Starting phenix.real_space_refine on Tue Feb 11 05:32:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jtw_36654/02_2025/8jtw_36654.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jtw_36654/02_2025/8jtw_36654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jtw_36654/02_2025/8jtw_36654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jtw_36654/02_2025/8jtw_36654.map" model { file = "/net/cci-nas-00/data/ceres_data/8jtw_36654/02_2025/8jtw_36654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jtw_36654/02_2025/8jtw_36654.cif" } resolution = 3.23 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= -0.004 sd= 0.179 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2793 2.51 5 N 705 2.21 5 O 750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4282 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3370 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 22, 'TRANS': 425} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 99 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 114} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.34, per 1000 atoms: 0.78 Number of scatterers: 4282 At special positions: 0 Unit cell: (60.2, 79.98, 125.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 750 8.00 N 705 7.00 C 2793 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 558.7 milliseconds 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1024 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 3 sheets defined 62.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 21 through 38 removed outlier: 4.263A pdb=" N LEU A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 33 " --> pdb=" O SER A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 38 through 43 removed outlier: 3.572A pdb=" N GLY A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 62 removed outlier: 4.021A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 141 through 147 removed outlier: 4.788A pdb=" N TRP A 146 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 4.192A pdb=" N GLN A 152 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.777A pdb=" N PHE A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 195 removed outlier: 3.537A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 3.595A pdb=" N MET A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 removed outlier: 3.519A pdb=" N LEU A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 277 Proline residue: A 271 - end of helix Processing helix chain 'A' and resid 333 through 339 removed outlier: 3.740A pdb=" N LEU A 337 " --> pdb=" O PHE A 334 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE A 338 " --> pdb=" O ALA A 335 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 372 removed outlier: 3.598A pdb=" N THR A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE A 348 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE A 349 " --> pdb=" O LYS A 345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 Processing helix chain 'A' and resid 387 through 396 removed outlier: 4.009A pdb=" N PHE A 391 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 422 removed outlier: 3.991A pdb=" N MET A 406 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY A 414 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 415 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 416 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N CYS A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 457 removed outlier: 3.627A pdb=" N ILE A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 447 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 487 removed outlier: 4.096A pdb=" N SER A 470 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 475 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.603A pdb=" N ILE A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 Processing helix chain 'B' and resid 27 through 32 removed outlier: 3.588A pdb=" N TYR B 31 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU B 32 " --> pdb=" O ILE B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 32' Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.692A pdb=" N LYS B 64 " --> pdb=" O ASP B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.507A pdb=" N HIS A 49 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.622A pdb=" N MET B 82 " --> pdb=" O LEU B 18 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 59 removed outlier: 3.996A pdb=" N ASN B 58 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL B 48 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N THR B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET B 34 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 91 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 118 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR B 116 " --> pdb=" O TYR B 93 " (cutoff:3.500A) 230 hydrogen bonds defined for protein. 