Starting phenix.real_space_refine on Thu Jul 18 22:37:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtw_36654/07_2024/8jtw_36654.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtw_36654/07_2024/8jtw_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtw_36654/07_2024/8jtw_36654.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtw_36654/07_2024/8jtw_36654.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtw_36654/07_2024/8jtw_36654.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtw_36654/07_2024/8jtw_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 Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 93": "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: 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: 2.58, per 1000 atoms: 0.60 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 - 3.50 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: 1.39 Conformation dependent library (CDL) restraints added in 573.9 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: 0.31 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: 0.82 Time building geometry restraints manager: 1.53 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: 100.37 - 107.09: 134 107.09 - 113.82: 2391 113.82 - 120.54: 1799 120.54 - 127.26: 1606 127.26 - 133.99: 53 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 2.440 nonbonded pdb=" OH TYR B 37 " pdb=" O TRP B 106 " model vdw 2.329 2.440 nonbonded pdb=" NH1 ARG B 66 " pdb=" O SER B 84 " model vdw 2.424 2.520 nonbonded pdb=" O VAL A 185 " pdb=" OG SER A 189 " model vdw 2.437 2.440 nonbonded pdb=" OD1 ASP B 72 " pdb=" N ASN B 73 " model vdw 2.442 2.520 ... (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 ========== 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: 0.810 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.700 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.500 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.455 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: 0.1673 time to fit residues: 11.0081 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 32 optimal weight: 0.0270 chunk 49 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4389 Z= 0.153 Angle : 0.528 10.971 5983 Z= 0.263 Chirality : 0.040 0.149 687 Planarity : 0.003 0.036 751 Dihedral : 3.730 14.765 610 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.45 % Allowed : 4.77 % Favored : 94.77 % 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: 1.38 (0.30), residues: 321 sheet: 0.70 (0.70), residues: 51 loop : -1.61 (0.47), residues: 188 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 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.451 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 0.1639 time to fit residues: 11.4130 Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 27 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 40 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4389 Z= 0.318 Angle : 0.649 9.530 5983 Z= 0.331 Chirality : 0.044 0.155 687 Planarity : 0.004 0.035 751 Dihedral : 4.244 18.428 610 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.14 % Allowed : 7.95 % Favored : 90.91 % 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: -0.08 (0.36), residues: 560 helix: 1.04 (0.30), residues: 313 sheet: 0.62 (0.69), residues: 51 loop : -2.10 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.005 0.002 HIS A 49 PHE 0.012 0.002 PHE A 273 TYR 0.009 0.001 TYR A 457 ARG 0.003 0.000 ARG A 486 *********************** 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 55 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.423 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 53 average time/residue: 0.1645 time to fit residues: 11.2642 Evaluate side-chains 52 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 62 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4389 Z= 0.161 Angle : 0.526 10.120 5983 Z= 0.267 Chirality : 0.040 0.140 687 Planarity : 0.004 0.034 751 Dihedral : 3.889 15.536 610 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.36 % Allowed : 9.77 % Favored : 88.86 % 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: 0.21 (0.37), residues: 560 helix: 1.32 (0.30), residues: 317 sheet: -0.08 (0.67), residues: 57 loop : -1.89 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.003 0.001 HIS A 49 PHE 0.019 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 fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.409 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 52 average time/residue: 0.1704 time to fit residues: 11.4665 Evaluate side-chains 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.448 ------------------------------------------------------------------------------- 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 44 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 0.0870 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.1641 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= 0.168 Angle : 0.531 9.683 5983 Z= 0.266 Chirality : 0.040 0.141 687 Planarity : 0.003 0.032 751 Dihedral : 3.821 15.185 610 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.05 % Allowed : 10.23 % Favored : 87.73 % 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: 0.41 (0.37), residues: 560 helix: 1.49 (0.31), residues: 316 sheet: -0.01 (0.66), residues: 57 loop : -1.81 (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 0.016 0.001 PHE A 460 TYR 0.011 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 56 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 time to evaluate : 0.436 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1531 time to fit residues: 10.3544 Evaluate side-chains 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 62 SER 