Starting phenix.real_space_refine on Thu Sep 10 23:16:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/43yy_82402/09_2026/43yy_82402.cif Found real_map, /net/cci-nas-00/data/ceres_data/43yy_82402/09_2026/43yy_82402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/43yy_82402/09_2026/43yy_82402.cif" } default_model = "/net/cci-nas-00/data/ceres_data/43yy_82402/09_2026/43yy_82402.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/43yy_82402/09_2026/43yy_82402.map" default_real_map = "/net/cci-nas-00/data/ceres_data/43yy_82402/09_2026/43yy_82402.map" } resolution = 2.3 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= 0.079 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 24 5.16 5 C 3194 2.51 5 N 830 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5020 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3149 Classifications: {'peptide': 403} Link IDs: {'PTRANS': 20, 'TRANS': 382} Chain breaks: 7 Chain: "H" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 937 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 803 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 8, 'TRANS': 101} 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 1.06, per 1000 atoms: 0.21 Number of scatterers: 5020 At special positions: 0 Unit cell: (102.3, 68.82, 94.86, 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 24 16.00 O 972 8.00 N 830 7.00 C 3194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.04 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.04 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 40 " - pdb=" SG CYS L 108 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA C 3 " - " MAN C 4 " ALPHA1-6 " BMA C 3 " - " MAN C 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 501 " - " ASN A 344 " " NAG A 502 " - " ASN A 216 " " NAG A 503 " - " ASN A 351 " " NAG B 1 " - " ASN A 324 " " NAG C 1 " - " ASN A 264 " Time building additional restraints: 0.46 Conformation dependent library (CDL) restraints added in 164.9 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 12 sheets defined 8.0% alpha, 48.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 31 through 38 removed outlier: 3.565A pdb=" N LYS A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.529A pdb=" N ALA H 110 " --> pdb=" O THR H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 52 Processing helix chain 'L' and resid 99 through 103 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 49 Processing sheet with id=AA2, first strand: chain 'A' and resid 73 through 74 removed outlier: 6.879A pdb=" N ALA A 121 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LYS A 152 " --> pdb=" O ALA A 121 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 123 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N PHE A 150 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE A 125 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N CYS A 148 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 180 through 183 Processing sheet with id=AA4, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.480A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 440 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL A 406 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 270 through 286 removed outlier: 5.480A pdb=" N LYS A 272 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N VAL A 453 " --> pdb=" O LYS A 272 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL A 274 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE A 451 " --> pdb=" O VAL A 274 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N ASN A 276 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ALA A 449 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N VAL A 447 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N SER A 443 " --> pdb=" O ASN A 282 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 284 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 441 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A 286 " --> pdb=" O TRP A 439 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N TRP A 439 " --> pdb=" O ALA A 286 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 298 removed outlier: 6.857A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE A 424 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 334 " --> pdb=" O ILE A 424 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR A 371 