Starting phenix.real_space_refine on Fri Jul 3 02:59:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dhm_27436/07_2026/8dhm_27436_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dhm_27436/07_2026/8dhm_27436.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dhm_27436/07_2026/8dhm_27436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dhm_27436/07_2026/8dhm_27436.map" model { file = "/net/cci-nas-00/data/ceres_data/8dhm_27436/07_2026/8dhm_27436_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dhm_27436/07_2026/8dhm_27436_trim.cif" } resolution = 2.73 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= 0.030 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: 6 Type Number sf(0) Gaussians K 4 8.98 5 S 38 5.16 5 C 3759 2.51 5 N 940 2.21 5 O 1057 1.98 5 H 5900 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11698 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5798 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Ad-hoc single atom residues: {' K': 2} Unusual residues: {'4AP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' K': 2} Chain breaks: 2 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Time building chain proxies: 2.25, per 1000 atoms: 0.19 Number of scatterers: 11698 At special positions: 0 Unit cell: (104.55, 70.55, 80.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 4 19.00 S 38 16.00 O 1057 8.00 N 940 7.00 C 3759 6.00 H 5900 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 285.5 milliseconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 4 sheets defined 89.6% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.197A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 102 removed outlier: 3.517A pdb=" N ASP B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG B 68 " --> pdb=" O GLN B 64 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 74 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 137 through 164 Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 173 Processing helix chain 'B' and resid 257 through 284 removed outlier: 5.135A pdb=" N LEU B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 333 removed outlier: 3.570A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 354 through 362 Processing helix chain 'B' and resid 368 through 398 removed outlier: 3.514A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP B 394 " --> pdb=" O GLN B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 5.257A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.560A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.197A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 102 removed outlier: 3.517A pdb=" N ASP A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ARG A 68 " --> pdb=" O GLN A 64 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N SER A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 137 through 164 Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 173 Processing helix chain 'A' and resid 257 through 284 removed outlier: 5.134A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ILE A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 333 removed outlier: 3.569A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 368 through 398 removed outlier: 3.513A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 5.256A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.560A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'B' and resid 255 through 256 removed outlier: 3.830A pdb=" N ALA B 337 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.831A pdb=" N ALA A 337 " --> pdb=" O LEU A 256 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1368 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: 2.23 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5882 1.03 - 1.22: 18 1.22 - 1.42: 2386 1.42 - 1.61: 3393 1.61 - 1.81: 58 Bond restraints: 11737 Sorted by residual: bond pdb=" C4 4AP B 703 " pdb=" N4 4AP B 703 " ideal model delta sigma weight residual 1.324 1.445 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C4 4AP B 703 " pdb=" C5 4AP B 703 " ideal model delta sigma weight residual 1.417 1.349 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C3 4AP B 703 " pdb=" C4 4AP B 703 " ideal model delta sigma weight residual 1.416 1.350 0.066 2.00e-02 2.50e+03 1.10e+01 bond pdb=" NH2 ARG A 97 " pdb="HH22 ARG A 97 " ideal model delta