Starting phenix.real_space_refine on Fri Jul 19 03:13:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/07_2024/8uyi_42807_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/07_2024/8uyi_42807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/07_2024/8uyi_42807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/07_2024/8uyi_42807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/07_2024/8uyi_42807_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uyi_42807/07_2024/8uyi_42807_neut.cif" } resolution = 3.13 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= 0.001 sd= 0.018 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 P 8 5.49 5 Mg 4 5.21 5 S 40 5.16 5 C 3804 2.51 5 N 1003 2.21 5 O 1121 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 5980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2966 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain breaks: 6 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2956 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain breaks: 6 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.34, per 1000 atoms: 0.73 Number of scatterers: 5980 At special positions: 0 Unit cell: (116.352, 74.336, 72.72, 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) S 40 16.00 P 8 15.00 Mg 4 11.99 O 1121 8.00 N 1003 7.00 C 3804 6.00 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 - 3.50 Amino acid : False - 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: 2.62 Conformation dependent library (CDL) restraints added in 1.0 seconds 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 6 sheets defined 45.0% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 120 through 136 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 203 through 215 removed outlier: 3.602A pdb=" N THR A 215 " --> pdb=" O MET A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.769A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 4.042A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.578A pdb=" N SER A 459 " --> pdb=" O ARG A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 484 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 557 through 572 removed outlier: 3.501A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 138 removed outlier: 3.541A pdb=" N CYS B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 203 through 215 removed outlier: 3.546A pdb=" N THR B 215 " --> pdb=" O MET B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 303 removed outlier: 3.564A pdb=" N ARG B 302 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.868A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.539A pdb=" N CYS B 360 " --> pdb=" O ASP B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.743A pdb=" N TRP B 410 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B 411 " --> pdb=" O SER B 407 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 removed outlier: 3.556A pdb=" N SER B 459 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 498 through 515 removed outlier: 3.624A pdb=" N LYS B 512 " --> pdb=" O CYS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 555 removed outlier: 3.897A pdb=" N ARG B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 167 removed outlier: 6.739A pdb=" N VAL A 173 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LYS A 167 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA4, first strand: chain 'B' and resid 159 through 167 removed outlier: 5.522A pdb=" N LEU B 161 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS B 177 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B 163 " --> pdb=" O SER B 175 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL B 173 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS B 167 " --> pdb=" O ALA B 171 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ALA B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR B 250 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.521A pdb=" N CYS B 295 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 370 through 372 266 hydrogen bonds defined for protein. 