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL A 390 " --> pdb=" O TYR A 371 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 382 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 22 through 26 Processing sheet with id=AA8, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.895A pdb=" N ILE H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY H 69 " --> pdb=" O ILE H 53 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP H 55 " --> pdb=" O LEU H 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 29 through 31 removed outlier: 3.568A pdb=" N LEU H 132 " --> pdb=" O ARG H 117 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 22 through 23 Processing sheet with id=AB2, first strand: chain 'L' and resid 27 through 30 removed outlier: 6.303A pdb=" N TRP L 55 " --> pdb=" O LEU L 67 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 27 through 30 removed outlier: 6.762A pdb=" N ASN L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 492 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: 0.84 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1590 1.35 - 1.47: 1434 1.47 - 1.60: 2090 1.60 - 1.73: 0 1.73 - 1.86: 31 Bond restraints: 5145 Sorted by residual: bond pdb=" N ASP A 481 " pdb=" CA ASP A 481 " ideal model delta sigma weight residual 1.454 1.479 -0.025 1.31e-02 5.83e+03 3.70e+00 bond pdb=" N ASP A 482 " pdb=" CA ASP A 482 " ideal model delta sigma weight residual 1.457 1.477 -0.020 1.31e-02 5.83e+03 2.40e+00 bond pdb=" CB CYS A 349 " pdb=" SG CYS A 349 " ideal model delta sigma weight residual 1.808 1.857 -0.049 3.30e-02 9.18e+02 2.24e+00 bond pdb=" N LEU A 480 " pdb=" CA LEU A 480 " ideal model delta sigma weight residual 1.455 1.474 -0.018 1.25e-02 6.40e+03 2.17e+00 bond pdb=" CE2 PHE A 374 " pdb=" CZ PHE A 374 " ideal model delta sigma weight residual 1.382 1.344 0.038 3.00e-02 1.11e+03 1.64e+00 ... (remaining 5140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 6842 2.17 - 4.33: 134 4.33 - 6.50: 16 6.50 - 8.67: 4 8.67 - 10.83: 1 Bond angle restraints: 6997 Sorted by residual: angle pdb=" C ASP A 482 " pdb=" CA ASP A 482 " pdb=" CB ASP A 482 " ideal model delta sigma weight residual 109.71 115.06 -5.35 1.39e+00 5.18e-01 1.48e+01 angle pdb=" CG ARG A 191 " pdb=" CD ARG A 191 " pdb=" NE ARG A 191 " ideal model delta sigma weight residual 112.00 119.98 -7.98 2.20e+00 2.07e-01 1.31e+01 angle pdb=" C2 NAG A 501 " pdb=" N2 NAG A 501 " pdb=" C7 NAG A 501 " ideal model delta sigma weight residual 124.56 135.39 -10.83 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CA GLY A 483 " pdb=" C GLY A 483 " pdb=" O GLY A 483 " ideal model delta sigma weight residual 121.87 118.44 3.43 1.02e+00 9.61e-01 1.13e+01 angle pdb=" C ASP A 481 " pdb=" CA ASP A 481 " pdb=" CB ASP A 481 " ideal model delta sigma weight residual 109.46 115.27 -5.81 1.84e+00 2.95e-01 9.98e+00 ... (remaining 6992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.57: 2825 15.57 - 31.14: 207 31.14 - 46.71: 45 46.71 - 62.28: 14 62.28 - 77.85: 6 Dihedral angle restraints: 3097 sinusoidal: 1295 harmonic: 1802 Sorted by residual: dihedral pdb=" CA GLN A 42 " pdb=" C GLN A 42 " pdb=" N ALA A 43 " pdb=" CA ALA A 43 " ideal model delta harmonic sigma weight residual -180.00 -152.55 -27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA CYS A 373 " pdb=" C CYS A 373 " pdb=" N PHE A 374 " pdb=" CA PHE A 374 " ideal model delta harmonic sigma weight residual 180.00 -157.80 -22.20 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA GLU A 98 " pdb=" C GLU A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual 180.00 158.97 21.03 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 3094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 644 0.065 - 0.129: 137 0.129 - 0.194: 12 0.194 - 0.259: 0 0.259 - 0.324: 1 Chirality restraints: 794 Sorted by residual: chirality pdb=" C2 NAG A 501 " pdb=" C1 NAG A 501 " pdb=" C3 NAG A 501 " pdb=" N2 NAG A 501 " both_signs ideal model delta sigma weight residual False -2.49 -2.17 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" C3 BMA C 3 " pdb=" C2 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" O3 BMA C 3 " both_signs ideal model delta sigma weight residual False 2.41 2.21 0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.09 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 791 not shown) Planarity restraints: 896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 