sigma weight residual 0.860 0.925 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" NH2 ARG B 97 " pdb="HH21 ARG B 97 " ideal model delta sigma weight residual 0.860 0.910 -0.050 2.00e-02 2.50e+03 6.28e+00 ... (remaining 11732 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.75: 21239 4.75 - 9.49: 19 9.49 - 14.24: 9 14.24 - 18.99: 3 18.99 - 23.73: 2 Bond angle restraints: 21272 Sorted by residual: angle pdb=" CG ARG A 97 " pdb=" CD ARG A 97 " pdb=" HD3 ARG A 97 " ideal model delta sigma weight residual 109.00 85.27 23.73 3.00e+00 1.11e-01 6.26e+01 angle pdb=" NE ARG A 97 " pdb=" CD ARG A 97 " pdb=" HD3 ARG A 97 " ideal model delta sigma weight residual 108.00 84.85 23.15 3.00e+00 1.11e-01 5.95e+01 angle pdb=" CB ARG A 97 " pdb=" CG ARG A 97 " pdb=" CD ARG A 97 " ideal model delta sigma weight residual 111.30 93.97 17.33 2.30e+00 1.89e-01 5.67e+01 angle pdb=" CB ARG B 97 " pdb=" CG ARG B 97 " pdb=" CD ARG B 97 " ideal model delta sigma weight residual 111.30 93.99 17.31 2.30e+00 1.89e-01 5.67e+01 angle pdb=" CG ARG B 97 " pdb=" CD ARG B 97 " pdb=" NE ARG B 97 " ideal model delta sigma weight residual 112.00 126.07 -14.07 2.20e+00 2.07e-01 4.09e+01 ... (remaining 21267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 4963 14.97 - 29.95: 402 29.95 - 44.92: 92 44.92 - 59.89: 59 59.89 - 74.87: 8 Dihedral angle restraints: 5524 sinusoidal: 2932 harmonic: 2592 Sorted by residual: dihedral pdb=" CA PHE A 99 " pdb=" C PHE A 99 " pdb=" N GLN A 100 " pdb=" CA GLN A 100 " ideal model delta harmonic sigma weight residual 180.00 154.72 25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA PHE B 99 " pdb=" C PHE B 99 " pdb=" N GLN B 100 " pdb=" CA GLN B 100 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA GLU B 282 " pdb=" C GLU B 282 " pdb=" N ASP B 283 " pdb=" CA ASP B 283 " ideal model delta harmonic sigma weight residual -180.00 -164.27 -15.73 0 5.00e+00 4.00e-02 9.89e+00 ... (remaining 5521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 555 0.030 - 0.061: 271 0.061 - 0.091: 106 0.091 - 0.121: 41 0.121 - 0.151: 5 Chirality restraints: 978 Sorted by residual: chirality pdb=" CB THR B 96 " pdb=" CA THR B 96 " pdb=" OG1 THR B 96 " pdb=" CG2 THR B 96 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.72e-01 chirality pdb=" CB THR A 96 " pdb=" CA THR A 96 " pdb=" OG1 THR A 96 " pdb=" CG2 THR A 96 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 60 " pdb=" N ILE B 60 " pdb=" C ILE B 60 " pdb=" CB ILE B 60 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 975 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 97 " -0.531 9.50e-02 1.11e+02 1.79e-01 4.23e+01 pdb=" NE ARG B 97 " 0.003 2.00e-02 2.50e+03 pdb=" CZ ARG B 97 " 0.047 2.00e-02 2.50e+03 pdb=" NH1 ARG B 97 " 0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG B 97 " 0.013 2.00e-02 2.50e+03 pdb="HH11 ARG B 97 " -0.012 2.00e-02 2.50e+03 pdb="HH12 ARG B 97 " -0.015 2.00e-02 2.50e+03 pdb="HH21 ARG B 97 " -0.007 2.00e-02 2.50e+03 pdb="HH22 ARG B 97 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 97 " 0.498 9.50e-02 1.11e+02 1.68e-01 3.81e+01 pdb=" NE ARG A 97 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 97 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 97 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 97 " 0.032 2.00e-02 2.50e+03 pdb="HH11 ARG A 97 " 0.012 2.00e-02 2.50e+03 pdb="HH12 ARG A 97 " -0.011 2.00e-02 2.50e+03 pdb="HH21 ARG A 97 " -0.031 2.00e-02 2.50e+03 pdb="HH22 ARG A 97 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 452 " 0.005 2.00e-02 2.50e+03 1.57e-02 3.69e+00 pdb=" CD GLN A 452 " -0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 452 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 GLN A 452 " 0.029 2.00e-02 2.50e+03 pdb="HE21 GLN A 452 " -0.011 2.00e-02 2.50e+03 pdb="HE22 GLN A 452 " -0.007 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.29: 1897 2.29 - 3.00: 32599 3.00 - 3.71: 44714 3.71 - 4.43: 66814 4.43 - 5.14: 103973 Nonbonded interactions: 249997 Sorted by model distance: nonbonded pdb="HH12 ARG B 77 " pdb=" O HOH B 802 " model vdw 1.572 2.450 nonbonded pdb="HH12 ARG A 77 " pdb=" O HOH A 802 " model vdw 1.573 2.450 nonbonded pdb=" H GLN A 452 " pdb="HE21 GLN A 452 " model vdw 1.595 2.100 nonbonded pdb=" H GLN B 452 " pdb="HE22 GLN B 452 " model vdw 1.602 2.100 nonbonded pdb=" OD1 ASP B 106 " pdb=" H LEU B 109 " model vdw 1.745 2.450 ... (remaining 249992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 30 through 702) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.100 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.960 Find NCS groups from input model: 0.140 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:6.