Starting phenix.real_space_refine on Fri Aug 22 15:41:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8csw_26973/08_2025/8csw_26973.cif Found real_map, /net/cci-nas-00/data/ceres_data/8csw_26973/08_2025/8csw_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/cci-nas-00/data/ceres_data/8csw_26973/08_2025/8csw_26973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8csw_26973/08_2025/8csw_26973.map" model { file = "/net/cci-nas-00/data/ceres_data/8csw_26973/08_2025/8csw_26973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8csw_26973/08_2025/8csw_26973.cif" } 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 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 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: 1.10, per 1000 atoms: 0.21 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: 0.26 Conformation dependent library (CDL) restraints added in 125.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.17 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: 0.83 Time building geometry restraints manager: 0.37 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: 2.310 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: 0.360 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.420 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- 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= 0.405 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.003 0.001 ARG X 450 TYR 0.017 0.002 TYR X 167 PHE 0.022 0.002 PHE X 639 TRP 0.009 0.002 TRP X 90 HIS 0.005 0.001 HIS X 632 Details of bonding type rmsd covalent geometry : bond 0.00650 ( 5273) covalent geometry : angle 0.86160 ( 7153) hydrogen bonds : bond 0.14040 ( 205) hydrogen bonds : angle 7.18321 ( 600) *********************** 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 : 0.209 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: 0.5818 time to fit residues: 78.0664 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 : 0.209 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 570 HIS ** X 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.125803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.100973 restraints weight = 5044.273| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.25 r_work: 0.2858 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5273 Z= 0.177 Angle : 0.559 5.608 7153 Z= 0.292 Chirality : 0.043 0.153 809 Planarity : 0.005 0.043 921 Dihedral : 6.623 59.583 719 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.51 % Allowed : 11.83 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.31), residues: 647 helix: 1.58 (0.46), residues: 116 sheet: 0.58 (0.31), residues: 247 loop : 0.41 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 259 TYR 0.016 0.002 TYR X 167 PHE 0.013 0.002 PHE X 639 TRP 0.009 0.001 TRP X 90 HIS 0.006 0.001 HIS X 570 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 5273) covalent geometry : angle 0.55904 ( 7153) hydrogen bonds : bond 0.04345 ( 205) hydrogen bonds : angle 5.50044 ( 600) *********************** 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: 14 poor density : 105 time to evaluate : 0.154 Fit side-chains REVERT: X 16 ARG cc_start: 0.7684 (ttm170) cc_final: 0.7480 (tmm-80) REVERT: X 127 LYS cc_start: 0.6394 (ttpp) cc_final: 0.5922 (ttpt) REVERT: X 133 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.7820 (mm110) REVERT: X 143 ARG cc_start: 0.8518 (ttp-170) cc_final: 0.7929 (ttm-80) REVERT: X 194 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7818 (ttp-110) REVERT: X 442 LEU cc_start: 0.8008 (mp) cc_final: 0.7648 (mm) REVERT: X 445 LYS cc_start: 0.8260 (tmtt) cc_final: 0.7918 (ttmt) REVERT: X 446 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7450 (tm-30) REVERT: X 452 GLU cc_start: 0.7622 (mm-30) cc_final: 0.6805 (mt-10) REVERT: X 483 SER cc_start: 0.8313 (p) cc_final: 0.8042 (m) REVERT: X 593 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8274 (tppt) REVERT: X 599 GLU cc_start: 0.8323 (tt0) cc_final: 0.7846 (tm-30) REVERT: X 638 ARG cc_start: 0.7882 (mpt90) cc_final: 0.5983 (mtm110) REVERT: X 647 THR cc_start: 0.8419 (m) cc_final: 0.8188 (p) REVERT: X 651 LYS cc_start: 0.7519 (mptt) cc_final: 0.7100 (ptmm) outliers start: 14 outliers final: 7 residues processed: 111 average time/residue: 0.6274 time to fit residues: 72.0640 Evaluate side-chains 107 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.251 ------------------------------------------------------------------------------- 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 534 THR Chi-restraints excluded: chain X residue 549 PHE Chi-restraints