Starting phenix.real_space_refine on Thu Oct 22 22:24:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9txi_56397/10_2026/9txi_56397.cif Found real_map, /net/cci-nas-00/data/ceres_data/9txi_56397/10_2026/9txi_56397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9txi_56397/10_2026/9txi_56397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9txi_56397/10_2026/9txi_56397.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9txi_56397/10_2026/9txi_56397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9txi_56397/10_2026/9txi_56397.map" } resolution = 3.02 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3915 2.51 5 N 1067 2.21 5 O 1211 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6213 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6101 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 773, 6080 Classifications: {'peptide': 773} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 735} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 773, 6080 Classifications: {'peptide': 773} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 735} Chain breaks: 2 bond proxies already assigned to first conformer: 6173 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.48, per 1000 atoms: 0.40 Number of scatterers: 6213 At special positions: 0 Unit cell: (78.75, 92.5, 118.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 1211 8.00 N 1067 7.00 C 3915 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 717 " - pdb=" SG CYS A 895 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 1 " - " ASN A 207 " " NAG C 1 " - " ASN A 517 " " NAG D 1 " - " ASN A 577 " " NAG E 1 " - " ASN A 81 " Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 565.9 milliseconds 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 7 sheets defined 19.8% alpha, 34.3% 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 98 through 103 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 218 through 223 removed outlier: 3.769A pdb=" N GLN A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 303 removed outlier: 4.045A pdb=" N GLN A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.007A pdb=" N ALA A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 407 Processing helix chain 'A' and resid 422 through 432 removed outlier: 3.549A pdb=" N LEU A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 457 removed outlier: 3.608A pdb=" N VAL A 457 " --> pdb=" O PHE A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.577A pdb=" N PHE A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 3.981A pdb=" N ARG A 546 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 582 removed outlier: 3.723A pdb=" N LEU A 571 " --> pdb=" O ASP A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 849 removed outlier: 3.649A pdb=" N PHE A 848 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 849 " --> pdb=" O GLY A 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 845 through 849' Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 206 removed outlier: 8.428A pdb=" N GLN A 173 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU A 38 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP A 175 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A 40 " --> pdb=" O ASP A 175 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N HIS A 177 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N SER A 42 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N PHE A 179 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N VAL A 44 " --> pdb=" O PHE A 179 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG A 56 " --> pdb=" O TYR A 36 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 38 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N THR A 54 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL A 40 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 52 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N SER A 42 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 50 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 44 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N PHE A 48 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLU A 147 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ILE A 79 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 16.847A pdb=" N PHE A 78 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 15.581A pdb=" N GLU A 97 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N THR A 80 