Starting phenix.real_space_refine on Thu Nov 14 08:36:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/11_2024/8csw_26973.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/11_2024/8csw_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_26973/11_2024/8csw_26973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/11_2024/8csw_26973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/11_2024/8csw_26973.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8csw_26973/11_2024/8csw_26973.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.272 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. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5332 Number of models: 1 Model: "" Number of chains: 2 Chain: "X" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5167 Classifications: {'peptide': 657} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 30, 'TRANS': 626} 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 Chain: "X" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Time building chain proxies: 4.78, per 1000 atoms: 0.90 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 644.5 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: 0.66 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: 2.35 Time building geometry restraints manager: 1.97 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: 0.00 - 1.78: 6768 1.78 - 3.56: 322 3.56 - 5.33: 50 5.33 - 7.11: 11 7.11 - 8.89: 2 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 3.040 nonbonded pdb=" O HOH X 768 " pdb=" O HOH X 798 " model vdw 2.236 3.040 nonbonded pdb=" O HOH X 792 " pdb=" O HOH X 838 " model vdw 2.261 3.040 nonbonded pdb=" O HOH X 755 " pdb=" O HOH X 839 " model vdw 2.271 3.040 nonbonded pdb=" O ASP X 426 " pdb=" O HOH X 701 " model vdw 2.283 3.040 ... (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: 5.380 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: 4.760 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 19.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:23.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.120 ------------------------------------------------------------------------------- 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 % Allowed : 8.24 % Favored : 89.43 % 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: 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP X 90 HIS 0.005 0.001 HIS X 632 PHE 0.022 0.002 PHE X 639 TYR 0.017 0.002 TYR X 167 ARG 0.003 0.001 ARG X 450 *********************** 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 to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 1.299 Fit side-chains REVERT: X 16 ARG cc_start: 0.7419 (ttm170) cc_final: 0.7217 (tmm-80) REVERT: X 88 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7557 (mmpt) REVERT: X 143 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7961 (ttm-80) REVERT: X 194 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7695 (ttp-110) REVERT: X 442 LEU cc_start: 0.8074 (mp) cc_final: 0.7733 (mm) REVERT: X 445 LYS cc_start: 0.8096 (tmtt) cc_final: 0.7647 (ttpp) REVERT: X 446 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7537 (tm-30) REVERT: X 452 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6893 (mt-10) REVERT: X 483 SER cc_start: 0.8344 (p) cc_final: 0.8047 (m) REVERT: X 508 GLN cc_start: 0.7339 (tt0) cc_final: 0.6839 (mt0) REVERT: X 593 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8154 (tppt) REVERT: X 638 ARG cc_start: 0.7856 (mpt90) cc_final: 0.6170 (mtm110) REVERT: X 647 THR cc_start: 0.8417 (m) cc_final: 0.8179 (p) REVERT: X 651 LYS cc_start: 0.7522 (mptt) cc_final: 0.7244 (pttp) outliers start: 13 outliers final: 6 residues processed: 130 average time/residue: 1.6877 time to fit residues: 227.3895 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 404 LEU Chi-restraints excluded: chain X residue 406 LEU Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 576 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 X 433 GLN X 559 ASN X 570 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 5273 Z= 0.143 Angle : 0.493 5.409 7153 Z= 0.258 Chirality : 0.041 0.145 809 Planarity : 0.004 0.041 921 Dihedral : 6.191 58.775 719 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.69 % Allowed : 11.47 % Favored : 85.84 % 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: 1.12 (0.31), residues: 647 helix: 1.80 (0.46), residues: 117 sheet: 0.63 (0.31), residues: 246 loop : 0.57 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 90 HIS 0.006 0.001 HIS X 570 PHE 0.010 0.001 PHE X 548 TYR 0.011 0.001 TYR X 167 ARG 0.008 0.000 ARG X 259 *********************** 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 119 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.585 Fit side-chains REVERT: X 16 ARG cc_start: 0.7344 (ttm170) cc_final: 0.7134 (tmm-80) REVERT: X 127 LYS cc_start: 0.6521 (ttpp) cc_final: 0.6112 (ttpt) REVERT: X 133 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.7686 (mm110) REVERT: X 143 ARG cc_start: 0.8185 (ttp-170) cc_final: 0.7955 (ttm-80) REVERT: X 194 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7619 (ttm110) REVERT: X 442 LEU cc_start: 0.7915 (mp) cc_final: 0.7651 (mm) REVERT: X 445 LYS cc_start: 0.8057 (tmtt) cc_final: 0.7654 (ttpp) REVERT: X 446 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7648 (tm-30) REVERT: X 452 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6860 (mt-10) REVERT: X 508 GLN cc_start: 0.7454 (tt0) cc_final: 0.6951 (mt0) REVERT: X 593 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8109 (tppt) REVERT: X 597 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7581 (mtmt) REVERT: X 599 GLU cc_start: 0.7961 (tt0) cc_final: 0.7584 (tm-30) REVERT: X 638 ARG cc_start: 0.7767 (mpt90) cc_final: 0.5961 (mtm110) REVERT: X 651 LYS cc_start: 0.7371 (mptt) cc_final: 0.7075 (pttp) outliers start: 15 outliers final: 5 residues processed: 110 average time/residue: 1.5024 time to fit residues: 171.5036 Evaluate side-chains 103 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 96 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 570 HIS Chi-restraints excluded: chain X residue 576 SER Chi-restraints excluded: chain X residue 597 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 570 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1323 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= 0.196 Angle : 0.520 5.551 7153 Z= 0.269 Chirality : 0.042 0.144 809 Planarity : 0.004 0.034 921 Dihedral : 5.026 45.814 713 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.15 % Allowed : 12.37 % Favored : 85.48 % 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: 1.12 (0.32), residues: 647 helix: 1.91 (0.46), residues: 116 sheet: 0.57 (0.31), residues: 246 loop : 0.57 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 PHE 0.012 0.002 PHE X 639 TYR 0.014 0.002 TYR X 167 ARG 0.006 0.000 ARG X 259 *********************** 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 110 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.986 Fit side-chains REVERT: X 16 ARG cc_start: 0.7344 (ttm170) cc_final: 0.7144 (tmm-80) REVERT: X 127 LYS cc_start: 0.6539 (ttpp) cc_final: 0.6185 (ttpt) REVERT: X 143 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7956 (ttm-80) REVERT: X 442 LEU cc_start: 0.7942 (mp) cc_final: 0.7675 (mm) REVERT: X 445 LYS cc_start: 0.8055 (tmtt) cc_final: 0.7655 (ttpp) REVERT: X 446 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7439 (tm-30) REVERT: X 452 GLU cc_start: 0.7474 (mm-30) cc_final: 0.6851 (mt-10) REVERT: X 593 LYS cc_start: 0.8347 (ttmm) cc_final: 0.8092 (ttmt) REVERT: X 599 GLU cc_start: 0.7960 (tt0) cc_final: 0.7540 (tm-30) REVERT: X 638 ARG cc_start: 0.7771 (mpt90) cc_final: 0.5942 (mtm110) REVERT: X 651 LYS cc_start: 0.7433 (mptt) cc_final: 0.6912 (mmtp) outliers start: 12 outliers final: 4 residues processed: 103 average time/residue: 1.6976 time to fit residues: 181.3406 Evaluate side-chains 100 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5273 Z= 0.157 Angle : 0.483 5.492 7153 Z= 0.249 Chirality : 0.041 0.137 809 Planarity : 0.004 0.041 921 Dihedral : 4.721 47.369 711 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.79 % Allowed : 13.44 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.32), residues: 647 helix: 2.01 (0.47), residues: 117 sheet: 0.52 (0.31), residues: 245 loop : 0.58 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 90 HIS 0.002 0.001 HIS X 22 PHE 0.009 0.001 PHE X 639 TYR 0.012 0.001 TYR X 167 ARG 0.007 0.000 ARG X 259 *********************** 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 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 104 time to evaluate : 0.538 Fit side-chains REVERT: X 127 LYS cc_start: 0.6546 (ttpp) cc_final: 0.6202 (ttpt) REVERT: X 143 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7941 (ttm-80) REVERT: X 405 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6325 (tp30) REVERT: X 406 LEU cc_start: 0.8752 (tp) cc_final: 0.8417 (tm) REVERT: X 442 LEU cc_start: 0.7924 (mp) cc_final: 0.7658 (mm) REVERT: X 445 LYS cc_start: 0.8043 (tmtt) cc_final: 0.7674 (ttpp) REVERT: X 446 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7436 (tm-30) REVERT: X 452 GLU cc_start: 0.7476 (mm-30) cc_final: 0.6835 (mt-10) REVERT: X 593 LYS cc_start: 0.8319 (ttmm) cc_final: 0.8073 (ttmt) REVERT: X 599 GLU cc_start: 0.7924 (tt0) cc_final: 0.7507 (tm-30) REVERT: X 638 ARG cc_start: 0.7743 (mpt90) cc_final: 0.5904 (mtm110) REVERT: X 651 LYS cc_start: 0.7400 (mptt) cc_final: 0.6881 (mmtp) REVERT: X 672 MET cc_start: 0.8481 (mmp) cc_final: 0.8187 (mmm) outliers start: 10 outliers final: 6 residues processed: 112 average time/residue: 1.5921 time to fit residues: 184.4215 Evaluate side-chains 108 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 9.9990 chunk 35 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 32 optimal weight: 0.4980 chunk 56 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- 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 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1480 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= 0.181 Angle : 0.495 5.544 7153 Z= 0.255 Chirality : 0.041 0.140 809 Planarity : 0.004 0.041 921 Dihedral : 4.787 47.670 711 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.05 % Allowed : 12.72 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.32), residues: 647 helix: 2.02 (0.47), residues: 116 sheet: 0.46 (0.31), residues: 249 loop : 0.55 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 PHE 0.011 0.001 PHE X 639 TYR 0.013 0.001 TYR X 167 ARG 0.010 0.000 ARG X 259 *********************** 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 120 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.585 Fit side-chains REVERT: X 127 LYS cc_start: 0.6573 (ttpp) cc_final: 0.6222 (ttpt) REVERT: X 133 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7771 (mm110) REVERT: X 143 ARG cc_start: 0.8192 (ttp-170) cc_final: 0.7941 (ttm-80) REVERT: X 194 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7578 (ttm110) REVERT: X 213 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7896 (mtt180) REVERT: X 405 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6321 (tp30) REVERT: X 442 LEU cc_start: 0.7936 (mp) cc_final: 0.7672 (mm) REVERT: X 445 LYS cc_start: 0.8053 (tmtt) cc_final: 0.7651 (ttpp) REVERT: X 446 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7425 (tm-30) REVERT: X 452 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6826 (mt-10) REVERT: X 533 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7240 (mt) REVERT: X 581 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: X 593 LYS cc_start: 0.8322 (ttmm) cc_final: 0.8079 (ttmt) REVERT: X 599 GLU cc_start: 0.7921 (tt0) cc_final: 0.7500 (tm-30) REVERT: X 638 ARG cc_start: 0.7748 (mpt90) cc_final: 0.5892 (mtm110) REVERT: X 651 LYS cc_start: 0.7421 (mptt) cc_final: 0.6906 (mmtp) outliers start: 17 outliers final: 8 residues processed: 113 average time/residue: 1.7499 time to fit residues: 204.2555 Evaluate side-chains 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 533 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 6.9990 chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 33 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 122 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5273 Z= 0.147 Angle : 0.477 5.678 7153 Z= 0.245 Chirality : 0.040 0.135 809 Planarity : 0.004 0.046 921 Dihedral : 4.687 48.978 711 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.69 % Allowed : 13.98 % Favored : 83.33 % 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: 1.12 (0.32), residues: 647 helix: 2.04 (0.47), residues: 117 sheet: 0.45 (0.32), residues: 243 loop : 0.64 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 90 HIS 0.002 0.001 HIS X 22 PHE 0.008 0.001 PHE X 639 TYR 0.012 0.001 TYR X 167 ARG 0.011 0.000 ARG X 259 *********************** 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 119 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.602 Fit side-chains REVERT: X 127 LYS cc_start: 0.6569 (ttpp) cc_final: 0.6279 (ttpt) REVERT: X 143 ARG cc_start: 0.8189 (ttp-170) cc_final: 0.7939 (ttm-80) REVERT: X 194 ARG cc_start: 0.8004 (ttp80) cc_final: 0.7562 (ttm110) REVERT: X 213 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7868 (mtt180) REVERT: X 405 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6342 (tp30) REVERT: X 406 LEU cc_start: 0.8705 (tp) cc_final: 0.8385 (tm) REVERT: X 439 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7118 (mp0) REVERT: X 442 LEU cc_start: 0.7923 (mp) cc_final: 0.7644 (mm) REVERT: X 445 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7590 (ttpp) REVERT: X 446 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7426 (tm-30) REVERT: X 452 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6805 (mt-10) REVERT: X 581 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7151 (mp0) REVERT: X 593 LYS cc_start: 0.8300 (ttmm) cc_final: 0.8066 (ttmt) REVERT: X 599 GLU cc_start: 0.7906 (tt0) cc_final: 0.7509 (tm-30) REVERT: X 638 ARG cc_start: 0.7722 (mpt90) cc_final: 0.5867 (mtm110) REVERT: X 651 LYS cc_start: 0.7393 (mptt) cc_final: 0.6877 (mmtp) REVERT: X 672 MET cc_start: 0.8483 (mmp) cc_final: 0.8209 (mmm) outliers start: 15 outliers final: 8 residues processed: 115 average time/residue: 1.6328 time to fit residues: 