedral : 3.739 15.818 1406 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.47 % Allowed : 20.54 % Favored : 77.99 % 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: 2.13 (0.24), residues: 1282 helix: 1.98 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 537 TYR 0.014 0.001 TYR C 288 PHE 0.026 0.001 PHE C 351 TRP 0.012 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (10934) covalent geometry : angle 0.60269 / 0.30 (14876) SS BOND : bond 0.00185 / 0.11 ( 2) SS BOND : angle 0.53007 / 0.26 ( 4) hydrogen bonds : bond 0.03709 / 2.44 ( 707) hydrogen bonds : angle 3.97218 / 2.86 ( 2091) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.405 Fit side-chains REVERT: A 50 GLU cc_start: 0.8634 (mp0) cc_final: 0.8421 (mp0) REVERT: A 98 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7963 (mmmm) REVERT: A 111 GLU cc_start: 0.7927 (mm-30) cc_final: 0.6874 (tm-30) REVERT: A 319 MET cc_start: 0.6823 (tpp) cc_final: 0.6550 (tpt) REVERT: A 320 ASP cc_start: 0.8482 (m-30) cc_final: 0.8142 (t0) REVERT: A 486 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: A 505 TRP cc_start: 0.8222 (OUTLIER) cc_final: 0.7725 (m100) REVERT: A 633 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: A 678 GLU cc_start: 0.7311 (pp20) cc_final: 0.6967 (tm-30) REVERT: C 111 GLU cc_start: 0.7815 (mm-30) cc_final: 0.6745 (tm-30) REVERT: C 322 MET cc_start: 0.7665 (tmm) cc_final: 0.7343 (tmm) REVERT: C 453 LEU cc_start: 0.8332 (mm) cc_final: 0.7979 (tp) REVERT: C 486 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7281 (m-80) REVERT: C 505 TRP cc_start: 0.8230 (OUTLIER) cc_final: 0.7760 (m100) REVERT: C 579 TYR cc_start: 0.9016 (m-80) cc_final: 0.8771 (m-80) REVERT: C 633 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.7848 (pm20) outliers start: 17 outliers final: 9 residues processed: 199 average time/residue: 0.0751 time to fit residues: 23.3427 Evaluate side-chains 200 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 184 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 486 TYR Chi-restraints excluded: chain A residue 505 TRP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 633 GLN Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 505 TRP Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 629 MET Chi-restraints excluded: chain C residue 633 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 0.0970 chunk 13 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.152905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.119203 restraints weight = 18422.140| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.69 r_work: 0.3421 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10936 Z= 0.130 Angle : 0.627 13.300 14880 Z= 0.307 Chirality : 0.042 0.368 1686 Planarity : 0.003 0.045 1832 Dihedral : 3.709 14.555 1406 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.56 % Allowed : 20.45 % Favored : 77.99 % 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: 2.12 (0.24), residues: 1282 helix: 1.97 (0.16), residues: 950 sheet: None (None), residues: 0 loop : -0.20 (0.36), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 552 TYR 0.011 0.001 TYR C 579 PHE 0.026 0.001 PHE C 195 TRP 0.013 0.001 TRP A 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10934) covalent geometry : angle 0.62655 / 0.31 (14876) SS BOND : bond 0.00429 / 0.24 ( 2) SS BOND : angle 0.60064 / 0.32 ( 4) hydrogen bonds : bond 0.03743 / 2.47 ( 707) hydrogen bonds : angle 3.97201 / 2.86 ( 2091) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.16 seconds wall clock time: 38 minutes 11.36 seconds (2291.36 seconds total)