Starting phenix.real_space_refine on Tue Feb 11 02:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkf_14040/02_2025/7qkf_14040.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkf_14040/02_2025/7qkf_14040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qkf_14040/02_2025/7qkf_14040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkf_14040/02_2025/7qkf_14040.map" model { file = "/net/cci-nas-00/data/ceres_data/7qkf_14040/02_2025/7qkf_14040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkf_14040/02_2025/7qkf_14040.cif" } resolution = 2.83 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= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1164 2.51 5 N 336 2.21 5 O 351 1.98 5 H 1926 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3783 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 804 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 457 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 804 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "D" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 457 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "E" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 804 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 457 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Time building chain proxies: 3.11, per 1000 atoms: 0.82 Number of scatterers: 3783 At special positions: 0 Unit cell: (70.04, 91.464, 33.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 351 8.00 N 336 7.00 C 1164 6.00 H 1926 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS B 322 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS D 322 " distance=2.04 Simple disulfide: pdb=" SG CYS E 322 " - pdb=" SG CYS F 322 " distance=2.02 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: 0.85 Conformation dependent library (CDL) restraints added in 246.2 milliseconds 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 432 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.709A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 317 through 322 Processing sheet with id=AA3, first strand: chain 'C' and resid 325 through 330 Processing sheet with id=AA4, first strand: chain 'C' and resid 339 through 340 removed outlier: 6.791A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 343 through 346 removed outlier: 6.255A pdb=" N LYS A 343 " --> pdb=" O LEU E 344 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N PHE E 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP A 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 349 through 350 removed outlier: 6.513A pdb=" N ARG A 349 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 353 through 356 removed outlier: 6.445A pdb=" N LYS A 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N SER E 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLY A 355 " --> pdb=" O SER E 356 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.422A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 313 through 324 removed outlier: 6.772A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N SER D 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 315 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL D 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N SER D 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N SER D 324 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLY B 323 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 328 through 329 removed outlier: 6.635A pdb=" N ILE B 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) 43 hydrogen bonds defined for protein. 129 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.14 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.55 - 0.80: 3 0.80 - 1.06: 480 1.06 - 1.31: 1771 1.31 - 1.56: 1542 1.56 - 1.81: 14 Bond restraints: 3810 Sorted by residual: bond pdb=" CG2 VAL A 313 " pdb="HG23 VAL A 313 " ideal model delta sigma weight residual 0.970 0.553 0.417 2.00e-02 2.50e+03 4.35e+02 bond pdb=" CG2 VAL A 313 " pdb="HG21 VAL A 313 " ideal model delta sigma weight residual 0.970 0.586 0.384 2.00e-02 2.50e+03 3.68e+02 bond pdb=" CG2 VAL A 313 " pdb="HG22 VAL A 313 " ideal model delta sigma weight residual 0.970 0.727 0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" NH1 ARG A 349 " pdb="HH12 ARG A 349 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N SER E 324 " pdb=" H SER E 324 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.57: 6876 7.57 - 15.14: 30 15.14 - 22.71: 17 22.71 - 30.28: 19 30.28 - 37.85: 9 Bond angle restraints: 6951 Sorted by residual: angle pdb=" CG1 VAL B 318 " pdb=" CB VAL B 318 " pdb=" HB VAL B 318 " ideal model delta sigma