765 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.55 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1895 1.34 - 1.46: 1213 1.46 - 1.58: 2905 1.58 - 1.69: 20 1.69 - 1.81: 62 Bond restraints: 6095 Sorted by residual: bond pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.84e+01 bond pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O2P TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 ... (remaining 6090 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.92: 161 105.92 - 113.47: 3426 113.47 - 121.02: 2927 121.02 - 128.57: 1703 128.57 - 136.12: 48 Bond angle restraints: 8265 Sorted by residual: angle pdb=" CB TPO A 305 " pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " ideal model delta sigma weight residual 119.31 107.32 11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" C THR B 215 " pdb=" N VAL B 216 " pdb=" CA VAL B 216 " ideal model delta sigma weight residual 120.33 123.43 -3.10 8.00e-01 1.56e+00 1.50e+01 angle pdb=" CB TPO B 305 " pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " ideal model delta sigma weight residual 119.31 108.58 10.73 3.00e+00 1.11e-01 1.28e+01 angle pdb=" OG1 TPO B 305 " pdb=" P TPO B 305 " pdb=" O1P TPO B 305 " ideal model delta sigma weight residual 100.43 111.06 -10.63 3.00e+00 1.11e-01 1.26e+01 angle pdb=" OG1 TPO A 305 " pdb=" P TPO A 305 " pdb=" O1P TPO A 305 " ideal model delta sigma weight residual 100.43 110.11 -9.68 3.00e+00 1.11e-01 1.04e+01 ... (remaining 8260 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.23: 3638 33.23 - 66.46: 60 66.46 - 99.69: 2 99.69 - 132.91: 0 132.91 - 166.14: 2 Dihedral angle restraints: 3702 sinusoidal: 1516 harmonic: 2186 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 133.86 166.14 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 89.85 -149.86 1 2.00e+01 2.50e-03 4.48e+01 dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 24.11 -84.11 1 2.00e+01 2.50e-03 2.15e+01 ... (remaining 3699 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 597 0.031 - 0.062: 220 0.062 - 0.093: 69 0.093 - 0.124: 38 0.124 - 0.155: 8 Chirality restraints: 932 Sorted by residual: chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE A 246 " pdb=" N ILE A 246 " pdb=" C ILE A 246 " pdb=" CB ILE A 246 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 chirality pdb=" CA ILE B 246 " pdb=" N ILE B 246 " pdb=" C ILE B 246 " pdb=" CB ILE B 246 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 929 not shown) Planarity restraints: 1029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 243 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO A 244 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 244 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 244 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 243 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 244 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 244 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 244 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 450 " -0.025 5.00e-02 4.00e+02 3.76e-02 2.26e+00 pdb=" N PRO B 451 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.021 5.00e-02 4.00e+02 ... (remaining 1026 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 67 2.63 - 3.19: 4804 3.19 - 3.76: 8944 3.76 - 4.33: 12969 4.33 - 4.90: 21241 Nonbonded interactions: 48025 Sorted by model distance: nonbonded pdb=" O2A ADP B 601 " pdb="MG MG B 603 " model vdw 2.057 2.170 nonbonded pdb=" OD1 ASP B 357 " pdb="MG MG B 602 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASN A 339 " pdb="MG MG A 603 " model vdw 2.105 2.170 nonbonded pdb=" OD1 ASN B 339 " pdb="MG MG B 603 " model vdw 2.205 2.170 nonbonded pdb=" OD2 ASP A 357 " pdb="MG MG A 603 " model vdw 2.240 2.170 ... (remaining 48020 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 122 through 223 or resid 237 through 572 or resid 601 thro \ ugh 603)) selection = (chain 'B' and (resid 122 through 136 or resid 148 through 572 or resid 601 thro \ ugh 603)) } 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.350 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 