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE A 95 " --> pdb=" O THR A 80 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N PHE A 82 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 74 Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 163 removed outlier: 3.826A pdb=" N PHE A 186 " --> pdb=" O ASP A 242 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASP A 809 " --> pdb=" O VAL A 813 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N VAL A 813 " --> pdb=" O ASP A 809 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 705 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU A 831 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N ARG A 715 " --> pdb=" O SER A 894 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N TRP A 896 " --> pdb=" O ARG A 715 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 900 " --> pdb=" O ASP A 719 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU A 899 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N SER A 875 " --> pdb=" O GLU A 899 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 251 through 255 removed outlier: 7.345A pdb=" N ALA A 494 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N VAL A 477 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS A 496 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 319 through 321 removed outlier: 5.981A pdb=" N LYS A 273 " --> pdb=" O GLN A 309 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ASN A 311 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 275 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 313 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE A 277 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE A 315 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE A 279 " --> pdb=" O PHE A 315 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER A 378 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N PHE A 413 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE A 380 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 415 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU A 382 " --> pdb=" O LEU A 415 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE A 417 " --> pdb=" O LEU A 382 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR A 384 " --> pdb=" O PHE A 417 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ARG A 438 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N CYS A 414 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ILE A 440 " --> pdb=" O CYS A 414 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLY A 416 " --> pdb=" O ILE A 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 484 through 486 removed outlier: 6.801A pdb=" N LEU A 485 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA A 464 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LYS A 512 " --> pdb=" O ALA A 464 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 727 through 732 removed outlier: 5.185A pdb=" N ASN A 728 " --> pdb=" O GLY A 741 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N GLY A 741 " --> pdb=" O ASN A 728 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 730 " --> pdb=" O VAL A 739 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU A 738 " --> pdb=" O VAL A 755 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N VAL A 755 " --> pdb=" O GLU A 738 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 740 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 753 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLN A 742 " --> pdb=" O SER A 751 " (cutoff:3.500A) 249 hydrogen bonds defined for protein. 693 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: 1.10 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1734 1.33 - 1.45: 1114 1.45 - 1.58: 3449 1.58 - 1.70: 1 1.70 - 1.82: 37 Bond restraints: 6335 Sorted by residual: bond pdb=" CA LEU A 900 " pdb=" C LEU A 900 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.19e-02 7.06e+03 1.25e+01 bond pdb=" CA GLU A 370 " pdb=" CB GLU A 370 " ideal model delta sigma weight residual 1.533 1.592 -0.059 2.15e-02 2.16e+03 7.46e+00 bond pdb=" N LEU A 900 " pdb=" CA LEU A 900 " ideal model delta sigma weight residual 1.454 1.430 0.024 1.18e-02 7.18e+03 4.20e+00 bond pdb=" C LEU A 900 " pdb=" O LEU A 900 " ideal model delta sigma weight residual 1.234 1.211 0.023 1.28e-02 6.10e+03 3.26e+00 bond pdb=" C1 NAG B 2 " pdb=" C2 NAG B 2 " ideal model delta sigma weight residual 1.532 1.562 