237 " -0.011 2.00e-02 2.50e+03 2.14e-02 9.19e+00 pdb=" CG TYR A 237 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR A 237 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TYR A 237 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 237 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 237 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 237 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 237 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 374 " 0.014 2.00e-02 2.50e+03 1.51e-02 4.00e+00 pdb=" CG PHE A 374 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 374 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 374 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 374 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 374 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 374 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 25 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" CD GLU H 25 " -0.034 2.00e-02 2.50e+03 pdb=" OE1 GLU H 25 " 0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU H 25 " 0.012 2.00e-02 2.50e+03 ... (remaining 893 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1553 2.84 - 3.35: 4072 3.35 - 3.87: 8877 3.87 - 4.38: 10198 4.38 - 4.90: 17024 Nonbonded interactions: 41724 Sorted by model distance: nonbonded pdb=" O ASP A 481 " pdb=" OH TYR A 485 " model vdw 2.322 3.040 nonbonded pdb=" O4 NAG C 2 " pdb=" O2 BMA C 3 " model vdw 2.578 2.432 nonbonded pdb=" O5 MAN C 4 " pdb=" O6 MAN C 4 " model vdw 2.582 2.432 nonbonded pdb=" N SER A 177 " pdb=" O SER A 177 " model vdw 2.592 2.496 nonbonded pdb=" N ASP A 466 " pdb=" O ASP A 466 " model vdw 2.593 2.496 ... (remaining 41719 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 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: 6.800 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.030 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 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 : 0.005 0.049 5163 Z= 0.214 Angle : 0.786 10.832 7043 Z= 0.402 Chirality : 0.054 0.324 794 Planarity : 0.005 0.043 891 Dihedral : 12.288 77.845 1933 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.34), residues: 618 helix: -1.73 (0.72), residues: 30 sheet: 0.30 (0.36), residues: 210 loop : -0.40 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 86 TYR 0.050 0.003 TYR A 237 PHE 0.035 0.003 PHE A 374 TRP 0.014 0.002 TRP H 66 HIS 0.007 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 ( 5145) covalent geometry : angle 0.76510 / 0.40 ( 6997) SS BOND : bond 0.00592 / 0.33 ( 8) SS BOND : angle 2.21999 / 1.38 ( 16) hydrogen bonds : bond 0.14938 / 8.93 ( 182) hydrogen bonds : angle 8.81866 / 6.34 ( 492) link_ALPHA1-3 : bond 0.00840 / 0.44 ( 1) link_ALPHA1-3 : angle 1.59457 / 1.02 ( 3) link_ALPHA1-6 : bond 0.01520 / 0.80 ( 1) link_ALPHA1-6 : angle 1.55550 / 0.95 ( 3) link_BETA1-4 : bond 0.00364 / 0.11 ( 3) link_BETA1-4 : angle 2.93183 / 1.73 ( 9) link_NAG-ASN : bond 0.00202 / 0.11 ( 5) link_NAG-ASN : angle 2.43919 / 1.58 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7706 (m-40) cc_final: 0.7148 (t0) REVERT: A 34 ARG cc_start: 0.8689 (ttm170) cc_final: 0.8488 (ttm170) REVERT: A 124 ARG cc_start: 0.8228 (mtm110) cc_final: 0.8023 (mtm110) REVERT: A 191 ARG cc_start: 0.7196 (tpm170) cc_final: 0.6534 (tmt170) REVERT: A 325 ASP cc_start: 0.8247 (t70) cc_final: 0.7894 (t0) REVERT: A 371 TYR cc_start: 0.7446 (m-10) cc_final: 0.7220 (m-10) REVERT: A 454 GLN cc_start: 0.8635 (tt0) cc_final: 0.8299 (tm-30) REVERT: H 21 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7546 (mt-10) REVERT: H 22 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7474 (tttm) REVERT: H 86 ARG cc_start: 0.8573 (mtm110) cc_final: 0.8303 (ttp80) REVERT: L 23 ILE cc_start: 0.8519 (mp) cc_final: 0.8300 (mp) REVERT: L 89 ASN cc_start: 0.7372 (m-40) cc_final: 0.6670 (p0) REVERT: L 128 LEU cc_start: 0.7598 (mt) cc_final: 0.7395 (mp) outliers start: 1 outliers final: 0 residues processed: 114 average time/residue: 0.5374 time to fit residues: 63.8468 Evaluate side-chains 92 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.0010 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 0.0470 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 127 GLN A 270 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.159998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.131774 restraints weight = 