6095 Z= 0.237 Angle : 0.673 11.987 8265 Z= 0.341 Chirality : 0.041 0.155 932 Planarity : 0.005 0.043 1029 Dihedral : 12.678 166.142 2272 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.08 % Allowed : 4.92 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.29), residues: 698 helix: -0.70 (0.24), residues: 299 sheet: -0.09 (0.56), residues: 92 loop : -0.35 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 489 HIS 0.003 0.001 HIS A 243 PHE 0.011 0.001 PHE A 253 TYR 0.007 0.001 TYR B 438 ARG 0.003 0.001 ARG B 469 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7676 (mt) cc_final: 0.7309 (mm) REVERT: A 194 MET cc_start: 0.8047 (ttt) cc_final: 0.7398 (tmm) REVERT: A 197 ASN cc_start: 0.8029 (t0) cc_final: 0.7664 (t0) REVERT: A 219 MET cc_start: 0.8061 (mtt) cc_final: 0.7833 (mtt) REVERT: A 236 PHE cc_start: 0.5701 (m-80) cc_final: 0.5054 (m-80) REVERT: A 318 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7616 (tt) REVERT: A 334 ASP cc_start: 0.7492 (t70) cc_final: 0.7116 (t0) REVERT: A 433 LEU cc_start: 0.8041 (mt) cc_final: 0.7794 (mp) REVERT: A 436 LYS cc_start: 0.7240 (tttt) cc_final: 0.6742 (ttpt) REVERT: A 452 PHE cc_start: 0.7155 (t80) cc_final: 0.6787 (t80) REVERT: A 456 ASN cc_start: 0.8273 (m-40) cc_final: 0.7861 (m-40) REVERT: A 558 LEU cc_start: 0.7429 (tp) cc_final: 0.7100 (tp) REVERT: B 129 TRP cc_start: 0.7335 (t60) cc_final: 0.6833 (t60) REVERT: B 298 LYS cc_start: 0.7700 (tttt) cc_final: 0.7418 (ttpt) REVERT: B 377 ASP cc_start: 0.5506 (t70) cc_final: 0.5239 (t0) REVERT: B 393 ASN cc_start: 0.7864 (m-40) cc_final: 0.7141 (m110) REVERT: B 401 TRP cc_start: 0.7061 (m100) cc_final: 0.6809 (m-90) REVERT: B 403 ASN cc_start: 0.8165 (t0) cc_final: 0.7454 (p0) REVERT: B 418 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7227 (tt0) REVERT: B 436 LYS cc_start: 0.6073 (tttt) cc_final: 0.4809 (mptt) REVERT: B 439 LYS cc_start: 0.7546 (mttt) cc_final: 0.7313 (mtpt) REVERT: B 442 ASP cc_start: 0.8205 (m-30) cc_final: 0.7741 (m-30) REVERT: B 471 ASP cc_start: 0.7209 (m-30) cc_final: 0.6912 (m-30) REVERT: B 501 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7540 (mt-10) REVERT: B 541 ARG cc_start: 0.5720 (mtt-85) cc_final: 0.5463 (mtm-85) REVERT: B 566 LYS cc_start: 0.8027 (tttt) cc_final: 0.7765 (ttpp) outliers start: 7 outliers final: 2 residues processed: 199 average time/residue: 0.1969 time to fit residues: 49.6594 Evaluate side-chains 145 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain B residue 500 ASN 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: 3.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 421 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN B 328 HIS B 504 GLN B 569 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6095 Z= 0.169 Angle : 0.555 6.231 8265 Z= 0.267 Chirality : 0.039 0.128 932 Planarity : 0.004 0.035 1029 Dihedral : 9.724 142.717 827 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.77 % Allowed : 11.54 % Favored : 85.69 % 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: 0.72 (0.32), residues: 698 helix: 1.25 (0.29), residues: 303 sheet: -0.28 (0.49), residues: 101 loop : 0.09 (0.38), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 505 HIS 0.013 0.002 HIS A 559 PHE 0.008 0.001 PHE A 452 TYR 0.014 0.001 TYR A 482 ARG 0.002 0.000 ARG A 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7648 (mt) cc_final: 0.7281 (mm) REVERT: A 194 MET cc_start: 0.7839 (ttt) cc_final: 0.7353 (tmm) REVERT: A 219 MET cc_start: 0.8065 (mtt) cc_final: 0.7856 (mtt) REVERT: A 236 PHE cc_start: 0.5772 (m-80) cc_final: 0.5198 (m-80) REVERT: A 249 MET cc_start: 0.7754 (ttm) cc_final: 0.7508 (ttm) REVERT: A 299 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7113 (pt0) REVERT: A 318 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7346 (tt) REVERT: A 334 ASP cc_start: 0.7453 (t70) cc_final: 0.6551 (t0) REVERT: A 418 GLU cc_start: 0.5864 (mt-10) cc_final: 0.5293 (mt-10) REVERT: A 433 LEU cc_start: 0.8010 (mt) cc_final: 0.7755 (mp) REVERT: A 436 LYS cc_start: 0.7166 (tttt) cc_final: 