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 6330 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 8374 2.33 - 4.66: 189 4.66 - 6.98: 21 6.98 - 9.31: 9 9.31 - 11.64: 4 Bond angle restraints: 8597 Sorted by residual: angle pdb=" CA GLU A 370 " pdb=" CB GLU A 370 " pdb=" CG GLU A 370 " ideal model delta sigma weight residual 114.10 124.49 -10.39 2.00e+00 2.50e-01 2.70e+01 angle pdb=" C GLN A 711 " pdb=" N SER A 712 " pdb=" CA SER A 712 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" CA ARG A 500 " pdb=" CB ARG A 500 " pdb=" CG ARG A 500 " ideal model delta sigma weight residual 114.10 121.89 -7.79 2.00e+00 2.50e-01 1.52e+01 angle pdb=" C GLU A 370 " pdb=" CA GLU A 370 " pdb=" CB GLU A 370 " ideal model delta sigma weight residual 110.35 117.13 -6.78 1.78e+00 3.16e-01 1.45e+01 angle pdb=" N ASN A 207 " pdb=" CA ASN A 207 " pdb=" C ASN A 207 " ideal model delta sigma weight residual 110.80 103.17 7.63 2.13e+00 2.20e-01 1.28e+01 ... (remaining 8592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 3520 17.58 - 35.17: 289 35.17 - 52.75: 90 52.75 - 70.34: 33 70.34 - 87.92: 11 Dihedral angle restraints: 3943 sinusoidal: 1699 harmonic: 2244 Sorted by residual: dihedral pdb=" CB CYS A 717 " pdb=" SG CYS A 717 " pdb=" SG CYS A 895 " pdb=" CB CYS A 895 " ideal model delta sinusoidal sigma weight residual -86.00 -166.95 80.95 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CA PHE A 540 " pdb=" C PHE A 540 " pdb=" N HIS A 541 " pdb=" CA HIS A 541 " ideal model delta harmonic sigma weight residual -180.00 -157.45 -22.55 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA LYS A 512 " pdb=" C LYS A 512 " pdb=" N LEU A 513 " pdb=" CA LEU A 513 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 3940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 964 0.124 - 0.248: 27 0.248 - 0.372: 2 0.372 - 0.496: 0 0.496 - 0.620: 1 Chirality restraints: 994 Sorted by residual: chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 207 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-01 2.50e+01 9.62e+00 chirality pdb=" C3 NAG B 1 " pdb=" C2 NAG B 1 " pdb=" C4 NAG B 1 " pdb=" O3 NAG B 1 " both_signs ideal model delta sigma weight residual False 2.45 2.14 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 517 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 991 not shown) Planarity restraints: 1120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 792 " 0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO A 793 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO A 793 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 793 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 207 " 0.028 2.00e-02 2.50e+03 2.78e-02 9.69e+00 pdb=" CG ASN A 207 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 207 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 207 " -0.024 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 586 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO A 587 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO A 587 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 587 " 0.041 5.00e-02 4.00e+02 ... (remaining 1117 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 2712 3.00 - 3.47: 5652 3.47 - 3.95: 9246 3.95 - 4.42: 10157 4.42 - 4.90: 18286 Nonbonded interactions: 46053 Sorted by model distance: nonbonded pdb=" N ASN A 207 " pdb=" O ASN A 207 " model vdw 2.520 2.496 nonbonded pdb=" N LEU A 900 " pdb=" O LEU A 900 " model vdw 2.568 2.496 nonbonded pdb=" N THR A 586 " pdb=" O THR A 586 " model vdw 2.579 2.496 nonbonded pdb=" N SER A 325 " pdb=" O SER A 325 " model vdw 2.585 2.496 nonbonded pdb=" N THR A 218 " pdb=" OG1 THR A 218 " model vdw 2.607 2.496 ... (remaining 46048 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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=0.47 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: 0.290 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.770 Find NCS groups from input model: 0.030 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 0.059 6344 Z= 0.203 Angle : 0.905 13.774 8623 Z= 0.451 Chirality : 0.058 0.620 994 Planarity : 0.008 0.079 1116 Dihedral : 15.841 87.921 2488 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.59 % Allowed : 9.94 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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 (0.29), residues: 771 helix: -2.13 (0.33), residues: 140 sheet: 1.00 (0.30), residues: 309 loop : -1.74 (0.29), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 500 TYR 0.019 0.002 TYR A 884 PHE 0.022 0.002 PHE A 789 TRP 0.007 0.001 TRP A 205 HIS 0.006 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 ( 6335) covalent geometry : angle 0.85830 / 0.44 ( 8597) SS BOND : bond 0.00118 / 0.07 ( 1) SS BOND : angle 2.06727 / 0.75 ( 2) hydrogen bonds : bond 0.10741 / 7.45 ( 249) hydrogen bonds : angle 5.59745 / 3.94 ( 693) link_BETA1-4 : bond 0.01717 / 1.07 ( 4) link_BETA1-4 : angle 4.48300 / 2.66 ( 12) link_NAG-ASN : bond 0.01694 / 0.94 ( 4) link_NAG-ASN : angle 6.31748 / 3.