4629.411| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.43 r_work: 0.3320 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5163 Z= 0.142 Angle : 0.646 9.597 7043 Z= 0.330 Chirality : 0.048 0.278 794 Planarity : 0.004 0.032 891 Dihedral : 7.085 56.241 888 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.76 % Allowed : 6.48 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.33), residues: 618 helix: -0.90 (0.86), residues: 31 sheet: 0.56 (0.36), residues: 204 loop : -0.36 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 117 TYR 0.021 0.002 TYR A 237 PHE 0.021 0.002 PHE A 374 TRP 0.006 0.001 TRP H 66 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 5145) covalent geometry : angle 0.61846 / 0.32 ( 6997) SS BOND : bond 0.00693 / 0.42 ( 8) SS BOND : angle 2.74268 / 1.95 ( 16) hydrogen bonds : bond 0.04573 / 2.85 ( 182) hydrogen bonds : angle 6.56117 / 4.70 ( 492) link_ALPHA1-3 : bond 0.00977 / 0.51 ( 1) link_ALPHA1-3 : angle 1.28705 / 0.75 ( 3) link_ALPHA1-6 : bond 0.01258 / 0.66 ( 1) link_ALPHA1-6 : angle 1.33353 / 0.83 ( 3) link_BETA1-4 : bond 0.00160 / 0.05 ( 3) link_BETA1-4 : angle 2.56213 / 1.48 ( 9) link_NAG-ASN : bond 0.00200 / 0.10 ( 5) link_NAG-ASN : angle 2.25926 / 1.41 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.130 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7736 (m-40) cc_final: 0.7133 (t0) REVERT: A 55 ILE cc_start: 0.8081 (mm) cc_final: 0.7698 (mm) REVERT: A 191 ARG cc_start: 0.7248 (tpm170) cc_final: 0.6583 (tmt170) REVERT: A 325 ASP cc_start: 0.8249 (t70) cc_final: 0.7880 (t0) REVERT: A 371 TYR cc_start: 0.7397 (m-10) cc_final: 0.7161 (m-10) REVERT: A 379 THR cc_start: 0.6957 (m) cc_final: 0.6658 (p) REVERT: A 454 GLN cc_start: 0.8411 (tt0) cc_final: 0.8206 (tm-30) REVERT: H 21 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7584 (mt-10) REVERT: H 22 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7419 (tttm) REVERT: L 89 ASN cc_start: 0.7372 (m-40) cc_final: 0.6736 (p0) REVERT: L 128 LEU cc_start: 0.7507 (mt) cc_final: 0.7306 (mp) outliers start: 4 outliers final: 2 residues processed: 103 average time/residue: 0.5182 time to fit residues: 55.5790 Evaluate side-chains 93 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 0.0570 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 58 optimal weight: 0.0970 chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.131400 restraints weight = 4623.353| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.44 r_work: 0.3313 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 5163 Z= 0.145 Angle : 0.699 13.469 7043 Z= 0.347 Chirality : 0.049 0.314 794 Planarity : 0.004 0.034 891 Dihedral : 6.865 55.781 888 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.90 % Allowed : 7.43 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.33), residues: 618 helix: -0.74 (0.84), residues: 31 sheet: 0.69 (0.36), residues: 204 loop : -0.34 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 172 TYR 0.015 0.002 TYR A 372 PHE 0.017 0.002 PHE A 374 TRP 0.005 0.001 TRP A 259 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 5145) covalent geometry : angle 0.66720 / 0.34 ( 6997) SS BOND : bond 0.01026 / 0.62 ( 8) SS BOND : angle 3.40248 / 2.73 ( 16) hydrogen bonds : bond 0.04038 / 2.52 ( 182) hydrogen bonds : angle 6.08894 / 4.37 ( 492) link_ALPHA1-3 : bond 0.00919 / 0.48 ( 1) link_ALPHA1-3 : angle 1.30332 / 0.76 ( 3) link_ALPHA1-6 : bond 0.01120 / 0.59 ( 1) link_ALPHA1-6 : angle 1.28820 / 0.81 ( 3) link_BETA1-4 : bond 0.00146 / 0.06 ( 3) link_BETA1-4 : angle 2.51369 / 1.45 ( 9) link_NAG-ASN : bond 0.00226 / 0.14 ( 5) link_NAG-ASN : angle 2.27977 / 1.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7752 (m-40) cc_final: 0.7160 (t0) REVERT: A 122 ARG cc_start: 0.7900 (tpm170) cc_final: 0.7682 (tpm170) REVERT: A 191 ARG cc_start: 0.7261 (tpm170) cc_final: 0.6624 (tmt170) REVERT: A 325 ASP cc_start: 0.8266 (t70) cc_final: 0.7935 (t0) REVERT: A 371 TYR cc_start: 0.7324 (m-10) cc_final: 0.7111 (m-10) REVERT: A 454 GLN cc_start: 0.8381 (tt0) cc_final: 0.8084 (tm-30) REVERT: H 21 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7600 (mt-10) REVERT: H 22 LYS cc_start: 0.7769 (mtpt) cc_final: 0.7417 (tttm) REVERT: L 89 ASN cc_start: 0.7370 (m-40) cc_final: 0.6683 (p0) REVERT: L 128 LEU cc_start: 0.7523 (mt) cc_final: 0.7320 (mp) outliers start: 10 outliers final: 8 residues processed: 97 average time/residue: 0.5281 time