0.6695 (ttpt) REVERT: A 452 PHE cc_start: 0.6987 (t80) cc_final: 0.6648 (t80) REVERT: A 456 ASN cc_start: 0.8240 (m-40) cc_final: 0.7869 (m110) REVERT: B 129 TRP cc_start: 0.7112 (t60) cc_final: 0.6639 (t60) REVERT: B 213 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7017 (mtt-85) REVERT: B 377 ASP cc_start: 0.5562 (t70) cc_final: 0.5311 (t0) REVERT: B 401 TRP cc_start: 0.7117 (m100) cc_final: 0.6832 (m-90) REVERT: B 403 ASN cc_start: 0.8126 (t0) cc_final: 0.7508 (p0) REVERT: B 436 LYS cc_start: 0.6136 (tttt) cc_final: 0.4908 (mptt) REVERT: B 442 ASP cc_start: 0.7983 (m-30) cc_final: 0.7752 (m-30) REVERT: B 501 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7576 (mt-10) REVERT: B 541 ARG cc_start: 0.5826 (mtt-85) cc_final: 0.5484 (mtm-85) REVERT: B 547 GLU cc_start: 0.6969 (tp30) cc_final: 0.6389 (tm-30) REVERT: B 566 LYS cc_start: 0.8014 (tttt) cc_final: 0.7705 (ttpp) REVERT: B 573 ILE cc_start: 0.7418 (mt) cc_final: 0.7185 (pt) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 0.1849 time to fit residues: 37.9760 Evaluate side-chains 146 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 0.0870 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6095 Z= 0.172 Angle : 0.541 6.189 8265 Z= 0.254 Chirality : 0.039 0.131 932 Planarity : 0.004 0.033 1029 Dihedral : 8.953 127.738 826 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.23 % Allowed : 12.31 % Favored : 84.46 % 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: 1.24 (0.33), residues: 698 helix: 1.93 (0.30), residues: 303 sheet: -0.19 (0.49), residues: 101 loop : 0.13 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.011 0.001 HIS A 559 PHE 0.011 0.001 PHE B 399 TYR 0.014 0.001 TYR A 482 ARG 0.002 0.000 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 0.696 Fit side-chains REVERT: A 161 LEU cc_start: 0.7660 (mt) cc_final: 0.7288 (mm) REVERT: A 194 MET cc_start: 0.8003 (ttt) cc_final: 0.7558 (tmm) REVERT: A 236 PHE cc_start: 0.5917 (m-80) cc_final: 0.5394 (m-80) REVERT: A 249 MET cc_start: 0.7740 (ttm) cc_final: 0.7451 (ttm) REVERT: A 299 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7124 (pt0) REVERT: A 318 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7370 (tt) REVERT: A 334 ASP cc_start: 0.7488 (t70) cc_final: 0.6583 (t0) REVERT: A 418 GLU cc_start: 0.5880 (mt-10) cc_final: 0.5614 (mt-10) REVERT: A 433 LEU cc_start: 0.8004 (mt) cc_final: 0.7737 (mp) REVERT: A 436 LYS cc_start: 0.7151 (tttt) cc_final: 0.6683 (ttpt) REVERT: A 439 LYS cc_start: 0.7110 (mttt) cc_final: 0.6575 (tttp) REVERT: A 456 ASN cc_start: 0.8186 (m-40) cc_final: 0.7894 (m110) REVERT: A 570 GLU cc_start: 0.7918 (tm-30) cc_final: 0.7501 (tt0) REVERT: B 129 TRP cc_start: 0.7089 (t60) cc_final: 0.6625 (t60) REVERT: B 213 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7035 (mtt-85) REVERT: B 401 TRP cc_start: 0.7161 (m100) cc_final: 0.6858 (m-90) REVERT: B 403 ASN cc_start: 0.8128 (t0) cc_final: 0.7497 (p0) REVERT: B 436 LYS cc_start: 0.6154 (tttt) cc_final: 0.4891 (mptt) REVERT: B 439 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7284 (mtpt) REVERT: B 442 ASP cc_start: 0.8073 (m-30) cc_final: 0.7846 (m-30) REVERT: B 541 ARG cc_start: 0.5822 (mtt-85) cc_final: 0.5439 (mtm-85) REVERT: B 547 GLU cc_start: 0.7064 (tp30) cc_final: 0.6467 (tm-30) REVERT: B 566 LYS cc_start: 0.8008 (tttt) cc_final: 0.7573 (ttpp) outliers start: 21 outliers final: 14 residues processed: 150 average time/residue: 0.2040 time to fit residues: 38.8227 Evaluate side-chains 141 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 326 ASN A 421 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 569 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6095 Z= 0.152 Angle : 0.550 14.784 8265 Z= 0.251 Chirality : 0.039 0.135 932 Planarity : 0.004 0.033 1029 Dihedral : 8.120 117.076 826 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.38 % Allowed : 12.92 % Favored : 83.69 % 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: 1.44 (0.33), residues: 698 helix: 2.14 (0.30), residues: 303 sheet: -0.12 (0.49), residues: 101 loop : 