Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:10:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/04_2023/8csw_26973.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/04_2023/8csw_26973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/04_2023/8csw_26973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/04_2023/8csw_26973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/04_2023/8csw_26973.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/04_2023/8csw_26973.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.272 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 23 5.16 5 C 3278 2.51 5 N 915 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5332 Number of models: 1 Model: "" Number of chains: 1 Chain: "X" Number of atoms: 5332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 822, 5332 Inner-chain residues flagged as termini: ['pdbres="ALA X 691 "'] Classifications: {'peptide': 657, 'water': 165} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 626, None: 165} Not linked: pdbres="ALA X 691 " pdbres="HOH X 701 " Not linked: pdbres="HOH X 701 " pdbres="HOH X 702 " Not linked: pdbres="HOH X 702 " pdbres="HOH X 703 " Not linked: pdbres="HOH X 703 " pdbres="HOH X 704 " Not linked: pdbres="HOH X 704 " pdbres="HOH X 705 " ... (remaining 160 not shown) Chain breaks: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.54, per 1000 atoms: 0.66 Number of scatterers: 5332 At special positions: 0 Unit cell: (95.45, 102.92, 71.795, 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 23 16.00 O 1116 8.00 N 915 7.00 C 3278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 761.0 milliseconds 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 10 sheets defined 21.2% alpha, 41.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'X' and resid 13 through 21 Processing helix chain 'X' and resid 51 through 58 removed outlier: 3.658A pdb=" N ALA X 55 " --> pdb=" O ALA X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 159 Processing helix chain 'X' and resid 187 through 197 Processing helix chain 'X' and resid 201 through 206 removed outlier: 3.998A pdb=" N SER X 206 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 227 Processing helix chain 'X' and resid 247 through 258 removed outlier: 4.118A pdb=" N ILE X 251 " --> pdb=" O GLY X 247 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 268 Processing helix chain 'X' and resid 269 through 283 removed outlier: 4.363A pdb=" N ALA X 273 " --> pdb=" O TRP X 269 " (cutoff:3.500A) Processing helix chain 'X' and resid 368 through 373 Processing helix chain 'X' and resid 381 through 389 removed outlier: 3.745A pdb=" N ILE X 389 " --> pdb=" O LEU X 385 " (cutoff:3.500A) Processing helix chain 'X' and resid 431 through 436 removed outlier: 3.869A pdb=" N TYR X 435 " --> pdb=" O ILE X 431 " (cutoff:3.500A) Processing helix chain 'X' and resid 441 through 459 Processing helix chain 'X' and resid 550 through 552 No H-bonds generated for 'chain 'X' and resid 550 through 552' Processing sheet with id=AA1, first strand: chain 'X' and resid 7 through 11 removed outlier: 3.509A pdb=" N GLU X 96 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N SER X 105 " --> pdb=" O VAL X 94 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N VAL X 94 " --> pdb=" O SER X 105 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR X 107 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA X 92 " --> pdb=" O THR X 107 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 31 through 34 removed outlier: 4.693A pdb=" N LEU X 31 " --> pdb=" O GLN X 133 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU X 130 " --> pdb=" O LEU X 121 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU X 121 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY X 132 " --> pdb=" O LEU X 119 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 163 through 169 Processing sheet with id=AA4, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.303A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR X 330 " --> pdb=" O LEU X 349 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER X 362 " --> pdb=" O SER X 352 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 322 through 327 removed outlier: 6.303A pdb=" N PHE X 326 " --> pdb=" O PHE X 292 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE X 292 " --> pdb=" O PHE X 326 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL X 288 " --> pdb=" O LYS X 421 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LYS X 421 " --> pdb=" O VAL X 288 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE X 292 " --> pdb=" O ASN X 417 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN X 417 " --> pdb=" O PHE X 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.068A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N CYS X 393 " --> pdb=" O SER X 409 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER X 409 " --> pdb=" O CYS X 393 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL X 395 " --> pdb=" O THR X 407 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER X 576 " --> pdb=" O LEU X 406 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU X 485 " --> pdb=" O CYS X 586 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 303 through 308 removed outlier: 6.068A pdb=" N ILE X 304 " --> pdb=" O VAL X 394 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TRP X 396 " --> pdb=" O ILE X 304 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU X 306 " --> pdb=" O TRP X 396 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N CYS X 398 " --> pdb=" O GLU X 306 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR X 308 " --> pdb=" O CYS X 398 " (cutoff:3.500A) removed outlier: 9.214A pdb=" N CYS X 393 " --> pdb=" O SER X 409 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N SER X 409 " --> pdb=" O CYS X 393 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N VAL X 395 " --> pdb=" O THR X 407 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER X 576 " --> pdb=" O LEU X 406 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LYS X 505 " --> pdb=" O LEU X 533 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU X 533 " --> pdb=" O LYS X 505 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL X 507 " --> pdb=" O LEU X 531 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU X 531 " --> pdb=" O VAL X 507 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU X 509 " --> pdb=" O LYS X 529 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS X 529 " --> pdb=" O LEU X 509 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ILE X 511 " --> pdb=" O TRP X 527 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP X 527 " --> pdb=" O ILE X 511 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N VAL X 513 " --> pdb=" O LYS X 525 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LYS X 525 " --> pdb=" O VAL X 513 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA X 515 " --> pdb=" O ALA X 523 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 475 through 480 Processing sheet with id=AA9, first strand: chain 'X' and resid 590 through 593 Processing sheet with id=AB1, first strand: chain 'X' and resid 597 through 599 removed outlier: 6.536A pdb=" N ALA X 598 " --> pdb=" O VAL X 685 " (cutoff:3.500A) 214 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 899 1.32 - 1.44: 1339 1.44 - 1.57: 3004 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5273 Sorted by residual: bond pdb=" N TRP X 89 " pdb=" CA TRP X 89 " ideal model delta sigma weight residual 1.454 1.493 -0.040 1.17e-02 7.31e+03 1.14e+01 bond pdb=" N GLU X 405 " pdb=" CA GLU X 405 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" N ILE X 104 " pdb=" CA ILE X 104 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA SER X 105 " pdb=" CB SER X 105 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.43e-02 4.89e+03 9.52e+00 bond pdb=" N VAL X 211 " pdb=" CA VAL X 211 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.19e-02 7.06e+03 9.17e+00 ... (remaining 5268 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.63: 164 106.63 - 113.57: 2909 113.57 - 120.51: 2000 120.51 - 127.45: 2013 127.45 - 134.39: 67 Bond angle restraints: 7153 Sorted by residual: angle pdb=" N ASP X 408 " pdb=" CA ASP X 408 " pdb=" C ASP X 408 " ideal model delta sigma weight residual 109.96 101.96 8.00 1.50e+00 4.44e-01 2.85e+01 angle pdb=" C THR X 403 " pdb=" N LEU X 404 " pdb=" CA LEU X 404 " ideal model delta sigma weight residual 123.11 117.38 5.73 1.42e+00 4.96e-01 1.63e+01 angle pdb=" C GLY X 85 " pdb=" N ASP X 86 " pdb=" CA ASP X 86 " ideal model delta sigma weight residual 121.99 116.05 5.94 1.49e+00 4.50e-01 1.59e+01 angle pdb=" CA LEU X 404 " pdb=" C LEU X 404 " pdb=" O LEU X 404 " ideal model delta sigma weight residual 120.46 116.22 4.24 1.07e+00 8.73e-01 1.57e+01 angle pdb=" CB ARG X 287 " pdb=" CG ARG X 287 " pdb=" CD ARG X 287 " ideal model delta sigma weight residual 111.30 102.41 8.89 2.30e+00 1.89e-01 1.49e+01 ... (remaining 7148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 2890 17.21 - 34.42: 199 34.42 - 51.63: 59 51.63 - 68.84: 21 68.84 - 86.04: 7 Dihedral angle restraints: 3176 sinusoidal: 1276 harmonic: 1900 Sorted by residual: dihedral pdb=" CA GLU X 185 " pdb=" C GLU X 185 " pdb=" N GLY X 186 " pdb=" CA GLY X 186 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ILE X 418 " pdb=" C ILE X 418 " pdb=" N SER X 419 " pdb=" CA SER X 419 " ideal model delta harmonic sigma weight residual -180.00 -163.11 -16.89 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" C ILE X 431 " pdb=" N ILE X 431 " pdb=" CA ILE X 431 " pdb=" CB ILE X 431 " ideal model delta harmonic sigma weight residual -122.00 -129.86 7.86 0 2.50e+00 1.60e-01 9.88e+00 ... (remaining 3173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 577 0.050 - 0.100: 168 0.100 - 0.150: 39 0.150 - 0.199: 17 0.199 - 0.249: 8 Chirality restraints: 809 Sorted by residual: chirality pdb=" CB VAL X 106 " pdb=" CA VAL X 106 " pdb=" CG1 VAL X 106 " pdb=" CG2 VAL X 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA LEU X 349 " pdb=" N LEU X 349 " pdb=" C LEU X 349 " pdb=" CB LEU X 349 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA SER X 329 " pdb=" N SER X 329 " pdb=" C SER X 329 " pdb=" CB SER X 329 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 806 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP X 364 " -0.016 2.00e-02 2.50e+03 3.29e-02 1.08e+01 pdb=" C ASP X 364 " 0.057 2.00e-02 2.50e+03 pdb=" O ASP X 364 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU X 365 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER X 576 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.21e+00 pdb=" C SER X 576 " -0.052 2.00e-02 2.50e+03 pdb=" O SER X 576 " 0.020 2.00e-02 2.50e+03 pdb=" N CYS X 577 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP X 89 " 0.013 2.00e-02 2.50e+03 2.65e-02 7.03e+00 pdb=" C TRP X 89 " -0.046 2.00e-02 2.50e+03 pdb=" O TRP X 89 " 0.017 2.00e-02 2.50e+03 pdb=" N TRP X 90 " 0.016 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 691 2.76 - 3.29: 4879 3.29 - 3.83: 9713 3.83 - 4.36: 11710 4.36 - 4.90: 19288 Nonbonded interactions: 46281 Sorted by model distance: nonbonded pdb=" O HOH X 738 " pdb=" O HOH X 851 " model vdw 2.219 