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.247 Fit side-chains REVERT: A 285 MET cc_start: 0.7686 (mmm) cc_final: 0.7482 (mmm) REVERT: A 389 THR cc_start: 0.8982 (m) cc_final: 0.8696 (p) REVERT: A 792 MET cc_start: 0.8750 (mtm) cc_final: 0.8091 (mtp) REVERT: A 884 TYR cc_start: 0.8649 (p90) cc_final: 0.8002 (p90) outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.0656 time to fit residues: 3.4154 Evaluate side-chains 32 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.095265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070523 restraints weight = 30722.512| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 5.11 r_work: 0.2880 rms_B_bonded: 5.01 restraints_weight: 2.0000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6344 Z= 0.201 Angle : 0.633 7.466 8623 Z= 0.314 Chirality : 0.048 0.259 994 Planarity : 0.005 0.060 1116 Dihedral : 8.419 62.600 1007 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.34 % Allowed : 10.24 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.41 (0.30), residues: 771 helix: -0.15 (0.41), residues: 146 sheet: 0.91 (0.30), residues: 307 loop : -1.54 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 396 TYR 0.018 0.002 TYR A 550 PHE 0.014 0.002 PHE A 142 TRP 0.007 0.001 TRP A 752 HIS 0.004 0.001 HIS A 770 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.20 ( 6335) covalent geometry : angle 0.61141 / 0.31 ( 8597) SS BOND : bond 0.00029 / 0.02 ( 1) SS BOND : angle 1.72042 / 0.63 ( 2) hydrogen bonds : bond 0.04094 / 2.94 ( 249) hydrogen bonds : angle 4.65175 / 3.31 ( 693) link_BETA1-4 : bond 0.00784 / 0.51 ( 4) link_BETA1-4 : angle 3.04645 / 1.72 ( 12) link_NAG-ASN : bond 0.00398 / 0.22 ( 4) link_NAG-ASN : angle 3.16616 / 1.61 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 26 time to evaluate : 0.292 Fit side-chains REVERT: A 792 MET cc_start: 0.9104 (mtm) cc_final: 0.8510 (mtp) outliers start: 9 outliers final: 2 residues processed: 34 average time/residue: 0.0884 time to fit residues: 4.1707 Evaluate side-chains 27 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 900 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [12, 42, 22, 37, 13, 57, 25, 60, 33, 61, 24] chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 22 optimal weight: 0.0030 chunk 37 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.099548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075627 restraints weight = 27138.286| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 4.77 r_work: 0.2931 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6344 Z= 0.094 Angle : 0.559 8.494 8623 Z= 0.271 Chirality : 0.045 0.274 994 Planarity : 0.005 0.054 1116 Dihedral : 7.551 55.085 1004 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.59 % Allowed : 11.42 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.00 (0.30), residues: 771 helix: 0.71 (0.44), residues: 146 sheet: 0.92 (0.30), residues: 309 loop : -1.29 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 500 TYR 0.011 0.001 TYR A 454 PHE 0.011 0.001 PHE A 142 TRP 0.003 0.000 TRP A 322 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 ( 6335) covalent geometry : angle 0.53424 / 0.26 ( 8597) SS BOND : bond 0.00319 / 0.20 ( 1) SS BOND : angle 1.63690 / 0.59 ( 2) hydrogen bonds : bond 0.03063 / 2.20 ( 249) hydrogen bonds : angle 4.41242 / 3.17 ( 693) link_BETA1-4 : bond 0.00984 / 0.60 ( 4) link_BETA1-4 : angle 3.19592 / 1.80 ( 12) link_NAG-ASN : bond 0.00688 / 0.43 ( 4) link_NAG-ASN : angle 3.11246 / 1.59 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.233 Fit side-chains REVERT: A 389 THR cc_start: 0.8970 (m) cc_final: 0.8754 (p) REVERT: A 792 MET cc_start: 0.9035 (mtm) cc_final: 0.8410 (mtp) outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.0729 time to fit residues: 3.2950 Evaluate side-chains 29 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 