0.18 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.010 0.001 HIS A 559 PHE 0.008 0.001 PHE A 253 TYR 0.015 0.001 TYR A 482 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 128 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 161 LEU cc_start: 0.7681 (mt) cc_final: 0.7297 (mm) REVERT: A 194 MET cc_start: 0.7920 (ttt) cc_final: 0.7661 (ttp) REVERT: A 236 PHE cc_start: 0.5910 (m-80) cc_final: 0.5459 (m-80) REVERT: A 299 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7105 (pt0) REVERT: A 318 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7372 (tt) REVERT: A 334 ASP cc_start: 0.7485 (t70) cc_final: 0.6582 (t0) REVERT: A 433 LEU cc_start: 0.7992 (mt) cc_final: 0.7727 (mp) REVERT: A 436 LYS cc_start: 0.7132 (tttt) cc_final: 0.6645 (ttpt) REVERT: A 456 ASN cc_start: 0.8134 (m-40) cc_final: 0.7843 (m110) REVERT: A 570 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7548 (tt0) REVERT: B 129 TRP cc_start: 0.7071 (t60) cc_final: 0.6623 (t60) REVERT: B 213 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7072 (mtt-85) REVERT: B 401 TRP cc_start: 0.7163 (m100) cc_final: 0.6821 (m-90) REVERT: B 403 ASN cc_start: 0.8140 (t0) cc_final: 0.7480 (p0) REVERT: B 436 LYS cc_start: 0.6087 (tttt) cc_final: 0.4800 (mptt) REVERT: B 440 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: B 442 ASP cc_start: 0.8083 (m-30) cc_final: 0.7875 (m-30) REVERT: B 541 ARG cc_start: 0.5836 (mtt-85) cc_final: 0.5419 (mtm-85) REVERT: B 547 GLU cc_start: 0.7045 (tp30) cc_final: 0.6457 (tm-30) REVERT: B 566 LYS cc_start: 0.7984 (tttt) cc_final: 0.7666 (ttpp) REVERT: B 573 ILE cc_start: 0.6137 (tp) cc_final: 0.5750 (pt) outliers start: 22 outliers final: 17 residues processed: 144 average time/residue: 0.2001 time to fit residues: 36.8513 Evaluate side-chains 144 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 326 ASN Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 440 GLU Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 326 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6095 Z= 0.186 Angle : 0.549 12.841 8265 Z= 0.254 Chirality : 0.040 0.151 932 Planarity : 0.004 0.033 1029 Dihedral : 7.806 114.784 824 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.69 % Allowed : 13.23 % Favored : 83.08 % 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: 1.38 (0.33), residues: 698 helix: 2.18 (0.30), residues: 303 sheet: -0.37 (0.47), residues: 109 loop : 0.15 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.009 0.001 HIS A 559 PHE 0.008 0.001 PHE A 253 TYR 0.015 0.001 TYR A 482 ARG 0.002 0.000 ARG A 248 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.756 Fit side-chains REVERT: A 161 LEU cc_start: 0.7682 (mt) cc_final: 0.7297 (mm) REVERT: A 194 MET cc_start: 0.7914 (ttt) cc_final: 0.7456 (tmm) REVERT: A 236 PHE cc_start: 0.5873 (m-80) cc_final: 0.5469 (m-80) REVERT: A 299 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7136 (pt0) REVERT: A 318 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 334 ASP cc_start: 0.7516 (t70) cc_final: 0.6628 (t0) REVERT: A 433 LEU cc_start: 0.7993 (mt) cc_final: 0.7716 (mp) REVERT: A 436 LYS cc_start: 0.7114 (tttt) cc_final: 0.6648 (ttpt) REVERT: A 439 LYS cc_start: 0.7116 (mttt) cc_final: 0.6604 (tttm) REVERT: A 570 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7617 (tt0) REVERT: B 129 TRP cc_start: 0.7085 (t60) cc_final: 0.6620 (t60) REVERT: B 213 ARG cc_start: 0.7723 (mtt180) cc_final: 0.6963 (mtt-85) REVERT: B 379 ASP cc_start: 0.6629 (p0) cc_final: 0.5596 (t0) REVERT: B 401 TRP cc_start: 0.7225 (m100) cc_final: 0.6874 (m-90) REVERT: B 403 ASN cc_start: 0.8154 (t0) cc_final: 0.7469 (p0) REVERT: B 436 LYS cc_start: 0.6178 (tttt) cc_final: 0.4851 (mptt) REVERT: B 442 ASP cc_start: 0.8087 (m-30) cc_final: 0.7866 (m-30) REVERT: B 541 ARG cc_start: 0.5858 (mtt-85) cc_final: 0.5461 (mtm-85) REVERT: B 547 GLU cc_start: 0.7045 (tp30) cc_final: 0.6446 (tm-30) REVERT: B 566 LYS cc_start: 0.7972 (tttt) cc_final: 0.7637 (ttpp) REVERT: B 573 ILE cc_start: 0.6079 (tp) cc_final: 0.5725 (pt) outliers start: 24 outliers final: 