to fit residues: 53.4230 Evaluate side-chains 95 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.5980 chunk 54 optimal weight: 0.0040 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.128935 restraints weight = 4606.712| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.43 r_work: 0.3284 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 5163 Z= 0.179 Angle : 0.729 18.791 7043 Z= 0.365 Chirality : 0.051 0.309 794 Planarity : 0.004 0.028 891 Dihedral : 7.015 55.943 888 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.71 % Allowed : 8.95 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.33), residues: 618 helix: -0.59 (0.85), residues: 31 sheet: 0.68 (0.36), residues: 206 loop : -0.32 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 172 TYR 0.015 0.002 TYR A 372 PHE 0.017 0.002 PHE A 374 TRP 0.006 0.001 TRP A 259 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 ( 5145) covalent geometry : angle 0.69905 / 0.36 ( 6997) SS BOND : bond 0.01105 / 0.69 ( 8) SS BOND : angle 3.18613 / 2.61 ( 16) hydrogen bonds : bond 0.04132 / 2.58 ( 182) hydrogen bonds : angle 5.99320 / 4.28 ( 492) link_ALPHA1-3 : bond 0.00738 / 0.39 ( 1) link_ALPHA1-3 : angle 1.40127 / 0.87 ( 3) link_ALPHA1-6 : bond 0.01360 / 0.72 ( 1) link_ALPHA1-6 : angle 1.33949 / 0.83 ( 3) link_BETA1-4 : bond 0.00289 / 0.09 ( 3) link_BETA1-4 : angle 2.77278 / 1.60 ( 9) link_NAG-ASN : bond 0.00191 / 0.10 ( 5) link_NAG-ASN : angle 2.36819 / 1.42 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7785 (m-40) cc_final: 0.7179 (t0) REVERT: A 122 ARG cc_start: 0.7890 (tpm170) cc_final: 0.7650 (tpm170) REVERT: A 191 ARG cc_start: 0.7283 (tpm170) cc_final: 0.6592 (ttt-90) REVERT: A 371 TYR cc_start: 0.7391 (m-10) cc_final: 0.7171 (m-10) REVERT: A 454 GLN cc_start: 0.8417 (tt0) cc_final: 0.8116 (tm-30) REVERT: H 21 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7598 (mt-10) REVERT: H 22 LYS cc_start: 0.7808 (mtpt) cc_final: 0.7418 (tttm) REVERT: L 89 ASN cc_start: 0.7404 (m-40) cc_final: 0.6721 (p0) REVERT: L 128 LEU cc_start: 0.7569 (mt) cc_final: 0.7330 (mp) outliers start: 9 outliers final: 5 residues processed: 86 average time/residue: 0.5314 time to fit residues: 47.6493 Evaluate side-chains 83 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 52 optimal weight: 0.0060 chunk 24 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.159743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.131288 restraints weight = 4760.220| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.46 r_work: 0.3313 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 5163 Z= 0.131 Angle : 0.666 15.977 7043 Z= 0.332 Chirality : 0.048 0.298 794 Planarity : 0.003 0.031 891 Dihedral : 6.664 55.775 888 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.33 % Allowed : 10.10 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.33), residues: 618 helix: -0.51 (0.86), residues: 31 sheet: 0.77 (0.36), residues: 207 loop : -0.34 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 172 TYR 0.011 0.001 TYR A 212 PHE 0.015 0.001 PHE A 374 TRP 0.004 0.001 TRP A 65 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 5145) covalent geometry : angle 0.63774 / 0.32 ( 6997) SS BOND : bond 0.00954 / 0.59 ( 8) SS BOND : angle 3.10338 / 2.35 ( 16) hydrogen bonds : bond 0.03634 / 2.25 ( 182) hydrogen bonds : angle 5.83688 / 4.17 ( 492) link_ALPHA1-3 : bond 0.00974 / 0.51 ( 1) link_ALPHA1-3 : angle 1.19649 / 0.68 ( 3) link_ALPHA1-6 : bond 0.01224 / 0.64 ( 1) link_ALPHA1-6 : angle 1.33818 / 0.84 ( 3) link_BETA1-4 : bond 0.00143 / 0.06 ( 3) link_BETA1-4 : angle 2.37591 / 1.37 ( 9) link_NAG-ASN : bond 0.00190 / 0.11 ( 5) link_NAG-ASN : angle 2.12339 / 1.29 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7773 (m-40) cc_final: 0.7177 (t0) REVERT: A 122 ARG cc_start: 0.7891 (tpm170) cc_final: 0.7628 (tpm170) REVERT: A 191 ARG cc_start: 0.7206 (tpm170) cc_final: 0.6533 (ttt-90) REVERT: A 371 TYR cc_start: 0.7343 (m-10) cc_final: 0.7102 (m-10) REVERT: A 416 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7125 (mt) REVERT: A 454 GLN cc_start: 0.8420 (tt0) cc_final: 0.8189 (tm-30) REVERT: H 21 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7609 (mt-10) REVERT: H 22 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7437 (ttmm) REVERT: L 89 ASN cc_start: 0.7374 (m-40) cc_final: 0.6685 (p0) REVERT: L 128 LEU cc_start: 0.7526 (mt) cc_final: 0.7318 (mp) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.5333 time to fit residues: 47.7591 Evaluate side-chains 90 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 53 optimal weight: 0.3980 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.159257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130708 restraints weight = 4761.249| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.46 r_work: 0.3305 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3191 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 5163 Z= 0.139 Angle : 0.669 18.484 7043 Z= 0.333 Chirality : 0.049 0.311 794 Planarity : 0.004 0.030 891 Dihedral : 6.564 55.755 888 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.33 % Allowed : 10.48 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.34), residues: 618 helix: -0.41 (0.87), residues: 31 sheet: 0.97 (0.37), residues: 201 loop : -0.29 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.015 0.002 TYR H 99 PHE 0.016 0.002 PHE A 374 TRP 0.005 0.001 TRP A 259 HIS 0.004 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 5145) covalent geometry : angle 0.64377 / 0.32 ( 6997) SS BOND : bond 0.01039 / 0.66 ( 8) SS BOND : angle 2.69261 / 2.12 ( 16) hydrogen bonds : bond 0.03675 / 2.29 ( 182) hydrogen bonds : angle 5.79508 / 4.14 ( 492) link_ALPHA1-3 : bond 0.00917 / 0.48 ( 1) link_ALPHA1-3 : angle 1.24556 / 0.72 ( 3) link_ALPHA1-6 : bond 0.01293 / 0.68 ( 1) link_ALPHA1-6 : angle 1.32266 / 0.83 ( 3) link_BETA1-4 : bond 0.00166 / 0.05 ( 3) link_BETA1-4 : angle 2.43443 / 1.40 ( 9) link_NAG-ASN : bond 0.00155 / 0.08 ( 5) link_NAG-ASN : angle 2.18218 / 1.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 82 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7795 (m-40) cc_final: 0.7179 (t0) REVERT: A 122 ARG cc_start: 0.7857 (tpm170) cc_final: 0.7582 (tpm170) REVERT: A 191 ARG cc_start: 0.7220 (tpm170) cc_final: 0.6565 (ttt-90) REVERT: A 416 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7163 (mt) REVERT: A 454 GLN cc_start: 0.8431 (tt0) cc_final: 0.8127 (tm-30) REVERT: H 22 LYS cc_start: 0.7784 (mtpt) cc_final: 0.7403 (ttmm) REVERT: L 89 ASN cc_start: 0.7377 (m-40) cc_final: 0.6716 (p0) REVERT: L 128 LEU cc_start: 0.7525 (mt) cc_final: 0.7303 (mp) outliers start: 7 outliers final: 5 residues processed: 86 average time/residue: 0.5527 time to fit residues: 49.4183 Evaluate side-chains 87 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS L 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128753 restraints weight = 4643.919| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.44 r_work: 0.3285 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 5163 Z= 0.173 Angle : 0.699 18.502 7043 Z= 0.350 Chirality : 0.050 0.334 794 Planarity : 0.004 0.033 891 Dihedral : 6.825 55.376 888 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.14 % Allowed : 10.86 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.34), residues: 618 helix: -0.46 (0.86), residues: 31 sheet: 0.76 (0.36), residues: 208 loop : -0.25 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.015 0.002 TYR A 212 PHE 0.019 0.002 PHE A 374 TRP 0.006 0.001 TRP A 259 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 5145) covalent geometry : angle 0.67343 / 0.34 ( 6997) SS BOND : bond 0.01056 / 0.66 ( 8) SS BOND : angle 2.58011 / 2.06 ( 16) hydrogen bonds : bond 0.04005 / 2.48 ( 182) hydrogen bonds : angle 5.87264 / 4.18 ( 492) link_ALPHA1-3 : bond 0.00801 / 0.42 ( 1) link_ALPHA1-3 : angle 1.35979 / 0.83 ( 3) link_ALPHA1-6 : bond 0.01318 / 0.69 ( 1) link_ALPHA1-6 : angle 1.32633 / 0.83 ( 3) link_BETA1-4 : bond 0.00288 / 0.09 ( 3) link_BETA1-4 : angle 2.68987 / 1.56 ( 9) link_NAG-ASN : bond 0.00214 / 0.12 ( 5) link_NAG-ASN : angle 2.34251 / 1.44 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7779 (m-40) cc_final: 0.7176 (t0) REVERT: A 122 ARG cc_start: 0.7923 (tpm170) cc_final: 0.7650 (tpm170) REVERT: A 191 ARG cc_start: 0.7229 (tpm170) cc_final: 0.6639 (ttt-90) REVERT: A 416 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7023 (mt) REVERT: A 454 GLN cc_start: 0.8425 (tt0) cc_final: 0.8122 (tm-30) REVERT: H 22 LYS cc_start: 0.7851 (mtpt) cc_final: 0.7426 (tttm) REVERT: L 89 ASN cc_start: 0.7399 (m-40) cc_final: 0.6707 (p0) REVERT: L 128 LEU cc_start: 0.7601 (mt) cc_final: 0.7355 (mp) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.5439 time to fit residues: 49.2213 Evaluate side-chains 