2.440 nonbonded pdb=" O HOH X 768 " pdb=" O HOH X 798 " model vdw 2.236 2.440 nonbonded pdb=" O HOH X 792 " pdb=" O HOH X 838 " model vdw 2.261 2.440 nonbonded pdb=" O HOH X 755 " pdb=" O HOH X 839 " model vdw 2.271 2.440 nonbonded pdb=" O ASP X 426 " pdb=" O HOH X 701 " model vdw 2.283 2.440 ... (remaining 46276 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: 1.340 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: 0.010 Extract box with map and model: 5.740 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 18.920 Find NCS groups from input model: 0.150 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 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 : 0.007 0.047 5273 Z= 0.429 Angle : 0.862 8.892 7153 Z= 0.555 Chirality : 0.057 0.249 809 Planarity : 0.006 0.038 921 Dihedral : 14.462 86.044 1944 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer Outliers : 2.33 % 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: 0.83 (0.31), residues: 647 helix: 0.80 (0.45), residues: 116 sheet: 0.87 (0.31), residues: 250 loop : 0.30 (0.34), residues: 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 0.612 Fit side-chains outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 1.4231 time to fit residues: 191.5946 Evaluate side-chains 110 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 104 time to evaluate : 0.617 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.0860 time to fit residues: 1.1555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 50.0000 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 50.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 64 GLN X 76 GLN X 133 GLN X 154 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 433 GLN X 570 HIS ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5273 Z= 0.262 Angle : 0.560 5.523 7153 Z= 0.291 Chirality : 0.043 0.150 809 Planarity : 0.005 0.043 921 Dihedral : 4.881 16.531 710 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.31), residues: 647 helix: 1.59 (0.46), residues: 116 sheet: 0.64 (0.30), residues: 254 loop : 0.49 (0.36), residues: 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.640 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 112 average time/residue: 1.3525 time to fit residues: 157.3680 Evaluate side-chains 105 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 98 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0978 time to fit residues: 0.9968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 74 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 66 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 25 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 154 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5273 Z= 0.175 Angle : 0.504 5.420 7153 Z= 0.258 Chirality : 0.041 0.132 809 Planarity : 0.004 0.035 921 Dihedral : 4.542 16.426 710 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.32), residues: 647 helix: 1.98 (0.47), residues: 116 sheet: 0.55 (0.30), residues: 254 loop : 0.63 (0.37), residues: 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.662 Fit side-chains outliers start: 17 outliers final: 8 residues processed: 107 average time/residue: 1.4767 time to fit residues: 163.7194 Evaluate side-chains 104 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 96 time to evaluate : 0.655 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 0.8184 time to fit residues: 2.5987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 50.0000 chunk 56 optimal weight: 0.0670 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5273 Z= 0.217 Angle : 0.521 5.515 7153 Z= 0.267 Chirality : 0.042 0.138 809 Planarity : 0.004 0.039 921 Dihedral : 4.674 16.531 710 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 3.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.32), residues: 647 helix: 1.91 (0.46), residues: 116 sheet: 0.51 (0.31), residues: 246 loop : 0.53 (0.36), residues: 285 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.564 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 106 average time/residue: 1.3890 time to fit residues: 152.6015 Evaluate side-chains 109 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.568 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 0.7398 time to fit residues: 3.9219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 59 optimal weight: 0.0050 chunk 32 optimal weight: 0.5980 chunk 67 optimal weight: 50.0000 chunk 54 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 20 optimal weight: 0.7980 overall best weight: 2.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 559 ASN ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 5273 Z= 0.237 Angle : 0.538 5.544 7153 Z= 0.275 Chirality : 0.042 0.140 809 Planarity : 0.004 0.040 921 Dihedral : 4.760 16.888 710 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.87 % 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: 0.95 (0.32), residues: 647 helix: 1.84 (0.46), residues: 116 sheet: 0.41 (0.31), residues: 245 loop : 0.49 (0.36), residues: 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.654 Fit side-chains outliers start: 16 outliers final: 11 residues processed: 109 average time/residue: 1.4351 time to fit residues: 162.2047 Evaluate side-chains 109 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.5942 time to fit residues: 2.