580 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [6, 8, 40, 42, 39, 21, 16, 3, 30, 11, 37] chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.091665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.066299 restraints weight = 21912.658| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.80 r_work: 0.2731 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 6344 Z= 0.276 Angle : 0.684 8.088 8623 Z= 0.342 Chirality : 0.049 0.218 994 Planarity : 0.005 0.052 1116 Dihedral : 7.359 52.914 1004 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.19 % Allowed : 11.57 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.29 (0.31), residues: 771 helix: 0.68 (0.44), residues: 151 sheet: 0.64 (0.30), residues: 318 loop : -1.56 (0.34), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 500 TYR 0.020 0.002 TYR A 550 PHE 0.020 0.002 PHE A 142 TRP 0.007 0.001 TRP A 752 HIS 0.005 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00683 / 0.28 ( 6335) covalent geometry : angle 0.66728 / 0.34 ( 8597) SS BOND : bond 0.01344 / 0.84 ( 1) SS BOND : angle 2.64209 / 0.97 ( 2) hydrogen bonds : bond 0.04620 / 3.29 ( 249) hydrogen bonds : angle 4.70978 / 3.35 ( 693) link_BETA1-4 : bond 0.00854 / 0.54 ( 4) link_BETA1-4 : angle 3.12249 / 1.75 ( 12) link_NAG-ASN : bond 0.00326 / 0.24 ( 4) link_NAG-ASN : angle 2.46775 / 1.19 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 25 time to evaluate : 0.242 Fit side-chains REVERT: A 830 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8224 (pt) REVERT: A 850 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8454 (mt0) outliers start: 7 outliers final: 3 residues processed: 31 average time/residue: 0.0950 time to fit residues: 4.0862 Evaluate side-chains 29 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 850 GLN Chi-restraints excluded: chain A residue 900 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [40, 13, 39, 5, 11, 67, 62, 3, 46, 72, 74] chunk 40 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 67 optimal weight: 0.0970 chunk 62 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.068877 restraints weight = 25069.050| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 5.09 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6344 Z= 0.101 Angle : 0.553 8.776 8623 Z= 0.270 Chirality : 0.045 0.245 994 Planarity : 0.004 0.049 1116 Dihedral : 6.803 48.789 1004 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.89 % Allowed : 12.17 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.02 (0.31), residues: 771 helix: 1.07 (0.44), residues: 151 sheet: 0.61 (0.30), residues: 322 loop : -1.27 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 500 TYR 0.013 0.001 TYR A 36 PHE 0.010 0.001 PHE A 789 TRP 0.003 0.000 TRP A 548 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6335) covalent geometry : angle 0.53069 / 0.26 ( 8597) SS BOND : bond 0.00018 / 0.01 ( 1) SS BOND : angle 1.72463 / 0.62 ( 2) hydrogen bonds : bond 0.03099 / 2.23 ( 249) hydrogen bonds : angle 4.41267 / 3.17 ( 693) link_BETA1-4 : bond 0.01039 / 0.64 ( 4) link_BETA1-4 : angle 3.12461 / 1.73 ( 12) link_NAG-ASN : bond 0.00618 / 0.41 ( 4) link_NAG-ASN : angle 2.79801 / 1.41 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.270 Fit side-chains REVERT: A 389 THR cc_start: 0.9118 (m) cc_final: 0.8899 (p) REVERT: A 850 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8424 (mt0) outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.0680 time to fit residues: 3.0500 Evaluate side-chains 30 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 850 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [24, 0, 11, 20, 10, 26, 14, 48, 54, 8, 75] chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068144 restraints weight = 19643.329| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.57 r_work: 0.2780 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6344 Z= 0.173 Angle : 0.591 8.388 8623 Z= 0.290 Chirality : 0.046 0.227 994 Planarity : 0.005 0.055 1116 Dihedral : 6.712 50.999 1004 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.19 % Allowed : 12.31 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.03 (0.31), residues: 771 helix: 1.09 (0.44), residues: 151 sheet: 0.66 (0.30), residues: 318 loop : -1.34 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 500 TYR 0.015 0.002 TYR A 550 PHE 0.015 0.002 PHE A 142 TRP 0.005 0.001 TRP A 752 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.17 ( 6335) covalent geometry : angle 0.57215 / 0.29 ( 8597) SS BOND : bond 0.00111 / 0.07 ( 1) SS BOND : angle 2.26041 / 0.84 ( 2) hydrogen bonds : bond 0.03680 / 2.64 ( 249) hydrogen bonds : angle 4.46179 / 3.19 ( 693) link_BETA1-4 : bond 0.00919 / 0.58 ( 4) link_BETA1-4 : angle 3.06076 / 1.70 ( 12) link_NAG-ASN : bond 0.00358 / 0.28 ( 4) link_NAG-ASN : angle 2.50272 / 1.