660 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: 1.17 Time building geometry restraints manager: 1.29 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: 1344 1.34 - 1.46: 1056 1.46 - 1.58: 1938 1.58 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 4389 Sorted by residual: bond pdb=" C VAL A 74 " pdb=" O VAL A 74 " ideal model delta sigma weight residual 1.247 1.230 0.017 1.23e-02 6.61e+03 1.90e+00 bond pdb=" CA LEU A 77 " pdb=" C LEU A 77 " ideal model delta sigma weight residual 1.532 1.515 0.017 1.41e-02 5.03e+03 1.49e+00 bond pdb=" CA THR A 45 " pdb=" CB THR A 45 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.58e-02 4.01e+03 6.50e-01 bond pdb=" N GLY A 78 " pdb=" CA GLY A 78 " ideal model delta sigma weight residual 1.443 1.453 -0.011 1.37e-02 5.33e+03 6.17e-01 bond pdb=" C VAL A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 1.332 1.341 -0.010 1.30e-02 5.92e+03 5.60e-01 ... (remaining 4384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 5900 1.98 - 3.95: 67 3.95 - 5.93: 15 5.93 - 7.91: 0 7.91 - 9.88: 1 Bond angle restraints: 5983 Sorted by residual: angle pdb=" C LEU A 456 " pdb=" N TYR A 457 " pdb=" CA TYR A 457 " ideal model delta sigma weight residual 122.15 112.27 9.88 3.47e+00 8.31e-02 8.11e+00 angle pdb=" CA VAL A 74 " pdb=" C VAL A 74 " pdb=" N PRO A 75 " ideal model delta sigma weight residual 119.37 116.83 2.54 1.13e+00 7.83e-01 5.07e+00 angle pdb=" N ILE A 387 " pdb=" CA ILE A 387 " pdb=" C ILE A 387 " ideal model delta sigma weight residual 108.88 113.56 -4.68 2.16e+00 2.14e-01 4.69e+00 angle pdb=" CA THR A 45 " pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 110.50 114.15 -3.65 1.70e+00 3.46e-01 4.61e+00 angle pdb=" N PRO A 79 " pdb=" CA PRO A 79 " pdb=" C PRO A 79 " ideal model delta sigma weight residual 113.47 110.41 3.06 1.43e+00 4.89e-01 4.58e+00 ... (remaining 5978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.65: 2298 16.65 - 33.30: 193 33.30 - 49.96: 42 49.96 - 66.61: 6 66.61 - 83.26: 3 Dihedral angle restraints: 2542 sinusoidal: 932 harmonic: 1610 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -150.22 64.22 1 1.00e+01 1.00e-02 5.42e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 156.81 -63.81 1 1.00e+01 1.00e-02 5.36e+01 dihedral pdb=" CA VAL A 461 " pdb=" C VAL A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual -180.00 -163.63 -16.37 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 2539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 459 0.034 - 0.068: 167 0.068 - 0.102: 41 0.102 - 0.136: 19 0.136 - 0.170: 1 Chirality restraints: 687 Sorted by residual: chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CA THR A 45 " pdb=" N THR A 45 " pdb=" C THR A 45 " pdb=" CB THR A 45 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE B 51 " pdb=" N ILE B 51 " pdb=" C ILE B 51 " pdb=" CB ILE B 51 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 ... (remaining 684 not shown) Planarity restraints: 751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 460 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C PHE A 460 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE A 460 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 461 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 461 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C VAL A 461 " -0.028 2.00e-02 2.50e+03 pdb=" O VAL A 461 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG A 462 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 387 " -0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 388 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.015 5.00e-02 4.00e+02 ... (remaining 748 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1276 2.83 - 3.35: 3838 3.35 - 3.86: 6280 3.86 - 4.38: 6620 4.38 - 4.90: 12477 Nonbonded interactions: 30491 Sorted by model distance: nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.309 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.329 3.040 nonbonded pdb=" NH1 ARG B 66 " pdb=" O SER B 84 " model vdw 2.424 3.120 nonbonded pdb=" O VAL A 185 " pdb=" OG SER A 189 " model vdw 2.437 3.040 nonbonded pdb=" OD1 ASP B 72 " pdb=" N ASN B 73 " model vdw 2.442 3.120 ... (remaining 30486 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.660 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.850 Find NCS groups from input model: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 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 : 0.002 0.027 4389 Z= 0.149 Angle : 0.556 9.884 5983 Z= 0.291 Chirality : 0.040 0.170 687 Planarity : 0.003 0.026 751 Dihedral : 13.050 83.260 1506 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.14 (0.37), residues: 560 helix: 1.12 (0.31), residues: 318 sheet: 0.81 (0.90), residues: 37 loop : -1.73 (0.42), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.015 0.001 PHE A 275 TYR 0.010 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 368 MET cc_start: 0.6794 (tmm) cc_final: 0.6575 (ttp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1704 time to fit residues: 11.1362 Evaluate side-chains 48 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 0.0770 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 49 optimal weight: 0.2980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.219607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.164597 restraints weight = 4564.670| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.72 r_work: 0.3695 