excluded: chain X residue 576 SER Chi-restraints excluded: chain X residue 659 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 0.0010 chunk 62 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 61 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 overall best weight: 1.2790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.128535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.103662 restraints weight = 4968.759| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.26 r_work: 0.2891 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5273 Z= 0.112 Angle : 0.494 5.493 7153 Z= 0.255 Chirality : 0.041 0.137 809 Planarity : 0.004 0.035 921 Dihedral : 5.466 59.965 715 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.15 % Allowed : 12.72 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.32), residues: 647 helix: 1.90 (0.47), residues: 117 sheet: 0.49 (0.31), residues: 245 loop : 0.54 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 259 TYR 0.012 0.001 TYR X 167 PHE 0.010 0.001 PHE X 639 TRP 0.009 0.001 TRP X 90 HIS 0.002 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 5273) covalent geometry : angle 0.49411 ( 7153) hydrogen bonds : bond 0.03531 ( 205) hydrogen bonds : angle 5.11913 ( 600) *********************** 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 to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.149 Fit side-chains REVERT: X 127 LYS cc_start: 0.6409 (ttpp) cc_final: 0.6018 (ttpt) REVERT: X 143 ARG cc_start: 0.8509 (ttp-170) cc_final: 0.7908 (ttm-80) REVERT: X 442 LEU cc_start: 0.7968 (mp) cc_final: 0.7591 (mm) REVERT: X 445 LYS cc_start: 0.8227 (tmtt) cc_final: 0.7678 (ttpp) REVERT: X 446 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7511 (tm-30) REVERT: X 452 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6762 (mt-10) REVERT: X 483 SER cc_start: 0.8269 (p) cc_final: 0.8054 (m) REVERT: X 593 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8208 (ttmt) REVERT: X 599 GLU cc_start: 0.8316 (tt0) cc_final: 0.7816 (tm-30) REVERT: X 638 ARG cc_start: 0.7817 (mpt90) cc_final: 0.5895 (mtm110) REVERT: X 651 LYS cc_start: 0.7485 (mptt) cc_final: 0.7069 (pttp) outliers start: 12 outliers final: 4 residues processed: 108 average time/residue: 0.6695 time to fit residues: 74.6579 Evaluate side-chains 104 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 100 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 448 LEU 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 25 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 5 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.129692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.105068 restraints weight = 4955.599| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.25 r_work: 0.2927 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1524 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= 0.100 Angle : 0.469 5.463 7153 Z= 0.242 Chirality : 0.040 0.134 809 Planarity : 0.004 0.040 921 Dihedral : 4.681 47.961 712 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.97 % Allowed : 13.26 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.12 (0.32), residues: 647 helix: 2.10 (0.47), residues: 117 sheet: 0.46 (0.31), residues: 248 loop : 0.61 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 259 TYR 0.011 0.001 TYR X 167 PHE 0.009 0.001 PHE X 639 TRP 0.008 0.001 TRP X 90 HIS 0.002 0.000 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 5273) covalent geometry : angle 0.46883 ( 7153) hydrogen bonds : bond 0.03181 ( 205) hydrogen bonds : angle 4.86384 ( 600) *********************** 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 to be fit. rotamer outliers: 11 poor density : 108 time to evaluate : 0.206 Fit side-chains REVERT: X 127 LYS cc_start: 0.6422 (ttpp) cc_final: 0.6048 (ttpt) REVERT: X 143 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.7895 (ttm-80) REVERT: X 405 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6525 (tp30) REVERT: X 406 LEU cc_start: 0.8693 (tp) cc_final: 0.8354 (tm) REVERT: X 442 LEU cc_start: 0.7945 (mp) cc_final: 0.7592 (mm) REVERT: X 445 LYS cc_start: 0.8213 (tmtt) cc_final: 0.7673 (ttpp) REVERT: X 446 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7422 (tm-30) REVERT: X 452 GLU cc_start: 0.7611 (mm-30) cc_final: 0.6768 (mt-10) REVERT: X 599 GLU cc_start: 0.8253 (tt0) cc_final: 0.7763 (tm-30) REVERT: X 638 ARG cc_start: 0.7786 (mpt90) cc_final: 0.5858 (mtm110) REVERT: X 651 LYS cc_start: 0.7459 (mptt) cc_final: 0.7053 (ptmm) REVERT: X 672 MET cc_start: 0.8472 (mmp) cc_final: 0.8161 (mmm) outliers start: 11 