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.235 Fit side-chains REVERT: A 500 ARG cc_start: 0.8477 (ttm110) cc_final: 0.8271 (ttm-80) outliers start: 7 outliers final: 3 residues processed: 29 average time/residue: 0.0833 time to fit residues: 3.4503 Evaluate side-chains 26 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [69, 0, 30, 57, 71, 12, 64, 56, 11, 67, 29] chunk 69 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 0.0030 chunk 12 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 11 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.066937 restraints weight = 34179.277| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 5.72 r_work: 0.2731 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6344 Z= 0.148 Angle : 0.570 8.514 8623 Z= 0.279 Chirality : 0.046 0.249 994 Planarity : 0.004 0.051 1116 Dihedral : 6.450 49.575 1004 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.59 % Allowed : 12.91 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.01 (0.31), residues: 771 helix: 1.14 (0.44), residues: 151 sheet: 0.66 (0.31), residues: 310 loop : -1.27 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 500 TYR 0.013 0.001 TYR A 550 PHE 0.012 0.001 PHE A 142 TRP 0.004 0.001 TRP A 548 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 6335) covalent geometry : angle 0.54948 / 0.27 ( 8597) SS BOND : bond 0.00029 / 0.02 ( 1) SS BOND : angle 2.03069 / 0.74 ( 2) hydrogen bonds : bond 0.03404 / 2.44 ( 249) hydrogen bonds : angle 4.40491 / 3.16 ( 693) link_BETA1-4 : bond 0.00981 / 0.62 ( 4) link_BETA1-4 : angle 3.03757 / 1.67 ( 12) link_NAG-ASN : bond 0.00448 / 0.33 ( 4) link_NAG-ASN : angle 2.65118 / 1.34 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.224 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.0807 time to fit residues: 3.4484 Evaluate side-chains 30 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 27 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [17, 6, 5, 16, 7, 12, 30, 37, 2, 24, 9] chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.094212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.068634 restraints weight = 19574.680| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.72 r_work: 0.2783 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6344 Z= 0.106 Angle : 0.542 8.496 8623 Z= 0.264 Chirality : 0.045 0.248 994 Planarity : 0.004 0.055 1116 Dihedral : 6.230 50.164 1004 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.74 % Allowed : 12.76 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.09 (0.31), residues: 771 helix: 1.27 (0.44), residues: 151 sheet: 0.76 (0.32), residues: 300 loop : -1.23 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 500 TYR 0.011 0.001 TYR A 36 PHE 0.010 0.001 PHE A 142 TRP 0.004 0.001 TRP A 548 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 ( 6335) covalent geometry : angle 0.51980 / 0.26 ( 8597) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 2.34414 / 0.87 ( 2) hydrogen bonds : bond 0.03046 / 2.20 ( 249) hydrogen bonds : angle 4.29546 / 3.09 ( 693) link_BETA1-4 : bond 0.00994 / 0.62 ( 4) link_BETA1-4 : angle 3.02849 / 1.67 ( 12) link_NAG-ASN : bond 0.00477 / 0.35 ( 4) link_NAG-ASN : angle 2.67705 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 27 time to evaluate : 0.234 Fit side-chains REVERT: A 389 THR cc_start: 0.8998 (m) cc_final: 0.8789 (p) REVERT: A 500 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8315 (ttm-80) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.0702 time to fit residues: 3.2031 Evaluate side-chains 29 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [73, 52, 27, 72, 33, 26, 23, 54, 2, 19, 60] chunk 73 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.064639 restraints weight = 38766.997| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 6.37 r_work: 0.2676 rms_B_bonded: 5.91 restraints_weight: 2.0000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6344 Z= 0.182 Angle : 0.593 8.197 8623 Z= 0.294 Chirality : 0.046 0.255 994 Planarity : 0.005 0.057 1116 Dihedral : 6.318 51.169 