Starting phenix.real_space_refine on Wed Mar 4 07:13:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dhm_27436/03_2026/8dhm_27436_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dhm_27436/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dhm_27436/03_2026/8dhm_27436_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dhm_27436/03_2026/8dhm_27436_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dhm_27436/03_2026/8dhm_27436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dhm_27436/03_2026/8dhm_27436.map" } 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-5986/lib/python3.9/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, 9 Unusual residues: {' K': 2, '4AP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 2.42, per 1000 atoms: 0.21 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: 0.98 Conformation dependent library (CDL) restraints added in 331.2 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: 0.28 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: 2.41 Time building geometry restraints manager: 1.37 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: 4.380 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: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.830 Find NCS groups from input model: 0.130 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 covalent geometry : bond 0.00606 ( 5837) covalent geometry : angle 0.76218 ( 7954) hydrogen bonds : bond 0.15573 ( 468) hydrogen bonds : angle 6.60180 ( 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 : 0.316 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: 1.2793 time to fit residues: 154.5857 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 : 0.224 ------------------------------------------------------------------------------- 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: 0.4980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.100637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.076220 restraints weight = 27135.693| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.29 r_work: 0.3000 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2336 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= 0.158 Angle : 0.565 4.603 7954 Z= 0.299 Chirality : 0.038 0.137 978 Planarity : 0.005 0.052 975 Dihedral : 4.129 26.543 780 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.16 % Allowed : 9.39 % Favored : 90.45 % 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: 2.24 (0.33), residues: 726 helix: 1.74 (0.22), residues: 612 sheet: None (None), residues: 0 loop : 0.30 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 474 TYR 0.011 0.001 TYR B 359 PHE 0.012 0.001 PHE B 99 TRP 0.014 0.002 TRP A 394 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 5837) covalent geometry : angle 0.56534 ( 7954) hydrogen bonds : bond 0.05803 ( 468) hydrogen bonds : angle 4.40461 ( 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 68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.271 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: 0.8009 (mmt) cc_final: 0.7624 (mmt) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 1.5994 time to fit residues: 110.9371 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 : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.099071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.075400 restraints weight = 27491.028| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.22 r_work: 0.2957 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2834 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= 0.159 Angle : 0.513 4.408 7954 Z= 0.273 Chirality : 0.037 0.133 978 Planarity : 0.004 0.049 975 Dihedral : 4.001 25.250 780 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.32 % Allowed : 9.06 % 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: 2.85 (0.33), residues: 726 helix: 2.19 (0.22), residues: 612 sheet: None (None), residues: 0 loop : 0.33 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 474 TYR 0.008 0.001 TYR A 359 PHE 0.015 0.001 PHE A 365 TRP 0.013 0.002 TRP B 394 HIS 0.008 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 5837) covalent geometry : angle 0.51306 ( 7954) hydrogen bonds : bond 0.05280 ( 468) hydrogen bonds : angle 4.07290 ( 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 67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.292 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: B 59 GLU cc_start: 0.7425 (pp20) cc_final: 0.7200 (pp20) REVERT: B 289 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8550 (mmmt) REVERT: B 293 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8077 (mp0) REVERT: A 59 GLU cc_start: 0.7431 (pp20) cc_final: 0.7205 (pp20) REVERT: A 289 LYS cc_start: 0.8986 (mmmt) cc_final: 0.8565 (mmmt) REVERT: A 293 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8081 (mp0) REVERT: A 451 MET cc_start: 0.7905 (mmt) cc_final: 0.7702 (mmt) outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 1.6201 time to fit residues: 110.7157 Evaluate side-chains 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 0.9980 chunk 44 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074190 restraints weight = 27549.456| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.24 r_work: 0.2931 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.3063 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= 0.145 Angle : 0.503 5.167 7954 Z= 0.266 Chirality : 0.036 0.132 978 Planarity : 0.004 0.049 975 Dihedral : 3.943 25.054 780 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.65 % Allowed : 8.74 % 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: 3.18 (0.32), residues: 726 helix: 2.45 (0.22), residues: 610 sheet: None (None), residues: 0 loop : 0.26 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 97 TYR 0.008 0.001 TYR B 359 PHE 0.012 0.001 PHE B 99 TRP 0.012 0.002 TRP A 394 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5837) covalent geometry : angle 0.50335 ( 7954) hydrogen bonds : bond 0.04897 ( 468) hydrogen bonds : angle 3.89634 ( 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: 4 poor density : 60 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7500 (pp20) cc_final: 0.7158 (pp20) REVERT: B 420 PHE cc_start: 0.8193 (OUTLIER) cc_final: 0.7976 (t80) REVERT: A 59 GLU cc_start: 0.7504 (pp20) cc_final: 0.7163 (pp20) REVERT: A 370 ARG cc_start: 0.7310 (tpp-160) cc_final: 0.7102 (tpp-160) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 1.3595 time to fit residues: 84.9894 Evaluate side-chains 55 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain B residue 453 ILE 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: 0.8980 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.097655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.074125 restraints weight = 27699.228| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.23 r_work: 0.2901 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3250 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= 0.163 Angle : 0.506 5.293 7954 Z= 0.268 Chirality : 0.037 0.134 978 Planarity : 0.004 0.049 975 Dihedral : 3.905 24.977 780 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 9.55 % 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: 3.32 (0.32), residues: 726 helix: 2.57 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.16 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 309 TYR 0.008 0.001 TYR A 359 PHE 0.015 0.001 PHE B 365 TRP 0.011 0.002 TRP A 394 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5837) covalent geometry : angle 0.50624 ( 7954) hydrogen bonds : bond 0.05033 ( 468) hydrogen bonds : angle 3.91251 ( 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 57 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7535 (pp20) cc_final: 0.7208 (pp20) REVERT: B 259 GLU cc_start: 0.8163 (mp0) cc_final: 0.7919 (mp0) REVERT: B 289 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8580 (mmmt) REVERT: B 293 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8251 (mp0) REVERT: A 59 GLU cc_start: 0.7533 (pp20) cc_final: 0.7208 (pp20) REVERT: A 259 GLU cc_start: 0.8150 (mp0) cc_final: 0.7899 (mp0) REVERT: A 289 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8598 (mmmt) REVERT: A 293 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8217 (mp0) REVERT: A 370 ARG cc_start: 0.7349 (tpp-160) cc_final: 0.7137 (tpp-160) outliers start: 3 outliers final: 0 residues processed: 54 average time/residue: 1.4972 time to fit residues: 84.1189 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 : 0.297 ------------------------------------------------------------------------------- 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: 0.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.097815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.074303 restraints weight = 27665.274| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.21 r_work: 0.2920 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3384 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= 0.135 Angle : 0.483 4.237 7954 Z= 0.255 Chirality : 0.036 0.129 978 Planarity : 0.004 0.049 975 Dihedral : 3.858 24.350 780 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.81 % Allowed : 9.22 % 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: 3.50 (0.32), residues: 726 helix: 2.71 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.09 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 370 TYR 0.007 0.001 TYR B 359 PHE 0.012 0.001 PHE B 99 TRP 0.012 0.002 TRP B 394 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5837) covalent geometry : angle 0.48343 ( 7954) hydrogen bonds : bond 0.04680 ( 468) hydrogen bonds : angle 3.79009 ( 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 63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7572 (pp20) cc_final: 0.7229 (pp20) REVERT: B 259 GLU cc_start: 0.8166 (mp0) cc_final: 0.7909 (mp0) REVERT: A 59 GLU cc_start: 0.7560 (pp20) cc_final: 0.7219 (pp20) REVERT: A 259 GLU cc_start: 0.8143 (mp0) cc_final: 0.7895 (mp0) outliers start: 5 outliers final: 0 residues processed: 58 average time/residue: 1.4305 time to fit residues: 86.3861 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 : 0.295 ------------------------------------------------------------------------------- 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: 0.4980 chunk 67 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.072788 restraints weight = 28018.490| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.25 r_work: 0.2899 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3521 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= 0.139 Angle : 0.484 4.543 7954 Z= 0.255 Chirality : 0.036 0.130 978 Planarity : 0.004 0.049 975 Dihedral : 3.830 24.079 780 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.16 % Allowed : 10.19 % 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: 3.59 (0.32), residues: 726 helix: 2.76 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.14 (0.62), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 370 TYR 0.007 0.001 TYR B 359 PHE 0.021 0.001 PHE B 365 TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5837) covalent geometry : angle 0.48399 ( 7954) hydrogen bonds : bond 0.04630 ( 468) hydrogen bonds : angle 3.71987 ( 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 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.313 Fit side-chains REVERT: B 59 GLU cc_start: 0.7568 (pp20) cc_final: 0.7223 (pp20) REVERT: B 259 GLU cc_start: 0.8053 (mp0) cc_final: 0.7804 (mp0) REVERT: B 289 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8379 (mmmt) REVERT: B 292 LYS cc_start: 0.9264 (ttmm) cc_final: 0.8956 (ttmm) REVERT: B 293 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8200 (mp0) REVERT: A 59 GLU cc_start: 0.7565 (pp20) cc_final: 0.7223 (pp20) REVERT: A 259 GLU cc_start: 0.8060 (mp0) cc_final: 0.7804 (mp0) REVERT: A 289 LYS cc_start: 0.8959 (mmmt) cc_final: 0.8395 (mmmt) REVERT: A 292 LYS cc_start: 0.9260 (ttmm) cc_final: 0.8942 (ttmm) REVERT: A 293 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8165 (mp0) outliers start: 1 outliers final: 0 residues processed: 57 average time/residue: 1.4462 time to fit residues: 85.7551 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 : 0.310 ------------------------------------------------------------------------------- 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: 0.9980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3405 r_free = 0.3405 target = 0.095787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.072588 restraints weight = 28194.348| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.26 r_work: 0.2909 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5837 Z= 0.142 Angle : 0.483 4.481 7954 Z= 0.254 Chirality : 0.036 0.133 978 Planarity : 0.004 0.049 975 Dihedral : 3.826 23.999 780 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 9.71 % Favored : 89.81 % 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: 3.65 (0.32), residues: 726 helix: 2.79 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.22 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 309 TYR 0.007 0.001 TYR B 359 PHE 0.013 0.001 PHE B 99 TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 5837) covalent geometry : angle 0.48293 ( 7954) hydrogen bonds : bond 0.04590 ( 468) hydrogen bonds : angle 3.67989 ( 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 61 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7609 (pp20) cc_final: 0.7276 (pp20) REVERT: B 259 GLU cc_start: 0.8119 (mp0) cc_final: 0.7861 (mp0) REVERT: B 289 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8533 (mmmt) REVERT: B 293 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8167 (mp0) REVERT: A 59 GLU cc_start: 0.7602 (pp20) cc_final: 0.7276 (pp20) REVERT: A 259 GLU cc_start: 0.8121 (mp0) cc_final: 0.7876 (mp0) REVERT: A 289 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8544 (mmmt) REVERT: A 293 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8135 (mp0) outliers start: 3 outliers final: 0 residues processed: 58 average time/residue: 1.4279 time to fit residues: 86.1800 Evaluate side-chains 53 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 0.8980 chunk 37 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3422 r_free = 0.3422 target = 0.095650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.071274 restraints weight = 27575.826| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.30 r_work: 0.2912 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5837 Z= 0.164 Angle : 0.497 4.240 7954 Z= 0.262 Chirality : 0.037 0.128 978 Planarity : 0.004 0.048 975 Dihedral : 3.833 24.182 780 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.49 % Allowed : 9.71 % Favored : 89.81 % 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: 3.62 (0.32), residues: 726 helix: 2.75 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.29 (0.66), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 370 TYR 0.008 0.001 TYR B 359 PHE 0.026 0.001 PHE B 365 TRP 0.010 0.002 TRP A 394 HIS 0.004 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 5837) covalent geometry : angle 0.49660 ( 7954) hydrogen bonds : bond 0.04744 ( 468) hydrogen bonds : angle 3.68268 ( 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 59 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7636 (pp20) cc_final: 0.7401 (pp20) REVERT: B 259 GLU cc_start: 0.8487 (mp0) cc_final: 0.8259 (mp0) REVERT: B 289 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8644 (mmmt) REVERT: B 293 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8208 (mp0) REVERT: B 419 MET cc_start: 0.8992 (tpp) cc_final: 0.8569 (tpt) REVERT: A 59 GLU cc_start: 0.7633 (pp20) cc_final: 0.7392 (pp20) REVERT: A 259 GLU cc_start: 0.8492 (mp0) cc_final: 0.8274 (mp0) REVERT: A 289 LYS cc_start: 0.9051 (mmmt) cc_final: 0.8659 (mmmt) REVERT: A 293 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8227 (mp0) REVERT: A 419 MET cc_start: 0.8995 (tpp) cc_final: 0.8569 (tpt) outliers start: 3 outliers final: 2 residues processed: 56 average time/residue: 1.4597 time to fit residues: 84.8993 Evaluate side-chains 55 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain A residue 415 GLU 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: 0.9980 chunk 38 optimal weight: 0.9980 chunk 41 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 14 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 68 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3437 r_free = 0.3437 target = 0.096524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.072198 restraints weight = 27716.810| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.31 r_work: 0.2926 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5837 Z= 0.125 Angle : 0.482 4.824 7954 Z= 0.253 Chirality : 0.036 0.130 978 Planarity : 0.004 0.048 975 Dihedral : 3.817 24.229 780 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 3.75 (0.32), residues: 726 helix: 2.84 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.35 (0.67), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 370 TYR 0.007 0.001 TYR B 359 PHE 0.012 0.001 PHE A 99 TRP 0.012 0.002 TRP A 394 HIS 0.003 0.001 HIS B 328 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5837) covalent geometry : angle 0.48225 ( 7954) hydrogen bonds : bond 0.04466 ( 468) hydrogen bonds : angle 3.63072 ( 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: 1 poor density : 55 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLU cc_start: 0.7628 (pp20) cc_final: 0.7367 (pp20) REVERT: B 259 GLU cc_start: 0.8477 (mp0) cc_final: 0.8266 (mp0) REVERT: B 289 LYS cc_start: 0.9062 (mmmt) cc_final: 0.8657 (mmmt) REVERT: B 293 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8213 (mp0) REVERT: B 419 MET cc_start: 0.8973 (tpp) cc_final: 0.8558 (tpt) REVERT: A 59 GLU cc_start: 0.7611 (pp20) cc_final: 0.7374 (pp20) REVERT: A 259 GLU cc_start: 0.8482 (mp0) cc_final: 0.8275 (mp0) REVERT: A 289 LYS cc_start: 0.9075 (mmmt) cc_final: 0.8672 (mmmt) REVERT: A 293 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8253 (mp0) REVERT: A 419 MET cc_start: 0.8972 (tpp) cc_final: 0.8555 (tpt) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 1.5066 time to fit residues: 86.0898 Evaluate side-chains 53 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.302 ------------------------------------------------------------------------------- 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: 0.9980 chunk 33 optimal weight: 0.0980 chunk 34 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3444 r_free = 0.3444 target = 0.096974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.072835 restraints weight = 27475.959| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.29 r_work: 0.2940 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5837 Z= 0.116 Angle : 0.475 4.256 7954 Z= 0.248 Chirality : 0.036 0.129 978 Planarity : 0.004 0.048 975 Dihedral : 3.785 23.971 780 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % 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: 3.88 (0.32), residues: 726 helix: 2.94 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.33 (0.67), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 35 TYR 0.006 0.001 TYR B 359 PHE 0.024 0.001 PHE A 365 TRP 0.012 0.001 TRP A 394 HIS 0.003 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5837) covalent geometry : angle 0.47476 ( 7954) hydrogen bonds : bond 0.04265 ( 468) hydrogen bonds : angle 3.58678 ( 1368) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4163.13 seconds wall clock time: 71 minutes 2.68 seconds (4262.68 seconds total)