outliers final: 6 residues processed: 115 average time/residue: 0.6518 time to fit residues: 77.5990 Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 103 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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 310 GLU 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 28 optimal weight: 0.0070 chunk 25 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 122 GLN X 133 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.128038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.103103 restraints weight = 5067.383| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.26 r_work: 0.2886 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1479 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= 0.129 Angle : 0.494 5.546 7153 Z= 0.254 Chirality : 0.041 0.138 809 Planarity : 0.004 0.040 921 Dihedral : 4.768 48.115 711 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.69 % Allowed : 13.80 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.32), residues: 647 helix: 2.06 (0.47), residues: 116 sheet: 0.48 (0.31), residues: 244 loop : 0.59 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 259 TYR 0.013 0.001 TYR X 167 PHE 0.013 0.001 PHE X 639 TRP 0.006 0.001 TRP X 90 HIS 0.003 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5273) covalent geometry : angle 0.49430 ( 7153) hydrogen bonds : bond 0.03414 ( 205) hydrogen bonds : angle 4.94477 ( 600) *********************** 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: 15 poor density : 105 time to evaluate : 0.158 Fit side-chains REVERT: X 127 LYS cc_start: 0.6436 (ttpp) cc_final: 0.6050 (ttpt) REVERT: X 133 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.7811 (mm110) REVERT: X 143 ARG cc_start: 0.8491 (ttp-170) cc_final: 0.7902 (ttm-80) REVERT: X 194 ARG cc_start: 0.8133 (ttp80) cc_final: 0.7686 (ttm110) REVERT: X 405 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6524 (tp30) REVERT: X 442 LEU cc_start: 0.7958 (mp) cc_final: 0.7576 (mm) REVERT: X 445 LYS cc_start: 0.8204 (tmtt) cc_final: 0.7653 (ttpp) REVERT: X 446 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7422 (tm-30) REVERT: X 452 GLU cc_start: 0.7635 (mm-30) cc_final: 0.6746 (mt-10) REVERT: X 581 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7424 (mp0) REVERT: X 593 LYS cc_start: 0.8479 (ttmm) cc_final: 0.8026 (mttp) REVERT: X 599 GLU cc_start: 0.8304 (tt0) cc_final: 0.7795 (tm-30) REVERT: X 638 ARG cc_start: 0.7820 (mpt90) cc_final: 0.5869 (mtm110) REVERT: X 651 LYS cc_start: 0.7518 (mptt) cc_final: 0.7087 (ptmm) outliers start: 15 outliers final: 6 residues processed: 113 average time/residue: 0.6619 time to fit residues: 77.3467 Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 448 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 23 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** X 646 ASN ** 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 = 0.3301 r_free = 0.3301 target = 0.125742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.100617 restraints weight = 5085.875| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.27 r_work: 0.2866 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 5273 Z= 0.211 Angle : 0.576 5.700 7153 Z= 0.296 Chirality : 0.044 0.150 809 Planarity : 0.004 0.042 921 Dihedral : 5.129 46.045 711 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.41 % Allowed : 13.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.32), residues: 647 helix: 1.78 (0.46), residues: 116 sheet: 0.37 (0.31), residues: 249 loop : 0.42 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 259 TYR 0.017 0.002 TYR X 167 PHE 0.013 0.002 PHE X 639 TRP 0.005 0.001 TRP X 90 HIS 0.004 0.001 HIS X 22 Details of bonding type rmsd covalent geometry : bond 0.00478 ( 5273) covalent geometry : angle 0.57554 ( 7153) hydrogen bonds : bond 0.04017 ( 205) hydrogen bonds : angle 5.22782 ( 600) *********************** 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 121 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.222 Fit side-chains REVERT: X 96 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: X 143 ARG cc_start: 0.8489 (ttp-170) cc_final: 0.7908 (ttm-80) REVERT: X 194 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7678 (ttm110) REVERT: X 405 GLU cc_start: 0.7114 (mt-10) cc_final: 0.6525 (tp30) REVERT: X 406 LEU cc_start: 0.8769 (tt) cc_final: 0.8531 (tp) REVERT: X 439 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: X 442 LEU cc_start: 0.8005 (mp) cc_final: 0.7614 (mm) REVERT: X 445 LYS cc_start: 0.8245 (tmtt) cc_final: 0.7666 (ttpp) REVERT: X 