1004 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.89 % Allowed : 12.76 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: 0.00 (0.31), residues: 771 helix: 1.17 (0.44), residues: 151 sheet: 0.73 (0.31), residues: 306 loop : -1.34 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 500 TYR 0.014 0.002 TYR A 454 PHE 0.014 0.002 PHE A 142 TRP 0.006 0.001 TRP A 752 HIS 0.003 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 ( 6335) covalent geometry : angle 0.57465 / 0.29 ( 8597) SS BOND : bond 0.00074 / 0.05 ( 1) SS BOND : angle 2.45629 / 0.92 ( 2) hydrogen bonds : bond 0.03694 / 2.65 ( 249) hydrogen bonds : angle 4.42171 / 3.17 ( 693) link_BETA1-4 : bond 0.00931 / 0.59 ( 4) link_BETA1-4 : angle 2.98835 / 1.65 ( 12) link_NAG-ASN : bond 0.00352 / 0.28 ( 4) link_NAG-ASN : angle 2.53279 / 1.28 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.250 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 31 average time/residue: 0.0875 time to fit residues: 3.8754 Evaluate side-chains 30 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 699 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [17, 34, 47, 0, 18, 37, 67, 61, 68, 56, 60] chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.092141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.064293 restraints weight = 36340.911| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 6.17 r_work: 0.2664 rms_B_bonded: 5.80 restraints_weight: 2.0000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6344 Z= 0.214 Angle : 0.635 8.022 8623 Z= 0.314 Chirality : 0.047 0.267 994 Planarity : 0.005 0.056 1116 Dihedral : 6.409 50.265 1004 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.89 % Allowed : 12.91 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.16 (0.31), residues: 771 helix: 1.06 (0.44), residues: 151 sheet: 0.61 (0.31), residues: 306 loop : -1.44 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 500 TYR 0.015 0.002 TYR A 550 PHE 0.015 0.002 PHE A 142 TRP 0.006 0.001 TRP A 752 HIS 0.004 0.001 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.21 ( 6335) covalent geometry : angle 0.61746 / 0.31 ( 8597) SS BOND : bond 0.00046 / 0.03 ( 1) SS BOND : angle 2.65226 / 0.99 ( 2) hydrogen bonds : bond 0.03989 / 2.85 ( 249) hydrogen bonds : angle 4.53819 / 3.25 ( 693) link_BETA1-4 : bond 0.00872 / 0.55 ( 4) link_BETA1-4 : angle 2.93920 / 1.63 ( 12) link_NAG-ASN : bond 0.00346 / 0.26 ( 4) link_NAG-ASN : angle 2.60668 / 1.33 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1542 Ramachandran restraints generated. 771 Oldfield, 0 Emsley, 771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.241 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 29 average time/residue: 0.0925 time to fit residues: 3.7165 Evaluate side-chains 29 residues out of total 670 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 699 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: [22, 51, 46, 53, 24, 73, 30, 0, 38, 50, 43] chunk 22 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.093019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.066156 restraints weight = 33507.383| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 5.76 r_work: 0.2725 rms_B_bonded: 5.53 restraints_weight: 2.0000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6344 Z= 0.118 Angle : 0.565 8.257 8623 Z= 0.276 Chirality : 0.045 0.268 994 Planarity : 0.005 0.058 1116 Dihedral : 6.112 49.403 1004 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.74 % Allowed : 13.06 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.41 % 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: -0.02 (0.31), residues: 771 helix: 1.26 (0.44), residues: 151 sheet: 0.68 (0.32), residues: 300 loop : -1.33 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 500 TYR 0.012 0.001 TYR A 36 PHE 0.010 0.001 PHE A 142 TRP 0.004 0.001 TRP A 322 HIS 0.002 0.001 HIS A 541 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 6335) covalent geometry : angle 0.54390 / 0.27 ( 8597) SS BOND : bond 0.00019 / 0.01 ( 1) SS BOND : angle 2.23429 / 0.82 ( 2) hydrogen bonds : bond 0.03164 / 2.28 ( 249) hydrogen bonds : angle 4.34286 / 3.13 ( 693) link_BETA1-4 : bond 0.00978 / 0.61 ( 4) link_BETA1-4 : angle 2.96133 / 1.64 ( 12) link_NAG-ASN : bond 0.00462 / 0.32 ( 4) link_NAG-ASN : angle 2.80973 / 1.46 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.47 seconds wall clock time: 28 minutes 45.51 seconds (1725.51 seconds total)