88 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 19 optimal weight: 0.0770 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS L 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.129321 restraints weight = 4655.089| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.44 r_work: 0.3290 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 5163 Z= 0.163 Angle : 0.700 18.431 7043 Z= 0.350 Chirality : 0.050 0.328 794 Planarity : 0.004 0.031 891 Dihedral : 6.847 55.496 888 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.14 % Allowed : 11.05 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.34), residues: 618 helix: -0.38 (0.87), residues: 31 sheet: 0.80 (0.36), residues: 208 loop : -0.28 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 172 TYR 0.014 0.002 TYR A 212 PHE 0.017 0.002 PHE A 374 TRP 0.006 0.001 TRP A 259 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5145) covalent geometry : angle 0.66765 / 0.34 ( 6997) SS BOND : bond 0.01058 / 0.66 ( 8) SS BOND : angle 3.28180 / 2.33 ( 16) hydrogen bonds : bond 0.03889 / 2.40 ( 182) hydrogen bonds : angle 5.81290 / 4.14 ( 492) link_ALPHA1-3 : bond 0.00848 / 0.45 ( 1) link_ALPHA1-3 : angle 1.27981 / 0.76 ( 3) link_ALPHA1-6 : bond 0.01250 / 0.66 ( 1) link_ALPHA1-6 : angle 1.33079 / 0.84 ( 3) link_BETA1-4 : bond 0.00240 / 0.07 ( 3) link_BETA1-4 : angle 2.62060 / 1.52 ( 9) link_NAG-ASN : bond 0.00389 / 0.24 ( 5) link_NAG-ASN : angle 2.39312 / 1.48 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.213 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7775 (m-40) cc_final: 0.7169 (t0) REVERT: A 122 ARG cc_start: 0.7938 (tpm170) cc_final: 0.7657 (tpm170) REVERT: A 191 ARG cc_start: 0.7231 (tpm170) cc_final: 0.6656 (ttt-90) REVERT: A 416 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.6993 (mt) REVERT: A 454 GLN cc_start: 0.8429 (tt0) cc_final: 0.8126 (tm-30) REVERT: H 22 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7617 (ttmt) REVERT: L 89 ASN cc_start: 0.7400 (m-40) cc_final: 0.6707 (p0) REVERT: L 128 LEU cc_start: 0.7602 (mt) cc_final: 0.7361 (mp) outliers start: 6 outliers final: 5 residues processed: 87 average time/residue: 0.5420 time to fit residues: 49.0791 Evaluate side-chains 89 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS L 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.157985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.129446 restraints weight = 4677.983| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.45 r_work: 0.3291 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 5163 Z= 0.162 Angle : 0.691 18.283 7043 Z= 0.346 Chirality : 0.050 0.329 794 Planarity : 0.004 0.032 891 Dihedral : 6.820 55.290 888 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.33 % Allowed : 10.86 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.34), residues: 618 helix: -0.33 (0.88), residues: 31 sheet: 0.84 (0.36), residues: 208 loop : -0.33 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 172 TYR 0.015 0.002 TYR A 212 PHE 0.017 0.002 PHE A 374 TRP 0.006 0.001 TRP A 259 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 5145) covalent geometry : angle 0.66149 / 0.34 ( 6997) SS BOND : bond 0.01023 / 0.64 ( 8) SS BOND : angle 3.04319 / 2.24 ( 16) hydrogen bonds : bond 0.03899 / 2.42 ( 182) hydrogen bonds : angle 5.79878 / 4.13 ( 492) link_ALPHA1-3 : bond 0.00843 / 0.44 ( 1) link_ALPHA1-3 : angle 1.29072 / 0.76 ( 3) link_ALPHA1-6 : bond 0.01320 / 0.69 ( 1) link_ALPHA1-6 : angle 1.33347 / 0.83 ( 3) link_BETA1-4 : bond 0.00255 / 0.08 ( 3) link_BETA1-4 : angle 2.62770 / 1.52 ( 9) link_NAG-ASN : bond 0.00307 / 0.19 ( 5) link_NAG-ASN : angle 2.37247 / 1.43 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.206 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7784 (m-40) cc_final: 0.7181 (t0) REVERT: A 191 ARG cc_start: 0.7231 (tpm170) cc_final: 0.6662 (ttt-90) REVERT: A 416 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.6993 (mt) REVERT: A 454 GLN cc_start: 0.8426 (tt0) cc_final: 0.8123 (tm-30) REVERT: H 22 LYS cc_start: 0.7885 (mtpt) cc_final: 0.7616 (ttmt) REVERT: H 102 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8169 (mtm) REVERT: L 89 ASN cc_start: 0.7410 (m-40) cc_final: 0.6730 (p0) REVERT: L 128 LEU cc_start: 0.7609 (mt) cc_final: 0.7362 (mp) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 0.5559 time to fit residues: 50.3333 Evaluate side-chains 91 