446 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7414 (tm-30) REVERT: X 452 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6767 (mt-10) REVERT: X 581 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: X 593 LYS cc_start: 0.8467 (ttmm) cc_final: 0.8155 (ttmt) REVERT: X 599 GLU cc_start: 0.8285 (tt0) cc_final: 0.7804 (tm-30) REVERT: X 638 ARG cc_start: 0.7876 (mpt90) cc_final: 0.5934 (mtm110) REVERT: X 651 LYS cc_start: 0.7559 (mptt) cc_final: 0.7123 (ptmm) outliers start: 19 outliers final: 9 residues processed: 113 average time/residue: 0.6419 time to fit residues: 74.9970 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 LEU Chi-restraints excluded: chain X residue 534 THR Chi-restraints excluded: chain X residue 576 SER 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 19 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** X 646 ASN X 658 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.128701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.103991 restraints weight = 5012.195| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.25 r_work: 0.2901 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1581 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= 0.114 Angle : 0.490 5.493 7153 Z= 0.253 Chirality : 0.041 0.136 809 Planarity : 0.004 0.047 921 Dihedral : 4.768 48.338 711 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.33 % Allowed : 14.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.32), residues: 647 helix: 1.97 (0.47), residues: 117 sheet: 0.39 (0.31), residues: 243 loop : 0.58 (0.36), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 259 TYR 0.012 0.001 TYR X 167 PHE 0.008 0.001 PHE X 39 TRP 0.009 0.001 TRP X 90 HIS 0.002 0.001 HIS X 658 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 5273) covalent geometry : angle 0.49027 ( 7153) hydrogen bonds : bond 0.03224 ( 205) hydrogen bonds : angle 4.93028 ( 600) *********************** 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 112 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.130 Fit side-chains REVERT: X 96 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: X 127 LYS cc_start: 0.6417 (ttpp) cc_final: 0.5944 (ttpt) REVERT: X 143 ARG cc_start: 0.8497 (ttp-170) cc_final: 0.7905 (ttm-80) REVERT: X 194 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7662 (ttm110) REVERT: X 405 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6659 (tp30) REVERT: X 439 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7216 (mp0) REVERT: X 442 LEU cc_start: 0.7978 (mp) cc_final: 0.7602 (mm) REVERT: X 445 LYS cc_start: 0.8201 (tmtt) cc_final: 0.7637 (ttpp) REVERT: X 446 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7421 (tm-30) REVERT: X 452 GLU cc_start: 0.7605 (mm-30) cc_final: 0.6700 (mt-10) REVERT: X 581 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7367 (mp0) REVERT: X 593 LYS cc_start: 0.8452 (ttmm) cc_final: 0.8033 (mttp) REVERT: X 599 GLU cc_start: 0.8273 (tt0) cc_final: 0.7774 (tm-30) REVERT: X 638 ARG cc_start: 0.7795 (mpt90) cc_final: 0.5843 (mtm110) REVERT: X 651 LYS cc_start: 0.7495 (mptt) cc_final: 0.7062 (ptmm) outliers start: 13 outliers final: 5 residues processed: 106 average time/residue: 0.6581 time to fit residues: 71.9236 Evaluate side-chains 107 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 99 time to evaluate : 0.133 ------------------------------------------------------------------------------- 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 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 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 51 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.125714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.100758 restraints weight = 4957.302| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 1.25 r_work: 0.2857 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5273 Z= 0.200 Angle : 0.570 5.668 7153 Z= 0.293 Chirality : 0.043 0.147 809 Planarity : 0.004 0.049 921 Dihedral : 5.122 46.117 711 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.69 % Allowed : 14.