Starting phenix.real_space_refine on Mon Dec 30 00:33:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dhm_27436/12_2024/8dhm_27436_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dhm_27436/12_2024/8dhm_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_27436/12_2024/8dhm_27436.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dhm_27436/12_2024/8dhm_27436.map" model { file = "/net/cci-nas-00/data/ceres_data/8dhm_27436/12_2024/8dhm_27436_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dhm_27436/12_2024/8dhm_27436_trim.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.01, per 1000 atoms: 0.60 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: 3.51 Conformation dependent library (CDL) restraints added in 972.8 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: 1.11 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: 4.21 Time building geometry restraints manager: 4.03 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 476 or resid 701 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: 5.610 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: 0.220 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.720 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.940 ------------------------------------------------------------------------------- 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= 0.375 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.017 0.003 TRP B 394 HIS 0.007 0.002 HIS B 328 PHE 0.013 0.001 PHE B 99 TYR 0.013 0.002 TYR A 359 ARG 0.025 0.001 ARG B 97 *********************** 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 : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 116 average time/residue: 2.7068 time to fit residues: 328.7556 Evaluate side-chains 62 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5837 Z= 0.283 Angle : 0.582 4.694 7954 Z= 0.309 Chirality : 0.038 0.138 978 Planarity : 0.005 0.062 975 Dihedral : 4.132 26.717 780 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.49 % Allowed : 9.22 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.33), residues: 726 helix: 1.66 (0.22), residues: 612 sheet: None (None), residues: 0 loop : 0.20 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 394 HIS 0.006 0.001 HIS B 57 PHE 0.015 0.001 PHE B 99 TYR 0.012 0.002 TYR B 359 ARG 0.006 0.001 ARG A 474 *********************** 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 64 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 1.016 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: B 420 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7577 (t80) REVERT: A 420 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7589 (t80) REVERT: A 451 MET cc_start: 0.7245 (mmt) cc_final: 0.6659 (mmt) outliers start: 3 outliers final: 0 residues processed: 62 average time/residue: 3.4614 time to fit residues: 223.1759 Evaluate side-chains 60 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 420 PHE Chi-restraints excluded: chain A residue 420 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 58 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2847 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= 0.209 Angle : 0.513 4.360 7954 Z= 0.272 Chirality : 0.037 0.130 978 Planarity : 0.004 0.046 975 Dihedral : 4.044 25.093 780 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.93 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.77 (0.33), residues: 726 helix: 2.15 (0.22), residues: 610 sheet: None (None), residues: 0 loop : 0.20 (0.62), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 394 HIS 0.007 0.001 HIS B 57 PHE 0.018 0.001 PHE B 365 TYR 0.008 0.001 TYR B 359 ARG 0.003 0.000 ARG B 97 *********************** 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 60 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 MET cc_start: 0.7222 (mmt) cc_final: 0.6738 (mmt) outliers start: 2 outliers final: 1 residues processed: 60 average time/residue: 3.3261 time to fit residues: 208.3352 Evaluate side-chains 54 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.3980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3094 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= 0.225 Angle : 0.529 7.140 7954 Z= 0.276 Chirality : 0.037 0.134 978 Planarity : 0.004 0.047 975 Dihedral : 3.971 24.899 780 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.65 % Allowed : 9.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.32), residues: 726 helix: 2.39 (0.22), residues: 610 sheet: None (None), residues: 0 loop : 0.35 (0.61), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 394 HIS 0.004 0.001 HIS B 57 PHE 0.016 0.001 PHE A 365 TYR 0.008 0.001 TYR A 359 ARG 0.002 0.000 ARG B 97 *********************** 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 62 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.987 Fit side-chains REVERT: B 420 PHE cc_start: 0.7813 (OUTLIER) cc_final: 0.7607 (t80) REVERT: A 420 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7596 (t80) REVERT: A 451 MET cc_start: 0.7220 (mmt) cc_final: 0.6818 (mmt) outliers start: 4 outliers final: 3 residues processed: 58 average time/residue: 2.8280 time to fit residues: 172.3205 Evaluate side-chains 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 420 PHE 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 57 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 1 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3252 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= 0.210 Angle : 0.528 8.359 7954 Z= 0.275 Chirality : 0.037 0.131 978 Planarity : 0.004 0.048 975 Dihedral : 3.913 24.447 780 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.65 % Allowed : 9.