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.0050 chunk 47 optimal weight: 0.6980 chunk 24 optimal weight: 0.0970 chunk 11 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS L 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.129196 restraints weight = 4675.595| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.45 r_work: 0.3288 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 5163 Z= 0.165 Angle : 0.692 18.299 7043 Z= 0.347 Chirality : 0.050 0.332 794 Planarity : 0.004 0.031 891 Dihedral : 6.852 55.245 888 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.33 % Allowed : 11.05 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.34), residues: 618 helix: -0.36 (0.87), residues: 31 sheet: 0.69 (0.36), residues: 216 loop : -0.29 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 172 TYR 0.014 0.002 TYR H 99 PHE 0.018 0.002 PHE A 374 TRP 0.006 0.001 TRP A 259 HIS 0.005 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 5145) covalent geometry : angle 0.66381 / 0.34 ( 6997) SS BOND : bond 0.01023 / 0.65 ( 8) SS BOND : angle 2.85347 / 2.13 ( 16) hydrogen bonds : bond 0.03928 / 2.44 ( 182) hydrogen bonds : angle 5.80096 / 4.13 ( 492) link_ALPHA1-3 : bond 0.00851 / 0.45 ( 1) link_ALPHA1-3 : angle 1.28872 / 0.76 ( 3) link_ALPHA1-6 : bond 0.01272 / 0.67 ( 1) link_ALPHA1-6 : angle 1.33072 / 0.83 ( 3) link_BETA1-4 : bond 0.00262 / 0.08 ( 3) link_BETA1-4 : angle 2.66144 / 1.54 ( 9) link_NAG-ASN : bond 0.00336 / 0.21 ( 5) link_NAG-ASN : angle 2.39171 / 1.44 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 29 ASN cc_start: 0.7789 (m-40) cc_final: 0.7181 (t0) REVERT: A 122 ARG cc_start: 0.7857 (tpt170) cc_final: 0.7632 (tpt170) REVERT: A 191 ARG cc_start: 0.7229 (tpm170) cc_final: 0.6659 (ttt-90) REVERT: A 416 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7000 (mt) REVERT: A 454 GLN cc_start: 0.8424 (tt0) cc_final: 0.8119 (tm-30) REVERT: H 22 LYS cc_start: 0.7905 (mtpt) cc_final: 0.7629 (ttmt) REVERT: H 102 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8149 (mtm) REVERT: L 89 ASN cc_start: 0.7420 (m-40) cc_final: 0.6723 (p0) REVERT: L 128 LEU cc_start: 0.7617 (mt) cc_final: 0.7367 (mp) outliers start: 7 outliers final: 5 residues processed: 88 average time/residue: 0.5404 time to fit residues: 49.5099 Evaluate side-chains 90 residues out of total 525 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 416 LEU Chi-restraints excluded: chain A residue 479 ASP Chi-restraints excluded: chain H residue 44 SER Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain L residue 83 SER Chi-restraints excluded: chain L residue 126 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 26 optimal weight: 4.9990 chunk 31 optimal weight: 0.3980 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 0.2980 chunk 59 optimal weight: 7.9990 chunk 10 optimal weight: 4.9990 chunk 41 optimal weight: 0.1980 chunk 33 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS L 99 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.133747 restraints weight = 4797.209| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.47 r_work: 0.3344 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 5163 Z= 0.109 Angle : 0.625 16.822 7043 Z= 0.311 Chirality : 0.048 0.286 794 Planarity : 0.003 0.029 891 Dihedral : 6.241 55.765 888 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.14 % Allowed : 11.62 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.34), residues: 618 helix: -0.23 (0.90), residues: 31 sheet: 0.73 (0.36), residues: 209 loop : -0.31 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 172 TYR 0.016 0.001 TYR H 99 PHE 0.011 0.001 PHE A 150 TRP 0.005 0.001 TRP L 55 HIS 0.002 0.000 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 5145) covalent geometry : angle 0.60182 / 0.30 ( 6997) SS BOND : bond 0.00810 / 0.53 ( 8) SS BOND : angle 2.59611 / 1.97 ( 16) hydrogen bonds : bond 0.03349 / 2.07 ( 182) hydrogen bonds : angle 5.57385 / 4.00 ( 492) link_ALPHA1-3 : bond 0.01065 / 0.56 ( 1) link_ALPHA1-3 : angle 1.05426 / 0.51 ( 3) link_ALPHA1-6 : bond 0.01242 / 0.65 ( 1) link_ALPHA1-6 : angle 1.37074 / 0.85 ( 3) link_BETA1-4 : bond 0.00197 / 0.10 ( 3) link_BETA1-4 : angle 2.07486 / 1.19 ( 9) link_NAG-ASN : bond 0.00303 / 0.19 ( 5) link_NAG-ASN : angle 2.05934 / 1.22 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2425.10 seconds wall clock time: 42 minutes 29.15 seconds (2549.15 seconds total)