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.32), residues: 647 helix: 1.74 (0.46), residues: 116 sheet: 0.37 (0.31), residues: 249 loop : 0.43 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG X 259 TYR 0.016 0.002 TYR X 167 PHE 0.014 0.002 PHE X 639 TRP 0.005 0.001 TRP X 90 HIS 0.004 0.001 HIS X 658 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 5273) covalent geometry : angle 0.56962 ( 7153) hydrogen bonds : bond 0.03906 ( 205) hydrogen bonds : angle 5.21766 ( 600) *********************** 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 115 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.210 Fit side-chains REVERT: X 96 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: X 127 LYS cc_start: 0.6467 (ttpp) cc_final: 0.5965 (ttpt) REVERT: X 133 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.7815 (mm110) REVERT: X 143 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.7916 (ttm-80) REVERT: X 194 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7681 (ttm110) REVERT: X 405 GLU cc_start: 0.7127 (mt-10) cc_final: 0.6531 (tp30) REVERT: X 439 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: X 442 LEU cc_start: 0.8000 (mp) cc_final: 0.7599 (mm) REVERT: X 445 LYS cc_start: 0.8243 (tmtt) cc_final: 0.7657 (ttpp) REVERT: X 446 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7419 (tm-30) REVERT: X 452 GLU cc_start: 0.7659 (mm-30) cc_final: 0.6752 (mt-10) REVERT: X 581 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: X 593 LYS cc_start: 0.8475 (ttmm) cc_final: 0.8170 (ttmt) REVERT: X 599 GLU cc_start: 0.8285 (tt0) cc_final: 0.7794 (tm-30) REVERT: X 638 ARG cc_start: 0.7859 (mpt90) cc_final: 0.5922 (mtm110) REVERT: X 651 LYS cc_start: 0.7560 (mptt) cc_final: 0.7133 (ptmm) REVERT: X 672 MET cc_start: 0.8588 (mmp) cc_final: 0.8353 (mmm) outliers start: 15 outliers final: 8 residues processed: 110 average time/residue: 0.7032 time to fit residues: 79.9012 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 177 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 534 THR Chi-restraints excluded: chain X residue 576 SER Chi-restraints excluded: chain X residue 581 GLU Chi-restraints excluded: chain X residue 586 CYS Chi-restraints excluded: chain X residue 653 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 39 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.126670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.101812 restraints weight = 4982.929| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.25 r_work: 0.2871 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1474 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= 0.166 Angle : 0.545 5.812 7153 Z= 0.281 Chirality : 0.042 0.144 809 Planarity : 0.004 0.052 921 Dihedral : 5.071 46.607 711 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.51 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.32), residues: 647 helix: 1.75 (0.46), residues: 116 sheet: 0.34 (0.31), residues: 244 loop : 0.46 (0.35), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG X 259 TYR 0.015 0.002 TYR X 167 PHE 0.010 0.002 PHE X 549 TRP 0.007 0.001 TRP X 90 HIS 0.005 0.001 HIS X 658 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 5273) covalent geometry : angle 0.54540 ( 7153) hydrogen bonds : bond 0.03710 ( 205) hydrogen bonds : angle 5.16433 ( 600) *********************** 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 113 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.214 Fit side-chains REVERT: X 96 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: X 127 LYS cc_start: 0.6468 (ttpp) cc_final: 0.5974 (ttpt) REVERT: X 133 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7826 (mm110) REVERT: X 143 ARG cc_start: 0.8519 (ttp-170) cc_final: 0.7924 (ttm-80) REVERT: X 194 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7692 (ttm110) REVERT: X 405 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6663 (tp30) REVERT: X 439 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7305 (mp0) REVERT: X 442 LEU cc_start: 0.7996 (mp) cc_final: 0.7600 (mm) REVERT: X 445 LYS cc_start: 0.8242 (tmtt) cc_final: 0.7660 (ttpp) REVERT: X 446 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7423 (tm-30) REVERT: X 452 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6753 (mt-10) REVERT: X 581 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: X 593 LYS cc_start: 0.8459 (ttmm) cc_final: 0.8156 (ttmt) REVERT: X 599 GLU cc_start: 0.8278 (tt0) cc_final: 0.7792 (tm-30) REVERT: X 638 ARG cc_start: 0.7861 (mpt90) cc_final: 0.5914 (mtm110) REVERT: X 651 LYS cc_start: 0.7547 (mptt) cc_final: 0.6985 (mmtp) REVERT: X 672 MET cc_start: 0.8591 (mmp) cc_final: 0.8364 (mmm) outliers start: 14 outliers final: 8 residues processed: 109 average time/residue: 0.6462 time to fit residues: 72.7194 Evaluate side-chains 109 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 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 Chi-restraints excluded: chain X residue 653 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 41 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.125873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.100780 restraints weight = 5052.109| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.26 r_work: 0.2857 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5273 Z= 0.184 Angle : 0.563 5.641 7153 Z= 0.290 Chirality : 0.043 0.146 809 Planarity : 0.004 0.055 921 Dihedral : 5.161 46.311 711 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.51 % Allowed : 15.