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.006 0.121 5837 Z= 0.260 Angle : 0.762 17.325 7954 Z= 0.412 Chirality : 0.042 0.151 978 Planarity : 0.011 0.219 975 Dihedral : 12.980 74.866 2034 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.65 % Allowed : 0.65 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.33), residues: 726 helix: 0.68 (0.22), residues: 606 sheet: None (None), residues: 0 loop : 0.07 (0.65), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG B 97 TYR 0.013 0.002 TYR A 359 PHE 0.013 0.001 PHE B 99 TRP 0.017 0.003 TRP B 394 HIS 0.007 0.002 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.26 ( 5837) covalent geometry : angle 0.76218 / 0.41 ( 7954) hydrogen bonds : bond 0.15573 / 10.68 ( 468) hydrogen bonds : angle 6.60180 / 4.80 ( 1368) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 116 average time/residue: 1.1800 time to fit residues: 143.2679 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.1980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3506 r_free = 0.3506 target = 0.100515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.076066 restraints weight = 27431.167| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.32 r_work: 0.2997 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5837 Z= 0.161 Angle : 0.573 4.623 7954 Z= 0.305 Chirality : 0.038 0.137 978 Planarity : 0.005 0.047 975 Dihedral : 4.138 26.589 780 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.49 % Allowed : 8.25 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.33), residues: 726 helix: 1.76 (0.22), residues: 612 sheet: None (None), residues: 0 loop : 0.28 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 474 TYR 0.010 0.001 TYR B 359 PHE 0.013 0.001 PHE B 99 TRP 0.014 0.002 TRP B 394 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 ( 5837) covalent geometry : angle 0.57317 / 0.30 ( 7954) hydrogen bonds : bond 0.05626 / 3.82 ( 468) hydrogen bonds : angle 4.36695 / 3.20 ( 1368) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.8019 (mmt) cc_final: 0.7666 (mmt) outliers start: 3 outliers final: 1 residues processed: 68 average time/residue: 1.3993 time to fit residues: 98.9469 Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 0.0970 chunk 6 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.098519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.075346 restraints weight = 27873.603| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.22 r_work: 0.2978 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5837 Z= 0.147 Angle : 0.510 4.438 7954 Z= 0.271 Chirality : 0.037 0.134 978 Planarity : 0.004 0.049 975 Dihedral : 4.012 25.267 780 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.16 % Allowed : 9.22 % Favored : 90.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.81 (0.33), residues: 726 helix: 2.16 (0.22), residues: 612 sheet: None (None), residues: 0 loop : 0.32 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 97 TYR 0.008 0.001 TYR B 359 PHE 0.013 0.001 PHE B 99 TRP 0.013 0.002 TRP B 394 HIS 0.007 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 5837) covalent geometry : angle 0.51008 / 0.27 ( 7954) hydrogen bonds : bond 0.05255 / 3.56 ( 468) hydrogen bonds : angle 4.10229 / 3.01 ( 1368) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7463 (pp20) cc_final: 0.7250 (pp20) REVERT: A 59 GLU cc_start: 0.7476 (pp20) cc_final: 0.7264 (pp20) REVERT: A 289 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8585 (mmmt) REVERT: A 293 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8043 (mp0) REVERT: A 403 GLU cc_start: 0.8743 (mp0) cc_final: 0.8524 (mp0) REVERT: A 451 MET cc_start: 0.8170 (mmt) cc_final: 0.7871 (mmt) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 1.4547 time to fit residues: 95.1933 Evaluate side-chains 56 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3449 r_free = 0.3449 target = 0.096910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073432 restraints weight = 27853.855| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.25 