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.32), residues: 726 helix: 2.55 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.22 (0.60), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.016 0.001 PHE B 365 TYR 0.008 0.001 TYR A 359 ARG 0.002 0.000 ARG A 309 *********************** 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 58 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.934 Fit side-chains REVERT: A 451 MET cc_start: 0.7106 (mmt) cc_final: 0.6736 (mmt) outliers start: 4 outliers final: 0 residues processed: 54 average time/residue: 2.8592 time to fit residues: 161.9235 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 : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3413 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= 0.266 Angle : 0.545 8.276 7954 Z= 0.285 Chirality : 0.037 0.130 978 Planarity : 0.004 0.048 975 Dihedral : 3.892 24.584 780 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.31 (0.32), residues: 726 helix: 2.57 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.05 (0.60), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS A 328 PHE 0.020 0.001 PHE A 365 TYR 0.008 0.001 TYR B 359 ARG 0.002 0.000 ARG A 35 *********************** 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 60 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.926 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 55 average time/residue: 2.9354 time to fit residues: 168.9922 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 : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 1.9990 chunk 39 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3507 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= 0.185 Angle : 0.516 9.079 7954 Z= 0.268 Chirality : 0.036 0.132 978 Planarity : 0.004 0.047 975 Dihedral : 3.870 24.287 780 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.49 % Allowed : 9.39 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.55 (0.32), residues: 726 helix: 2.72 (0.21), residues: 610 sheet: None (None), residues: 0 loop : 0.24 (0.63), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 394 HIS 0.003 0.001 HIS B 328 PHE 0.022 0.001 PHE B 365 TYR 0.007 0.001 TYR B 313 ARG 0.002 0.000 ARG B 309 *********************** 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 54 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 1.011 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 52 average time/residue: 2.7048 time to fit residues: 148.2264 Evaluate side-chains 51 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 292 LYS Chi-restraints excluded: chain B residue 415 GLU Chi-restraints excluded: chain A residue 415 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5837 Z= 0.258 Angle : 0.550 9.122 7954 Z= 0.285 Chirality : 0.037 0.128 978 Planarity : 0.004 0.046 975 Dihedral : 3.864 24.148 780 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.32 % Allowed : 10.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.32), residues: 726 helix: 2.68 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.16 (0.64), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 394 HIS 0.004 0.001 HIS B 328 PHE 0.019 0.001 PHE A 365 TYR 0.007 0.001 TYR B 359 ARG 0.001 0.000 ARG A 35 *********************** 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 53 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.944 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 51 average time/residue: 2.9631 time to fit residues: 158.6563 Evaluate side-chains 48 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 50 optimal weight: 0.1980 chunk 19 optimal weight: 0.0870 chunk 58 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.3158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5837 Z= 0.158 Angle : 0.519 9.660 7954 Z= 0.267 Chirality : 0.036 0.128 978 Planarity : 0.004 0.046 975 Dihedral : 3.838 23.937 780 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 10.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.73 (0.32), residues: 726 helix: 2.84 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.30 (0.65), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 394 HIS 0.003 0.001 HIS B 57 PHE 0.025 0.001 PHE B 365 TYR 0.007 0.001 TYR A 313 ARG 0.002 0.000 ARG A 377 *********************** 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 52 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.926 Fit side-chains outliers start: 0 outliers final: 2 residues processed: 52 average time/residue: 2.3889 time to fit residues: 131.6023 Evaluate side-chains 52 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.0970 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.004 0.052 5837 Z= 0.244 Angle : 0.572 9.512 7954 Z= 0.298 Chirality : 0.036 0.127 978 Planarity : 0.004 0.046 975 Dihedral : 3.876 23.821 780 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.65 % Allowed : 9.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.70 (0.32), residues: 726 helix: 2.83 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.20 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 394 HIS 0.003 0.001 HIS B 328 PHE 0.024 0.001 PHE A 365 TYR 0.007 0.001 TYR B 359 ARG 0.002 0.000 ARG A 414 ********************** 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: 4 poor density : 52 time to evaluate : 0.844 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 2.5416 time to fit residues: 139.4026 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.1980 chunk 50 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.096607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.072228 restraints weight = 27488.044| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.31 r_work: 0.2923 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5837 Z= 0.227 Angle : 0.537 9.480 7954 Z= 0.278 Chirality : 0.037 0.129 978 Planarity : 0.004 0.046 975 Dihedral : 3.883 24.012 780 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.16 % Allowed : 9.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.71 (0.32), residues: 726 helix: 2.84 (0.21), residues: 612 sheet: None (None), residues: 0 loop : 0.18 (0.63), residues: 114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 394 HIS 0.004 0.001 HIS B 328 PHE 0.023 0.001 PHE B 365 TYR 0.007 0.001 TYR A 359 ARG 0.001 0.000 ARG A 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4781.43 seconds wall clock time: 86 minutes 4.45 seconds (5164.45 seconds total)