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.80 (0.31), residues: 647 helix: 1.70 (0.46), residues: 116 sheet: 0.33 (0.31), residues: 246 loop : 0.38 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 259 TYR 0.016 0.002 TYR X 167 PHE 0.023 0.002 PHE X 548 TRP 0.006 0.001 TRP X 90 HIS 0.005 0.001 HIS X 658 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 5273) covalent geometry : angle 0.56299 ( 7153) hydrogen bonds : bond 0.03863 ( 205) hydrogen bonds : angle 5.20793 ( 600) ********************** 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 to be fit. rotamer outliers: 14 poor density : 98 time to evaluate : 0.285 Fit side-chains REVERT: X 96 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: X 127 LYS cc_start: 0.6474 (ttpp) cc_final: 0.5971 (ttpt) REVERT: X 133 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.7820 (mm110) REVERT: X 143 ARG cc_start: 0.8529 (ttp-170) cc_final: 0.7925 (ttm-80) REVERT: X 194 ARG cc_start: 0.8141 (ttp80) cc_final: 0.7688 (ttm110) REVERT: X 405 GLU cc_start: 0.7124 (mt-10) cc_final: 0.6664 (tp30) REVERT: X 439 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: X 442 LEU cc_start: 0.7994 (mp) cc_final: 0.7608 (mm) REVERT: X 445 LYS cc_start: 0.8252 (tmtt) cc_final: 0.7663 (ttpp) REVERT: X 446 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7421 (tm-30) REVERT: X 452 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6763 (mt-10) REVERT: X 581 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7382 (mp0) REVERT: X 593 LYS cc_start: 0.8472 (ttmm) cc_final: 0.8164 (ttmt) REVERT: X 599 GLU cc_start: 0.8277 (tt0) cc_final: 0.7788 (tm-30) REVERT: X 638 ARG cc_start: 0.7865 (mpt90) cc_final: 0.5936 (mtm110) REVERT: X 651 LYS cc_start: 0.7556 (mptt) cc_final: 0.6992 (mmtp) REVERT: X 672 MET cc_start: 0.8617 (mmp) cc_final: 0.8383 (mmm) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 0.6665 time to fit residues: 73.7872 Evaluate side-chains 111 residues out of total 563 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain X residue 96 GLU Chi-restraints excluded: chain X residue 133 GLN Chi-restraints excluded: chain X residue 177 GLU Chi-restraints excluded: chain X residue 281 CYS Chi-restraints excluded: chain X residue 310 GLU Chi-restraints excluded: chain X residue 362 SER Chi-restraints excluded: chain X residue 439 GLU Chi-restraints excluded: chain X residue 448 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 Chi-restraints excluded: chain X residue 653 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6171 > 50: distance: 51 - 56: 34.028 distance: 58 - 59: 19.740 distance: 62 - 65: 40.810 distance: 63 - 69: 41.182 distance: 69 - 70: 32.279 distance: 70 - 71: 34.535 distance: 70 - 73: 33.896 distance: 71 - 75: 41.771 distance: 75 - 76: 44.129 distance: 76 - 79: 40.140 distance: 77 - 78: 21.376 distance: 77 - 86: 17.521 distance: 79 - 80: 5.958 distance: 80 - 81: 16.095 distance: 81 - 82: 23.771 distance: 82 - 83: 40.368 distance: 83 - 84: 40.672 distance: 83 - 85: 39.872 distance: 86 - 87: 56.161 distance: 87 - 90: 40.926 distance: 91 - 92: 36.401 distance: 95 - 96: 39.770 distance: 97 - 98: 56.660 distance: 98 - 99: 39.685 distance: 98 - 100: 57.501 distance: 99 - 101: 6.695 distance: 100 - 102: 39.573 distance: 101 - 102: 57.009 distance: 103 - 104: 30.407 distance: 104 - 105: 28.839 distance: 104 - 107: 26.013 distance: 105 - 106: 39.060 distance: 105 - 111: 50.446 distance: 107 - 108: 42.080 distance: 108 - 109: 56.701 distance: 108 - 110: 56.234 distance: 111 - 112: 31.735 distance: 111 - 162: 32.975 distance: 112 - 115: 23.399 distance: 114 - 159: 35.920 distance: 116 - 117: 6.395 distance: 117 - 118: 16.929 distance: 117 - 120: 23.076 distance: 118 - 119: 17.774 distance: 118 - 124: 13.982 distance: 120 - 121: 43.246 distance: 120 - 122: 18.904 distance: 121 - 123: 5.250 distance: 124 - 149: 34.189 distance: 125 - 126: 9.344 distance: 125 - 128: 32.936 distance: 126 - 127: 29.739 distance: 126 - 133: 24.626 distance: 127 - 146: 24.095 distance: 128 - 129: 53.404 distance: 129 - 130: 40.681 distance: 130 - 131: 41.384 distance: 131 - 132: 36.775 distance: 181 - 238: 3.316 distance: 186 - 226: 3.100