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 4389 Z= 0.142 Angle : 0.524 10.965 5983 Z= 0.262 Chirality : 0.040 0.146 687 Planarity : 0.003 0.036 751 Dihedral : 3.713 14.218 610 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.68 % Allowed : 4.32 % Favored : 95.00 % 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: 0.54 (0.37), residues: 560 helix: 1.43 (0.30), residues: 319 sheet: 0.66 (0.69), residues: 51 loop : -1.62 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.014 0.001 PHE A 275 TYR 0.014 0.001 TYR A 457 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.439 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 0.1665 time to fit residues: 11.7809 Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.0570 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.215522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.163491 restraints weight = 4527.848| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.25 r_work: 0.3658 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4389 Z= 0.163 Angle : 0.523 10.525 5983 Z= 0.262 Chirality : 0.040 0.135 687 Planarity : 0.003 0.035 751 Dihedral : 3.737 15.058 610 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.91 % Allowed : 7.73 % Favored : 91.36 % 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: 0.55 (0.37), residues: 560 helix: 1.52 (0.30), residues: 319 sheet: 0.83 (0.68), residues: 51 loop : -1.84 (0.45), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.008 0.001 PHE A 275 TYR 0.011 0.001 TYR A 457 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.468 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.1894 time to fit residues: 12.9712 Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 0.0010 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.214226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.160391 restraints weight = 4464.763| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.34 r_work: 0.3632 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4389 Z= 0.169 Angle : 0.529 10.079 5983 Z= 0.265 Chirality : 0.040 0.138 687 Planarity : 0.003 0.033 751 Dihedral : 3.750 15.670 610 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.14 % Allowed : 9.77 % Favored : 89.09 % 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: 0.51 (0.37), residues: 560 helix: 1.59 (0.30), residues: 316 sheet: 0.08 (0.65), residues: 57 loop : -1.83 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.020 0.001 PHE A 460 TYR 0.011 0.001 TYR A 457 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.451 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.1871 time to fit residues: 12.2917 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.212322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159406 restraints weight = 4566.680| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.27 r_work: 0.3619 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4389 Z= 0.186 Angle : 0.535 9.884 5983 Z= 0.271 Chirality : 0.041 0.140 687 Planarity : 0.003 0.030 751 Dihedral : 3.843 15.348 610 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.14 % Allowed : 11.36 % Favored : 87.50 % 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: 0.46 (0.37), residues: 560 helix: 1.52 (0.30), residues: 316 sheet: 0.12 (0.65), residues: 57 loop : -1.81 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.014 0.001 PHE A 460 TYR 0.010 0.001 TYR A 457 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.438 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 52 average time/residue: 0.1882 time to fit residues: 12.3978 Evaluate side-chains 50 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 51 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.0870 chunk 20 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.212883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158652 restraints weight = 4533.125| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.37 r_work: 0.3627 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4389 Z= 0.170 Angle : 0.523 9.514 5983 Z= 0.265 Chirality : 0.040 0.140 687 Planarity : 0.003 0.027 751 Dihedral : 3.823 14.919 610 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.91 % Allowed : 12.27 % Favored : 86.82 % 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: 0.53 (0.37), residues: 560 helix: 1.58 (0.30), residues: 316 sheet: 0.12 (0.65), residues: 57 loop : -1.77 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.013 0.001 PHE A 460 TYR 0.011 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.466 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 50 average time/residue: 0.1910 time to fit residues: 12.0633 Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 1 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.209268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154387 restraints weight = 4478.380| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.29 r_work: 0.3546 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4389 Z= 0.183 Angle : 0.532 9.065 5983 Z= 0.270 Chirality : 0.041 0.142 687 Planarity : 0.003 0.027 751 Dihedral : 3.857 15.369 610 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.36 % Allowed : 12.27 % Favored : 86.36 % 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: 0.47 (0.37), residues: 560 helix: 1.53 (0.30), residues: 316 sheet: -0.07 (0.62), residues: 64 loop : -1.78 (0.47), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.010 0.001 PHE A 460 TYR 0.011 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.472 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1924 time to fit residues: 12.6877 Evaluate side-chains 53 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.209227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154724 restraints weight = 4480.322| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 2.31 r_work: 0.3541 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4389 Z= 0.180 Angle : 0.528 8.932 5983 Z= 0.267 Chirality : 0.040 0.142 687 Planarity : 0.003 0.027 751 Dihedral : 3.843 15.177 610 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.36 % Allowed : 13.64 % Favored : 85.00 % 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: 0.49 (0.37), residues: 560 helix: 1.62 (0.31), residues: 310 sheet: -0.11 (0.62), residues: 64 loop : -1.80 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.010 0.001 PHE A 460 TYR 0.011 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.457 Fit side-chains REVERT: A 275 PHE cc_start: 0.5613 (OUTLIER) cc_final: 0.5105 (m-10) outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.1997 time to fit residues: 13.0762 Evaluate side-chains 52 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 0.0370 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 0.2980 chunk 42 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 25 optimal weight: 0.0170 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.213185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.159263 restraints weight = 4564.716| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.33 r_work: 0.3584 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4389 Z= 0.140 Angle : 0.498 9.196 5983 Z= 0.250 Chirality : 0.039 0.135 687 Planarity : 0.003 0.027 751 Dihedral : 3.687 13.421 610 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.14 % Allowed : 13.64 % Favored : 85.23 % 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: 0.66 (0.37), residues: 560 helix: 1.69 (0.31), residues: 317 sheet: -0.08 (0.61), residues: 64 loop : -1.70 (0.47), residues: 179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.013 0.001 PHE A 460 TYR 0.012 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.516 Fit side-chains REVERT: A 275 PHE cc_start: 0.5662 (OUTLIER) cc_final: 0.5106 (m-10) REVERT: A 408 MET cc_start: 0.7550 (tpp) cc_final: 0.7213 (mmm) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 0.1808 time to fit residues: 12.4905 Evaluate side-chains 51 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 32 optimal weight: 0.0170 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.213979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.162357 restraints weight = 4385.737| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 2.47 r_work: 0.3572 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4389 Z= 0.135 Angle : 0.491 8.912 5983 Z= 0.249 Chirality : 0.039 0.135 687 Planarity : 0.003 0.027 751 Dihedral : 3.601 14.172 610 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.91 % Allowed : 14.09 % Favored : 85.00 % 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: 0.68 (0.38), residues: 560 helix: 1.65 (0.31), residues: 324 sheet: -0.06 (0.61), residues: 64 loop : -1.72 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.013 0.001 PHE A 460 TYR 0.011 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1120 Ramachandran restraints generated. 560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.371 Fit side-chains REVERT: A 275 PHE cc_start: 0.5678 (OUTLIER) cc_final: 0.5116 (m-10) REVERT: A 408 MET cc_start: 0.7587 (tpp) cc_final: 0.7289 (mmm) outliers start: 4 outliers final: 3 residues processed: 48 average time/residue: 0.1832 time to fit residues: 11.3585 Evaluate side-chains 49 residues out of total 464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 275 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 7.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.208913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.154660 restraints weight = 4499.502| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.24 r_work: 0.3551 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4389 Z= 0.191 Angle : 0.539 8.612 5983 Z= 0.272 Chirality : 0.041 0.143 687 Planarity : 0.003 0.027 751 Dihedral : 3.792 15.067 610 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.14 % Allowed : 14.09 % Favored : 84.77 % 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: 0.52 (0.37), residues: 560 helix: 1.59 (0.31), residues: 316 sheet: -0.10 (0.62), residues: 64 loop : -1.78 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.009 0.001 PHE A 460 TYR 0.011 0.001 TYR A 457 ARG 0.004 0.000 ARG A 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2419.12 seconds wall clock time: 43 minutes 24.09 seconds (2604.09 seconds total)