194.2307 Evaluate side-chains 113 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 38 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5273 Z= 0.201 Angle : 0.509 5.568 7153 Z= 0.261 Chirality : 0.041 0.140 809 Planarity : 0.004 0.047 921 Dihedral : 4.845 48.072 711 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.33 % Allowed : 14.70 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.32), residues: 647 helix: 1.95 (0.47), residues: 116 sheet: 0.44 (0.31), residues: 249 loop : 0.54 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 PHE 0.012 0.002 PHE X 639 TYR 0.014 0.002 TYR X 167 ARG 0.012 0.000 ARG X 259 *********************** 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 to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.679 Fit side-chains REVERT: X 96 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7144 (tm-30) REVERT: X 143 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7947 (ttm-80) REVERT: X 194 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7565 (ttm110) REVERT: X 213 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.7911 (mtt180) REVERT: X 405 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6321 (tp30) REVERT: X 439 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: X 442 LEU cc_start: 0.7969 (mp) cc_final: 0.7694 (mm) REVERT: X 445 LYS cc_start: 0.8028 (tmtt) cc_final: 0.7632 (ttpp) REVERT: X 446 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7415 (tm-30) REVERT: X 452 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6812 (mt-10) REVERT: X 581 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: X 593 LYS cc_start: 0.8322 (ttmm) cc_final: 0.8082 (ttmt) REVERT: X 599 GLU cc_start: 0.7919 (tt0) cc_final: 0.7524 (tm-30) REVERT: X 638 ARG cc_start: 0.7758 (mpt90) cc_final: 0.5892 (mtm110) REVERT: X 651 LYS cc_start: 0.7445 (mptt) cc_final: 0.6926 (mmtp) outliers start: 13 outliers final: 8 residues processed: 114 average time/residue: 1.5336 time to fit residues: 180.9262 Evaluate side-chains 113 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 529 LYS Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 416 ASN X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5273 Z= 0.121 Angle : 0.463 6.623 7153 Z= 0.237 Chirality : 0.040 0.133 809 Planarity : 0.004 0.052 921 Dihedral : 4.517 52.423 711 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.61 % Allowed : 15.77 % Favored : 82.62 % 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: 1.23 (0.32), residues: 647 helix: 2.15 (0.48), residues: 117 sheet: 0.50 (0.32), residues: 243 loop : 0.72 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 90 HIS 0.002 0.000 HIS X 658 PHE 0.007 0.001 PHE X 326 TYR 0.010 0.001 TYR X 167 ARG 0.011 0.000 ARG X 259 *********************** 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 114 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.645 Fit side-chains REVERT: X 96 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7159 (tm-30) REVERT: X 127 LYS cc_start: 0.6557 (ttpp) cc_final: 0.6181 (ttpt) REVERT: X 143 ARG cc_start: 0.8182 (ttp-170) cc_final: 0.7930 (ttm-80) REVERT: X 194 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7540 (ttm110) REVERT: X 406 LEU cc_start: 0.8697 (tp) cc_final: 0.8480 (tm) REVERT: X 439 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: X 442 LEU cc_start: 0.7898 (mp) cc_final: 0.7632 (mm) REVERT: X 445 LYS cc_start: 0.8004 (tmtt) cc_final: 0.7587 (ttpp) REVERT: X 446 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7410 (tm-30) REVERT: X 452 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6781 (mt-10) REVERT: X 593 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7973 (mttp) REVERT: X 599 GLU cc_start: 0.7856 (tt0) cc_final: 0.7499 (tm-30) REVERT: X 638 ARG cc_start: 0.7680 (mpt90) cc_final: 0.5819 (mtm110) REVERT: X 651 LYS cc_start: 0.7343 (mptt) cc_final: 0.7030 (ptmm) REVERT: X 672 MET cc_start: 0.8455 (mmp) cc_final: 0.8211 (mmm) outliers start: 9 outliers final: 4 residues processed: 112 average time/residue: 1.5208 time to fit residues: 176.4269 Evaluate side-chains 110 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 104 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 chunk 52 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.0050 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 508 GLN ** 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: 0.8629 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5273 Z= 0.213 Angle : 0.525 5.943 7153 Z= 0.269 Chirality : 0.042 0.140 809 Planarity : 0.004 0.045 921 Dihedral : 4.871 49.205 711 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.97 % Allowed : 15.05 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.32), residues: 647 helix: 1.95 (0.47), residues: 116 sheet: 0.51 (0.32), residues: 244 loop : 0.63 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 90 HIS 0.004 0.001 HIS X 658 PHE 0.009 0.002 PHE X 549 TYR 0.015 0.002 TYR X 167 ARG 0.011 0.000 ARG X 259 *********************** 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 to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.617 Fit side-chains REVERT: X 96 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: X 127 LYS cc_start: 0.6581 (ttpp) cc_final: 0.6179 (ttpt) REVERT: X 143 ARG cc_start: 0.8198 (ttp-170) cc_final: 0.7949 (ttm-80) REVERT: X 194 ARG cc_start: 0.8006 (ttp80) cc_final: 0.7555 (ttm110) REVERT: X 213 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.7892 (mtt180) REVERT: X 439 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: X 442 LEU cc_start: 0.7964 (mp) cc_final: 0.7671 (mm) REVERT: X 445 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7581 (ttpp) REVERT: X 446 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7409 (tm-30) REVERT: X 452 GLU cc_start: 0.7480 (mm-30) cc_final: 0.6793 (mt-10) REVERT: X 593 LYS cc_start: 0.8302 (ttmm) cc_final: 0.8077 (ttmt) REVERT: X 599 GLU cc_start: 0.7904 (tt0) cc_final: 0.7518 (tm-30) REVERT: X 638 ARG cc_start: 0.7745 (mpt90) cc_final: 0.5871 (mtm110) REVERT: X 651 LYS cc_start: 0.7424 (mptt) cc_final: 0.6901 (mmtp) REVERT: X 672 MET cc_start: 0.8543 (mmp) cc_final: 0.8295 (mmm) outliers start: 11 outliers final: 4 residues processed: 110 average time/residue: 1.6338 time to fit residues: 185.9824 Evaluate side-chains 108 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 7 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5273 Z= 0.221 Angle : 0.535 5.769 7153 Z= 0.274 Chirality : 0.042 0.142 809 Planarity : 0.004 0.046 921 Dihedral : 4.931 47.440 711 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.97 % Allowed : 15.23 % Favored : 82.80 % 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: 0.99 (0.32), residues: 647 helix: 1.88 (0.47), residues: 116 sheet: 0.44 (0.31), residues: 246 loop : 0.52 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 PHE 0.009 0.002 PHE X 39 TYR 0.015 0.002 TYR X 167 ARG 0.012 0.000 ARG X 259 ********************** 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 115 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.632 Fit side-chains REVERT: X 96 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7133 (tm-30) REVERT: X 127 LYS cc_start: 0.6581 (ttpp) cc_final: 0.6187 (ttpt) REVERT: X 143 ARG cc_start: 0.8200 (ttp-170) cc_final: 0.7949 (ttm-80) REVERT: X 194 ARG cc_start: 0.8013 (ttp80) cc_final: 0.7555 (ttm110) REVERT: X 213 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7910 (mtt180) REVERT: X 439 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7194 (mp0) REVERT: X 442 LEU cc_start: 0.7976 (mp) cc_final: 0.7701 (mm) REVERT: X 445 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7631 (ttpp) REVERT: X 446 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7410 (tm-30) REVERT: X 452 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6784 (mt-10) REVERT: X 593 LYS cc_start: 0.8312 (ttmm) cc_final: 0.8076 (ttmt) REVERT: X 599 GLU cc_start: 0.7917 (tt0) cc_final: 0.7513 (tm-30) REVERT: X 638 ARG cc_start: 0.7766 (mpt90) cc_final: 0.5903 (mtm110) REVERT: X 651 LYS cc_start: 0.7452 (mptt) cc_final: 0.6927 (mmtp) REVERT: X 672 MET cc_start: 0.8574 (mmp) cc_final: 0.8326 (mmm) outliers start: 11 outliers final: 6 residues processed: 113 average time/residue: 1.5975 time to fit residues: 186.8744 Evaluate side-chains 112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 213 ARG Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 403 THR Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 68 GLN ** X 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 508 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.125796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.100981 restraints weight = 4997.297| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.25 r_work: 0.2860 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.1508 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= 0.279 Angle : 0.573 5.658 7153 Z= 0.294 Chirality : 0.043 0.146 809 Planarity : 0.004 0.046 921 Dihedral : 5.122 46.462 711 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 1.97 % Allowed : 15.59 % Favored : 82.44 % 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: 0.88 (0.32), residues: 647 helix: 1.85 (0.47), residues: 114 sheet: 0.37 (0.31), residues: 246 loop : 0.41 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X 90 HIS 0.006 0.001 HIS X 658 PHE 0.011 0.002 PHE X 184 TYR 0.016 0.002 TYR X 167 ARG 0.012 0.001 ARG X 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3838.28 seconds wall clock time: 70 minutes 49.66 seconds (4249.66 seconds total)