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 47 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 13 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4389 Z= 0.182 Angle : 0.533 9.440 5983 Z= 0.269 Chirality : 0.040 0.142 687 Planarity : 0.003 0.031 751 Dihedral : 3.837 15.269 610 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % 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: 0.41 (0.37), residues: 560 helix: 1.56 (0.31), residues: 310 sheet: 0.05 (0.66), residues: 57 loop : -1.85 (0.45), residues: 193 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 54 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.407 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1676 time to fit residues: 10.7833 Evaluate side-chains 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 47 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 62 SER 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 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1747 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= 0.136 Angle : 0.498 9.516 5983 Z= 0.251 Chirality : 0.039 0.135 687 Planarity : 0.003 0.030 751 Dihedral : 3.669 13.470 610 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.82 % Allowed : 12.73 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.65 (0.38), residues: 560 helix: 1.77 (0.31), residues: 310 sheet: -0.09 (0.62), residues: 64 loop : -1.74 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 261 HIS 0.003 0.000 HIS A 49 PHE 0.015 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 53 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.471 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 49 average time/residue: 0.1538 time to fit residues: 9.9626 Evaluate side-chains 49 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 62 SER 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 15 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 26 optimal weight: 0.0980 chunk 4 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4389 Z= 0.218 Angle : 0.568 8.796 5983 Z= 0.284 Chirality : 0.041 0.145 687 Planarity : 0.004 0.031 751 Dihedral : 3.890 15.767 610 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.14 % Allowed : 14.32 % Favored : 84.55 % 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: 0.40 (0.37), residues: 560 helix: 1.54 (0.31), residues: 310 sheet: 0.40 (0.64), residues: 58 loop : -1.97 (0.45), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS A 49 PHE 0.009 0.001 PHE A 275 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 51 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.445 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 48 average time/residue: 0.1953 time to fit residues: 11.7849 Evaluate side-chains 50 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 PHE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain B residue 62 SER 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 50 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 15 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 0.0070 chunk 31 optimal weight: 0.0050 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4389 Z= 0.128 Angle : 0.501 9.316 5983 Z= 0.248 Chirality : 0.039 0.136 687 Planarity : 0.003 0.030 751 Dihedral : 3.620 13.509 610 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.14 % Allowed : 14.55 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.38), residues: 560 helix: 1.85 (0.31), residues: 310 sheet: -0.06 (0.62), residues: 64 loop : -1.70 (0.46), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 261 HIS 0.002 0.000 HIS A 49 PHE 0.014 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 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.426 Fit side-chains REVERT: A 275 PHE cc_start: 0.5799 (OUTLIER) cc_final: 0.5175 (m-10) outliers start: 5 outliers final: 3 residues processed: 47 average time/residue: 0.1371 time to fit residues: 8.7855 Evaluate side-chains 46 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 34 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4389 Z= 0.205 Angle : 0.556 8.687 5983 Z= 0.277 Chirality : 0.041 0.146 687 Planarity : 0.003 0.031 751 Dihedral : 3.819 15.340 610 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.91 % Allowed : 15.45 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.37), residues: 560 helix: 1.57 (0.31), residues: 312 sheet: 0.43 (0.64), residues: 58 loop : -1.85 (0.45), residues: 190 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 0.003 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 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.419 Fit side-chains REVERT: A 275 PHE cc_start: 0.5796 (OUTLIER) cc_final: 0.5174 (m-10) outliers start: 4 outliers final: 3 residues processed: 47 average time/residue: 0.1718 time to fit residues: 10.4263 Evaluate side-chains 48 residues out of total 464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.211239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.156322 restraints weight = 4439.818| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.32 r_work: 0.3616 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4389 Z= 0.203 Angle : 0.557 8.650 5983 Z= 0.279 Chirality : 0.041 0.147 687 Planarity : 0.003 0.031 751 Dihedral : 3.868 15.558 610 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 1.14 % Allowed : 14.77 % Favored : 84.09 % 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: 0.40 (0.37), residues: 560 helix: 1.50 (0.31), residues: 312 sheet: -0.13 (0.62), residues: 64 loop : -1.78 (0.46), residues: 184 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 0.008 0.001 PHE A 275 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: 1308.95 seconds wall clock time: 23 minutes 51.00 seconds (1431.00 seconds total)