20 residues processed: 146 average time/residue: 0.1863 time to fit residues: 35.0898 Evaluate side-chains 148 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 570 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.2830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6095 Z= 0.140 Angle : 0.535 13.360 8265 Z= 0.246 Chirality : 0.039 0.134 932 Planarity : 0.003 0.032 1029 Dihedral : 7.521 112.355 824 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.38 % Allowed : 13.54 % Favored : 83.08 % 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: 1.52 (0.33), residues: 698 helix: 2.31 (0.30), residues: 303 sheet: -0.30 (0.47), residues: 109 loop : 0.23 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.009 0.001 HIS A 559 PHE 0.008 0.001 PHE A 253 TYR 0.015 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.721 Fit side-chains REVERT: A 123 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6463 (pp20) REVERT: A 161 LEU cc_start: 0.7774 (mt) cc_final: 0.7384 (mm) REVERT: A 194 MET cc_start: 0.7871 (ttt) cc_final: 0.7386 (tmm) REVERT: A 236 PHE cc_start: 0.5908 (m-80) cc_final: 0.5556 (m-80) REVERT: A 299 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7166 (pt0) REVERT: A 318 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7395 (tt) REVERT: A 334 ASP cc_start: 0.7503 (t70) cc_final: 0.6571 (t0) REVERT: A 439 LYS cc_start: 0.7035 (mttt) cc_final: 0.6548 (tttp) REVERT: A 456 ASN cc_start: 0.8159 (m-40) cc_final: 0.7935 (m110) REVERT: A 570 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7627 (tt0) REVERT: B 129 TRP cc_start: 0.7070 (t60) cc_final: 0.6668 (t60) REVERT: B 213 ARG cc_start: 0.7677 (mtt180) cc_final: 0.6955 (mtt-85) REVERT: B 376 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.5175 (tt0) REVERT: B 379 ASP cc_start: 0.6596 (p0) cc_final: 0.5606 (t0) REVERT: B 401 TRP cc_start: 0.7285 (m100) cc_final: 0.6859 (m-90) REVERT: B 403 ASN cc_start: 0.8126 (t0) cc_final: 0.7440 (p0) REVERT: B 436 LYS cc_start: 0.6158 (tttt) cc_final: 0.4834 (mptt) REVERT: B 442 ASP cc_start: 0.8060 (m-30) cc_final: 0.7858 (m-30) REVERT: B 541 ARG cc_start: 0.5886 (mtt-85) cc_final: 0.5489 (mtm-85) REVERT: B 547 GLU cc_start: 0.7048 (tp30) cc_final: 0.6440 (tm-30) REVERT: B 566 LYS cc_start: 0.7941 (tttt) cc_final: 0.7602 (ttpp) REVERT: B 573 ILE cc_start: 0.6013 (tp) cc_final: 0.5689 (pt) outliers start: 22 outliers final: 16 residues processed: 149 average time/residue: 0.1810 time to fit residues: 35.0704 Evaluate side-chains 146 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 8.9990 chunk 43 optimal weight: 0.0040 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6095 Z= 0.144 Angle : 0.541 15.643 8265 Z= 0.246 Chirality : 0.039 0.144 932 Planarity : 0.003 0.032 1029 Dihedral : 7.352 111.511 824 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.92 % Allowed : 14.15 % Favored : 82.92 % 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: 1.60 (0.33), residues: 698 helix: 2.38 (0.30), residues: 303 sheet: -0.20 (0.47), residues: 109 loop : 0.23 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.009 0.001 HIS A 559 PHE 0.009 0.001 PHE A 253 TYR 0.015 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 0.756 Fit side-chains REVERT: A 161 LEU cc_start: 0.7820 (mt) cc_final: 0.7434 (mm) REVERT: A 194 MET cc_start: 0.7817 (ttt) cc_final: 0.7330 (tmm) REVERT: A 299 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7164 (pt0) REVERT: A 318 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7401 (tt) REVERT: A 334 ASP cc_start: 0.7526 (t70) cc_final: 0.6591 (t0) REVERT: A 439 LYS cc_start: 0.7034 (mttt) cc_final: 0.6570 (tttp) REVERT: A 456 ASN cc_start: 0.8153 (m-40) cc_final: 0.7942 (m110) REVERT: A 557 ARG cc_start: 0.6912 (mmt90) cc_final: 0.6472 (mtm180) REVERT: A 570 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7702 (tt0) REVERT: B 129 TRP cc_start: 0.7078 (t60) cc_final: 0.6663 (t60) REVERT: B 213 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7061 (mtt-85) REVERT: B 379 ASP cc_start: 0.6621 (p0) cc_final: 0.5572 (t0) REVERT: B 401 TRP cc_start: 0.7281 (m100) cc_final: 0.6831 (m-90) REVERT: B 403 ASN cc_start: 0.8098 (t0) cc_final: 0.7371 (p0) REVERT: B 436 LYS cc_start: 0.6174 (tttt) cc_final: 0.4836 (mptt) REVERT: B 541 ARG cc_start: 0.5933 (mtt-85) cc_final: 0.5533 (mtm-85) REVERT: B 547 GLU cc_start: 0.7099 (tp30) cc_final: 0.6463 (tm-30) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.1866 time to fit residues: 34.0485 Evaluate side-chains 142 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 44 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6095 Z= 0.149 Angle : 0.552 16.572 8265 Z= 0.249 Chirality : 0.039 0.137 932 Planarity : 0.003 0.032 1029 Dihedral : 7.232 109.618 824 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.62 % Allowed : 14.62 % Favored : 82.77 % 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: 1.67 (0.33), residues: 698 helix: 2.44 (0.30), residues: 303 sheet: -0.14 (0.47), residues: 109 loop : 0.24 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 505 HIS 0.010 0.001 HIS A 559 PHE 0.009 0.001 PHE A 253 TYR 0.014 0.001 TYR A 494 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.716 Fit side-chains REVERT: A 125 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: A 161 LEU cc_start: 0.7710 (mt) cc_final: 0.7408 (mm) REVERT: A 194 MET cc_start: 0.7773 (ttt) cc_final: 0.7500 (ttp) REVERT: A 290 MET cc_start: 0.8189 (ptp) cc_final: 0.7908 (ptp) REVERT: A 299 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7162 (pt0) REVERT: A 318 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7411 (tt) REVERT: A 334 ASP cc_start: 0.7532 (t70) cc_final: 0.6591 (t0) REVERT: A 439 LYS cc_start: 0.6948 (mttt) cc_final: 0.6493 (tttp) REVERT: A 456 ASN cc_start: 0.8124 (m-40) cc_final: 0.7915 (m110) REVERT: A 557 ARG cc_start: 0.6908 (mmt90) cc_final: 0.6493 (mtm180) REVERT: A 570 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7702 (tt0) REVERT: B 129 TRP cc_start: 0.7142 (t60) cc_final: 0.6720 (t60) REVERT: B 213 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7154 (mtt-85) REVERT: B 401 TRP cc_start: 0.7311 (m100) cc_final: 0.6859 (m-90) REVERT: B 436 LYS cc_start: 0.6157 (tttt) cc_final: 0.4832 (mptt) REVERT: B 541 ARG cc_start: 0.5842 (mtt-85) cc_final: 0.5579 (mtm-85) REVERT: B 547 GLU cc_start: 0.7139 (tp30) cc_final: 0.6508 (tm-30) outliers start: 17 outliers final: 15 residues processed: 133 average time/residue: 0.1833 time to fit residues: 31.7590 Evaluate side-chains 140 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 311 SER Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.6980 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6095 Z= 0.140 Angle : 0.549 16.466 8265 Z= 0.247 Chirality : 0.039 0.136 932 Planarity : 0.003 0.031 1029 Dihedral : 7.123 106.915 824 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.92 % Allowed : 14.92 % Favored : 82.15 % 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: 1.73 (0.33), residues: 698 helix: 2.49 (0.30), residues: 303 sheet: -0.13 (0.47), residues: 109 loop : 0.29 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.010 0.001 HIS A 559 PHE 0.008 0.001 PHE A 253 TYR 0.014 0.001 TYR A 482 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.666 Fit side-chains REVERT: A 125 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: A 161 LEU cc_start: 0.7646 (mt) cc_final: 0.7334 (mm) REVERT: A 194 MET cc_start: 0.7757 (ttt) cc_final: 0.7246 (tmm) REVERT: A 290 MET cc_start: 0.8226 (ptp) cc_final: 0.7981 (ptp) REVERT: A 299 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7141 (pt0) REVERT: A 318 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7405 (tt) REVERT: A 334 ASP cc_start: 0.7531 (t70) cc_final: 0.6590 (t0) REVERT: A 377 ASP cc_start: 0.7690 (m-30) cc_final: 0.7338 (t0) REVERT: A 439 LYS cc_start: 0.6927 (mttt) cc_final: 0.6474 (tttp) REVERT: A 557 ARG cc_start: 0.6908 (mmt90) cc_final: 0.6520 (mtm180) REVERT: A 570 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7744 (tt0) REVERT: B 129 TRP cc_start: 0.7184 (t60) cc_final: 0.6773 (t60) REVERT: B 213 ARG cc_start: 