weight residual 108.00 70.15 37.85 3.00e+00 1.11e-01 1.59e+02 angle pdb=" CA VAL F 313 " pdb=" CB VAL F 313 " pdb=" CG1 VAL F 313 " ideal model delta sigma weight residual 110.40 130.74 -20.34 1.70e+00 3.46e-01 1.43e+02 angle pdb=" CA VAL B 318 " pdb=" CB VAL B 318 " pdb=" CG1 VAL B 318 " ideal model delta sigma weight residual 110.40 130.66 -20.26 1.70e+00 3.46e-01 1.42e+02 angle pdb=" CG1 VAL F 318 " pdb=" CB VAL F 318 " pdb=" HB VAL F 318 " ideal model delta sigma weight residual 108.00 72.50 35.50 3.00e+00 1.11e-01 1.40e+02 angle pdb=" CA VAL B 318 " pdb=" CB VAL B 318 " pdb=" HB VAL B 318 " ideal model delta sigma weight residual 109.00 75.33 33.67 3.00e+00 1.11e-01 1.26e+02 ... (remaining 6946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 1576 17.80 - 35.59: 106 35.59 - 53.39: 42 53.39 - 71.18: 42 71.18 - 88.98: 4 Dihedral angle restraints: 1770 sinusoidal: 1014 harmonic: 756 Sorted by residual: dihedral pdb=" C VAL A 337 " pdb=" N VAL A 337 " pdb=" CA VAL A 337 " pdb=" CB VAL A 337 " ideal model delta harmonic sigma weight residual -122.00 -137.87 15.87 0 2.50e+00 1.60e-01 4.03e+01 dihedral pdb=" CA LYS B 317 " pdb=" C LYS B 317 " pdb=" N VAL B 318 " pdb=" CA VAL B 318 " ideal model delta harmonic sigma weight residual 180.00 152.18 27.82 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA GLY A 334 " pdb=" C GLY A 334 " pdb=" N GLY A 335 " pdb=" CA GLY A 335 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 1767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.231: 262 0.231 - 0.462: 13 0.462 - 0.694: 2 0.694 - 0.925: 3 0.925 - 1.156: 5 Chirality restraints: 285 Sorted by residual: chirality pdb=" CB VAL D 318 " pdb=" CA VAL D 318 " pdb=" CG1 VAL D 318 " pdb=" CG2 VAL D 318 " both_signs ideal model delta sigma weight residual False -2.63 -1.47 -1.16 2.00e-01 2.50e+01 3.34e+01 chirality pdb=" CB VAL E 313 " pdb=" CA VAL E 313 " pdb=" CG1 VAL E 313 " pdb=" CG2 VAL E 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.50 -1.13 2.00e-01 2.50e+01 3.17e+01 chirality pdb=" CB VAL D 313 " pdb=" CA VAL D 313 " pdb=" CG1 VAL D 313 " pdb=" CG2 VAL D 313 " both_signs ideal model delta sigma weight residual False -2.63 -1.55 -1.08 2.00e-01 2.50e+01 2.90e+01 ... (remaining 282 not shown) Planarity restraints: 549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 307 " 0.048 2.00e-02 2.50e+03 4.78e-02 3.42e+01 pdb=" CD GLN B 307 " -0.019 2.00e-02 2.50e+03 pdb=" OE1 GLN B 307 " -0.046 2.00e-02 2.50e+03 pdb=" NE2 GLN B 307 " 0.025 2.00e-02 2.50e+03 pdb="HE21 GLN B 307 " -0.069 2.00e-02 2.50e+03 pdb="HE22 GLN B 307 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 330 " 0.054 2.00e-02 2.50e+03 3.89e-02 3.41e+01 pdb=" CG HIS E 330 " -0.046 2.00e-02 2.50e+03 pdb=" ND1 HIS E 330 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS E 330 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS E 330 " -0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS E 330 " -0.041 2.00e-02 2.50e+03 pdb=" HD2 HIS E 330 " 0.028 2.00e-02 2.50e+03 pdb=" HE1 HIS E 330 " 0.043 2.00e-02 2.50e+03 pdb=" HE2 HIS E 330 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 333 " 0.032 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" N GLY A 334 " -0.098 2.00e-02 2.50e+03 pdb=" CA GLY A 334 " 0.029 2.00e-02 2.50e+03 pdb=" H GLY A 334 " 0.038 2.00e-02 2.50e+03 ... (remaining 546 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 421 2.23 - 2.82: 7031 2.82 - 3.42: 10020 3.42 - 4.01: 13175 4.01 - 4.60: 18482 Nonbonded interactions: 49129 Sorted by model distance: nonbonded pdb=" HG SER A 356 " pdb=" OD1 ASP C 358 " model vdw 1.640 2.450 nonbonded pdb=" OD1 ASP A 358 " pdb=" HG SER E 356 " model vdw 1.653 2.450 nonbonded pdb=" HZ2 LYS A 331 " pdb=" OD1 ASP F 314 " model vdw 1.684 2.450 nonbonded pdb=" HG SER A 316 " pdb=" O SER C 316 " model vdw 1.717 2.450 nonbonded pdb=" OD2 ASP B 314 " pdb=" HZ2 LYS C 331 " model vdw 1.725 2.450 ... (remaining 49124 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } 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: 2.930 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: 0.070 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 13.810 Find NCS groups from input model: 0.080 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:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.012 0.136 1884 Z= 0.824 Angle : 2.232 20.336 2520 Z= 1.446 Chirality : 0.205 1.156 285 Planarity : 0.010 0.033 318 Dihedral : 13.419 88.978 717 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 0.