r_work: 0.2916 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5837 Z= 0.167 Angle : 0.514 4.551 7954 Z= 0.273 Chirality : 0.037 0.133 978 Planarity : 0.006 0.081 975 Dihedral : 4.007 25.197 780 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 8.90 % Favored : 90.61 % 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: 3.12 (0.32), residues: 726 helix: 2.40 (0.22), residues: 610 sheet: None (None), residues: 0 loop : 0.23 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 68 TYR 0.009 0.001 TYR B 359 PHE 0.012 0.001 PHE B 99 TRP 0.012 0.002 TRP B 394 HIS 0.007 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 5837) covalent geometry : angle 0.51402 / 0.27 ( 7954) hydrogen bonds : bond 0.05056 / 3.42 ( 468) hydrogen bonds : angle 3.92705 / 2.88 ( 1368) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7512 (pp20) cc_final: 0.7161 (pp20) REVERT: B 289 LYS cc_start: 0.8999 (mmmt) cc_final: 0.8626 (mmmt) REVERT: B 293 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8354 (mp0) REVERT: A 59 GLU cc_start: 0.7487 (pp20) cc_final: 0.7143 (pp20) REVERT: A 293 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8328 (mm-30) REVERT: A 370 ARG cc_start: 0.7321 (tpp-160) cc_final: 0.7109 (tpp-160) REVERT: A 403 GLU cc_start: 0.8690 (mp0) cc_final: 0.8441 (mp0) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 1.2636 time to fit residues: 81.5572 Evaluate side-chains 57 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.096778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.073500 restraints weight = 28046.629| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.24 r_work: 0.2934 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5837 Z= 0.154 Angle : 0.502 5.725 7954 Z= 0.265 Chirality : 0.037 0.130 978 Planarity : 0.005 0.052 975 Dihedral : 3.922 24.911 780 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.81 % Allowed : 8.90 % Favored : 90.29 % 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: 3.30 (0.32), residues: 726 helix: 2.54 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.22 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.008 0.001 TYR A 359 PHE 0.014 0.001 PHE A 365 TRP 0.012 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 ( 5837) covalent geometry : angle 0.50195 / 0.26 ( 7954) hydrogen bonds : bond 0.05027 / 3.38 ( 468) hydrogen bonds : angle 3.91710 / 2.88 ( 1368) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7497 (pp20) cc_final: 0.7173 (pp20) REVERT: B 259 GLU cc_start: 0.8177 (mp0) cc_final: 0.7947 (mp0) REVERT: A 59 GLU cc_start: 0.7490 (pp20) cc_final: 0.7164 (pp20) REVERT: A 259 GLU cc_start: 0.8160 (mp0) cc_final: 0.7920 (mp0) REVERT: A 403 GLU cc_start: 0.8730 (mp0) cc_final: 0.8451 (mp0) outliers start: 5 outliers final: 0 residues processed: 56 average time/residue: 1.2859 time to fit residues: 75.0342 Evaluate side-chains 54 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.096773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.073799 restraints weight = 28251.183| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.20 r_work: 0.2917 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5837 Z= 0.157 Angle : 0.500 4.646 7954 Z= 0.263 Chirality : 0.037 0.135 978 Planarity : 0.004 0.050 975 Dihedral : 3.896 24.746 780 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.65 % Allowed : 9.71 % Favored : 89.64 % 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: 3.36 (0.32), residues: 726 helix: 2.59 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.14 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 68 TYR 0.008 0.001 TYR B 359 PHE 0.013 0.001 PHE A 99 TRP 0.011 0.002 TRP B 394 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 5837) covalent geometry : angle 0.49953 / 0.26 ( 7954) hydrogen bonds : bond 0.04883 / 3.28 ( 468) hydrogen bonds : angle 3.82593 / 2.82 ( 1368) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7526 (pp20) cc_final: 0.7267 (pp20) REVERT: B 259 GLU cc_start: 0.8122 (mp0) cc_final: 0.7872 (mp0) REVERT: B 289 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8565 (mmmt) REVERT: B 293 GLU cc_start: 0.8505 (mm-30) cc_final: 0.8265 (mp0) REVERT: A 59 GLU cc_start: 0.7521 (pp20) cc_final: 0.7188 (pp20) REVERT: A 259 GLU cc_start: 0.8092 (mp0) cc_final: 0.7838 (mp0) REVERT: A 289 