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 8.9990 chunk 71 optimal weight: 50.0000 chunk 15 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 50.0000 chunk 65 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 76 optimal weight: 50.0000 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 5273 Z= 0.255 Angle : 0.549 5.550 7153 Z= 0.281 Chirality : 0.042 0.140 809 Planarity : 0.004 0.041 921 Dihedral : 4.830 17.549 710 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 3.41 % 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: 0.91 (0.32), residues: 647 helix: 1.81 (0.47), residues: 116 sheet: 0.41 (0.31), residues: 249 loop : 0.43 (0.36), residues: 282 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.666 Fit side-chains outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 1.5459 time to fit residues: 174.5138 Evaluate side-chains 112 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.582 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.6322 time to fit residues: 2.8994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 50.0000 chunk 79 optimal weight: 50.0000 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 5273 Z= 0.274 Angle : 0.560 5.576 7153 Z= 0.288 Chirality : 0.043 0.142 809 Planarity : 0.005 0.045 921 Dihedral : 4.918 18.161 710 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 3.05 % 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: 0.85 (0.32), residues: 647 helix: 1.77 (0.47), residues: 116 sheet: 0.37 (0.31), residues: 249 loop : 0.41 (0.36), residues: 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.564 Fit side-chains outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 1.4623 time to fit residues: 163.6206 Evaluate side-chains 110 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.635 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.5647 time to fit residues: 2.7013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 5273 Z= 0.288 Angle : 0.578 5.588 7153 Z= 0.296 Chirality : 0.043 0.141 809 Planarity : 0.005 0.048 921 Dihedral : 4.972 18.231 710 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.51 % 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: 0.79 (0.32), residues: 647 helix: 1.86 (0.47), residues: 114 sheet: 0.27 (0.31), residues: 249 loop : 0.38 (0.35), residues: 284 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 99 time to evaluate : 0.666 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 108 average time/residue: 1.5276 time to fit residues: 170.7938 Evaluate side-chains 108 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 0.6011 time to fit residues: 2.8580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 50.0000 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 66 optimal weight: 50.0000 chunk 69 optimal weight: 50.0000 chunk 73 optimal weight: 50.0000 chunk 48 optimal weight: 8.9990 chunk 77 optimal weight: 50.0000 chunk 47 optimal weight: 6.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 5273 Z= 0.306 Angle : 0.591 5.607 7153 Z= 0.303 Chirality : 0.043 0.144 809 Planarity : 0.005 0.052 921 Dihedral : 5.048 19.305 710 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 2.51 % 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: 0.76 (0.31), residues: 647 helix: 1.79 (0.47), residues: 114 sheet: 0.27 (0.31), residues: 246 loop : 0.35 (0.35), residues: 287 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.660 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 108 average time/residue: 1.4896 time to fit residues: 166.6079 Evaluate side-chains 108 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 0.648 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.8951 time to fit residues: 2.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 81 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 65 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 69 optimal weight: 50.0000 chunk 19 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 5273 Z= 0.250 Angle : 0.563 6.756 7153 Z= 0.289 Chirality : 0.042 0.147 809 Planarity : 0.004 0.055 921 Dihedral : 4.917 19.120 710 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer Outliers : 1.79 % 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: 0.83 (0.32), residues: 647 helix: 1.80 (0.47), residues: 116 sheet: 0.31 (0.31), residues: 245 loop : 0.41 (0.35), residues: 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1294 Ramachandran restraints generated. 647 Oldfield, 0 Emsley, 647 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 102 time to evaluate : 0.669 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 110 average time/residue: 1.3960 time to fit residues: 159.2500 Evaluate side-chains 110 residues out of total 563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 2 average time/residue: 0.6971 time to fit residues: 2.3345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 0.0970 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 66 optimal weight: 50.0000 chunk 8 optimal weight: 0.8980 chunk 12 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 10.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 133 GLN X 314 GLN X 434 ASN X 646 ASN ** X 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.127999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.103772 restraints weight = 5013.498| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.22 r_work: 0.2900 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 5273 Z= 0.140 Angle : 0.484 5.368 7153 Z= 0.249 Chirality : 0.040 0.133 809 Planarity : 0.004 0.056 921 Dihedral : 4.421 17.967 710 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.32), residues: 647 helix: 2.15 (0.48), residues: 117 sheet: 0.40 (0.31), residues: 252 loop : 0.63 (0.37), residues: 278 =============================================================================== Job complete usr+sys time: 3176.35 seconds wall clock time: 56 minutes 27.59 seconds (3387.59 seconds total)