0.7732 (mtt180) cc_final: 0.7135 (mtt-85) REVERT: B 401 TRP cc_start: 0.7356 (m100) cc_final: 0.6897 (m-90) REVERT: B 436 LYS cc_start: 0.6129 (tttt) cc_final: 0.4807 (mptt) REVERT: B 439 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7524 (mtpt) REVERT: B 541 ARG cc_start: 0.5968 (mtt-85) cc_final: 0.5593 (mtm-85) REVERT: B 547 GLU cc_start: 0.7156 (tp30) cc_final: 0.6540 (tm-30) outliers start: 19 outliers final: 17 residues processed: 136 average time/residue: 0.1964 time to fit residues: 35.1071 Evaluate side-chains 138 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6095 Z= 0.157 Angle : 0.562 17.087 8265 Z= 0.253 Chirality : 0.040 0.133 932 Planarity : 0.003 0.032 1029 Dihedral : 7.110 104.966 824 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.92 % Allowed : 14.77 % Favored : 82.31 % 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: 1.75 (0.33), residues: 698 helix: 2.50 (0.30), residues: 303 sheet: 0.20 (0.49), residues: 99 loop : 0.15 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.010 0.001 HIS A 559 PHE 0.010 0.001 PHE B 399 TYR 0.014 0.001 TYR A 482 ARG 0.002 0.000 ARG B 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1396 Ramachandran restraints generated. 698 Oldfield, 0 Emsley, 698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.866 Fit side-chains REVERT: A 125 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6511 (mp0) REVERT: A 161 LEU cc_start: 0.7652 (mt) cc_final: 0.7355 (mm) REVERT: A 194 MET cc_start: 0.7752 (ttt) cc_final: 0.7245 (tmm) REVERT: A 290 MET cc_start: 0.8237 (ptp) cc_final: 0.8015 (ptp) REVERT: A 299 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7138 (pt0) REVERT: A 318 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7414 (tt) REVERT: A 334 ASP cc_start: 0.7542 (t70) cc_final: 0.6600 (t0) REVERT: A 377 ASP cc_start: 0.7719 (m-30) cc_final: 0.7406 (t0) REVERT: A 439 LYS cc_start: 0.6958 (mttt) cc_final: 0.6507 (tttp) REVERT: A 456 ASN cc_start: 0.8195 (m-40) cc_final: 0.7965 (m110) REVERT: A 557 ARG cc_start: 0.6898 (mmt90) cc_final: 0.6526 (mtm180) REVERT: A 570 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7738 (tt0) REVERT: B 129 TRP cc_start: 0.7200 (t60) cc_final: 0.6789 (t60) REVERT: B 213 ARG cc_start: 0.7734 (mtt180) cc_final: 0.7132 (mtt-85) REVERT: B 401 TRP cc_start: 0.7351 (m100) cc_final: 0.6903 (m-90) REVERT: B 436 LYS cc_start: 0.6093 (tttt) cc_final: 0.4763 (mptt) REVERT: B 541 ARG cc_start: 0.5858 (mtt-85) cc_final: 0.5456 (mtm-85) REVERT: B 547 GLU cc_start: 0.7166 (tp30) cc_final: 0.6517 (tm-30) outliers start: 19 outliers final: 17 residues processed: 134 average time/residue: 0.2101 time to fit residues: 37.3546 Evaluate side-chains 140 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 376 GLU Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 500 ASN Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 338 ASP Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 473 ASP Chi-restraints excluded: chain B residue 500 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.0970 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 326 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.192912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.169463 restraints weight = 6910.990| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.94 r_work: 0.3803 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6095 Z= 0.152 Angle : 0.555 17.023 8265 Z= 0.250 Chirality : 0.039 0.132 932 Planarity : 0.004 0.037 1029 Dihedral : 7.047 102.675 824 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.08 % Allowed : 14.62 % Favored : 82.31 % 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: 1.79 (0.33), residues: 698 helix: 2.55 (0.30), residues: 303 sheet: 0.18 (0.49), residues: 99 loop : 0.17 (0.39), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.010 0.001 HIS A 559 PHE 0.008 0.001 PHE A 253 TYR 0.014 0.001 TYR A 482 ARG 0.002 0.000 ARG B 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1780.12 seconds wall clock time: 32 minutes 12.16 seconds (1932.16 seconds total)