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8528 (mmmt) REVERT: A 293 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8205 (mp0) REVERT: A 403 GLU cc_start: 0.8713 (mp0) cc_final: 0.8430 (mp0) outliers start: 4 outliers final: 0 residues processed: 55 average time/residue: 1.2254 time to fit residues: 70.3420 Evaluate side-chains 50 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.095558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.072567 restraints weight = 28306.475| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.25 r_work: 0.2906 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5837 Z= 0.140 Angle : 0.481 4.148 7954 Z= 0.253 Chirality : 0.036 0.126 978 Planarity : 0.004 0.050 975 Dihedral : 3.868 24.309 780 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.81 % Allowed : 8.90 % Favored : 90.29 % 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: 3.50 (0.32), residues: 726 helix: 2.69 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.15 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.007 0.001 TYR B 359 PHE 0.020 0.001 PHE A 365 TRP 0.012 0.002 TRP B 394 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 5837) covalent geometry : angle 0.48136 / 0.25 ( 7954) hydrogen bonds : bond 0.04663 / 3.13 ( 468) hydrogen bonds : angle 3.75045 / 2.76 ( 1368) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7516 (pp20) cc_final: 0.7260 (pp20) REVERT: B 259 GLU cc_start: 0.8071 (mp0) cc_final: 0.7812 (mp0) REVERT: B 289 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8598 (mmmt) REVERT: B 293 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8259 (mp0) REVERT: A 59 GLU cc_start: 0.7517 (pp20) cc_final: 0.7175 (pp20) REVERT: A 259 GLU cc_start: 0.8061 (mp0) cc_final: 0.7806 (mp0) REVERT: A 289 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8551 (mmmt) REVERT: A 293 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8170 (mp0) REVERT: A 403 GLU cc_start: 0.8692 (mp0) cc_final: 0.8487 (mp0) outliers start: 5 outliers final: 0 residues processed: 56 average time/residue: 1.3519 time to fit residues: 78.9239 Evaluate side-chains 52 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 0.0570 chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.074006 restraints weight = 28261.524| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.23 r_work: 0.2913 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5837 Z= 0.108 Angle : 0.463 4.391 7954 Z= 0.241 Chirality : 0.036 0.131 978 Planarity : 0.004 0.049 975 Dihedral : 3.805 23.867 780 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.32 % Allowed : 9.71 % Favored : 89.97 % 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: 3.75 (0.32), residues: 726 helix: 2.85 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.29 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 68 TYR 0.007 0.001 TYR A 313 PHE 0.011 0.001 PHE B 99 TRP 0.012 0.001 TRP B 394 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 5837) covalent geometry : angle 0.46270 / 0.24 ( 7954) hydrogen bonds : bond 0.04239 / 2.85 ( 468) hydrogen bonds : angle 3.62684 / 2.67 ( 1368) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7533 (pp20) cc_final: 0.7251 (pp20) REVERT: B 259 GLU cc_start: 0.8074 (mp0) cc_final: 0.7833 (mp0) REVERT: B 289 LYS cc_start: 0.8976 (mmmt) cc_final: 0.8592 (mmmt) REVERT: B 293 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8237 (mp0) REVERT: A 59 GLU cc_start: 0.7528 (pp20) cc_final: 0.7165 (pp20) REVERT: A 259 GLU cc_start: 0.8049 (mp0) cc_final: 0.7794 (mp0) REVERT: A 403 GLU cc_start: 0.8693 (mp0) cc_final: 0.8423 (mp0) outliers start: 2 outliers final: 0 residues processed: 57 average time/residue: 1.3920 time to fit residues: 82.8449 Evaluate side-chains 54 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.072457 restraints weight = 27790.722| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 2.20 r_work: 0.2925 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5837 Z= 0.173 Angle : 0.495 5.579 7954 Z= 0.260 Chirality : 0.037 0.127 978 Planarity : 0.004 0.049 975 Dihedral : 3.821 23.871 780 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.32 % Allowed : 9.71 % Favored : 89.97 % 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: 3.69 (0.32), residues: 726 helix: 2.79 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.36 (0.66), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.008 0.001 TYR A 359 PHE 0.021 0.001 PHE B 365 TRP 0.009 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 5837) covalent geometry : angle 0.49484 / 0.26 ( 7954) hydrogen bonds : bond 0.04690 / 3.16 ( 468) hydrogen bonds : angle 3.66994 / 2.70 ( 1368) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7588 (pp20) cc_final: 0.7327 (pp20) REVERT: B 259 GLU cc_start: 0.8447 (mp0) cc_final: 0.8226 (mp0) REVERT: B 419 MET cc_start: 0.8964 (tpp) cc_final: 0.8534 (tpt) REVERT: A 59 GLU cc_start: 0.7573 (pp20) cc_final: 0.7331 (pp20) REVERT: A 259 GLU cc_start: 0.8436 (mp0) cc_final: 0.8217 (mp0) REVERT: A 289 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8522 (mmmt) REVERT: A 292 LYS cc_start: 0.9270 (ttmm) cc_final: 0.8957 (ttmm) REVERT: A 293 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8060 (mp0) REVERT: A 403 GLU cc_start: 0.8824 (mp0) cc_final: 0.8579 (mp0) REVERT: A 419 MET cc_start: 0.8970 (tpp) cc_final: 0.8538 (tpt) outliers start: 2 outliers final: 0 residues processed: 56 average time/residue: 1.3144 time to fit residues: 76.8733 Evaluate side-chains 54 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 41 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 32 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.072663 restraints weight = 27958.949| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.30 r_work: 0.2931 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5837 Z= 0.125 Angle : 0.486 5.966 7954 Z= 0.254 Chirality : 0.036 0.129 978 Planarity : 0.004 0.048 975 Dihedral : 3.806 23.986 780 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % 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: 3.78 (0.32), residues: 726 helix: 2.86 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.42 (0.67), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 68 TYR 0.008 0.001 TYR B 359 PHE 0.012 0.001 PHE B 99 TRP 0.012 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 ( 5837) covalent geometry : angle 0.48642 / 0.25 ( 7954) hydrogen bonds : bond 0.04399 / 2.96 ( 468) hydrogen bonds : angle 3.62456 / 2.67 ( 1368) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7601 (pp20) cc_final: 0.7330 (pp20) REVERT: B 259 GLU cc_start: 0.8459 (mp0) cc_final: 0.8246 (mp0) REVERT: B 289 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8552 (mmmt) REVERT: B 293 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8096 (mp0) REVERT: B 419 MET cc_start: 0.8959 (tpp) cc_final: 0.8533 (tpt) REVERT: A 59 GLU cc_start: 0.7576 (pp20) cc_final: 0.7307 (pp20) REVERT: A 259 GLU cc_start: 0.8442 (mp0) cc_final: 0.8230 (mp0) REVERT: A 289 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8514 (mmmt) REVERT: A 292 LYS cc_start: 0.9273 (ttmm) cc_final: 0.8954 (ttmm) REVERT: A 293 GLU cc_start: 0.8277 (mm-30) cc_final: 0.8068 (mp0) REVERT: A 403 GLU cc_start: 0.8835 (mp0) cc_final: 0.8592 (mp0) REVERT: A 419 MET cc_start: 0.8966 (tpp) cc_final: 0.8541 (tpt) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 1.3673 time to fit residues: 80.0034 Evaluate side-chains 54 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.3980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN A 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.094795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.072441 restraints weight = 27753.411| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.14 r_work: 0.2934 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5837 Z= 0.146 Angle : 0.490 4.924 7954 Z= 0.255 Chirality : 0.036 0.127 978 Planarity : 0.004 0.048 975 Dihedral : 3.796 23.863 780 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.16 % Allowed : 10.36 % Favored : 89.48 % 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: 3.77 (0.32), residues: 726 helix: 2.85 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.36 (0.66), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 68 TYR 0.008 0.001 TYR B 359 PHE 0.025 0.001 PHE A 365 TRP 0.010 0.001 TRP B 394 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5837) covalent geometry : angle 0.48950 / 0.26 ( 7954) hydrogen bonds : bond 0.04495 / 3.03 ( 468) hydrogen bonds : angle 3.62269 / 2.67 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3916.01 seconds wall clock time: 66 minutes 58.90 seconds (4018.90 seconds total)