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Cbeta Deviations : 0.93 % 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: -2.72 (0.44), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.07 (0.33), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.004 HIS D 330 PHE 0.013 0.003 PHE C 346 TYR 0.035 0.009 TYR C 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 311 LYS cc_start: 0.6624 (mtpt) cc_final: 0.6148 (mttm) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 2.5564 time to fit residues: 181.7620 Evaluate side-chains 38 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN F 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.124076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111876 restraints weight = 7113.320| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 1.90 r_work: 0.3716 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 1884 Z= 0.315 Angle : 1.125 10.188 2520 Z= 0.579 Chirality : 0.244 1.410 285 Planarity : 0.005 0.039 318 Dihedral : 7.923 25.291 252 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.31 % Allowed : 14.35 % 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: -3.36 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 330 PHE 0.002 0.001 PHE E 346 TYR 0.012 0.002 TYR A 310 ARG 0.003 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.8014 (mttp) REVERT: E 311 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7776 (mttp) REVERT: E 353 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8430 (mtpp) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 2.5573 time to fit residues: 111.9837 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 353 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.0470 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.127862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115072 restraints weight = 6936.008| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 1.87 r_work: 0.3750 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3660 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1884 Z= 0.247 Angle : 1.071 10.831 2520 Z= 0.542 Chirality : 0.255 1.433 285 Planarity : 0.005 0.033 318 Dihedral : 6.734 22.352 252 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.31 % Allowed : 17.59 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.001 TYR A 310 ARG 0.003 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7874 (mttp) REVERT: A 340 LYS cc_start: 0.7968 (tmtm) cc_final: 0.7160 (mmtp) REVERT: E 311 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7758 (mttp) outliers start: 5 outliers final: 2 residues processed: 42 average time/residue: 2.6735 time to fit residues: 114.2605 Evaluate side-chains 40 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 4.9990 chunk 5 optimal weight: 0.0470 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.128388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.116304 restraints weight = 6765.301| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.76 r_work: 0.3746 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3662 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.265 Angle : 1.056 10.924 2520 Z= 0.532 Chirality : 0.254 1.426 285 Planarity : 0.005 0.036 318 Dihedral : 6.439 21.044 252 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.24 % Allowed : 18.52 % Favored : 78.24 % 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: -3.47 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.007 0.001 PHE E 346 TYR 0.010 0.001 TYR C 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8008 (tmtm) cc_final: 0.7228 (mmtp) REVERT: E 311 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7776 (mttp) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 2.6009 time to fit residues: 111.1839 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 3 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.128001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.115861 restraints weight = 6910.365| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.81 r_work: 0.3747 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3658 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.244 Angle : 1.043 10.914 2520 Z= 0.527 Chirality : 0.255 1.424 285 Planarity : 0.005 0.039 318 Dihedral : 6.197 22.323 252 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.31 % Allowed : 18.06 % Favored : 79.63 % 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: -3.49 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.005 0.001 PHE E 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7812 (mttp) REVERT: A 340 LYS cc_start: 0.8036 (tmtm) cc_final: 0.7226 (mmtp) REVERT: E 311 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7788 (mttp) outliers start: 5 outliers final: 4 residues processed: 40 average time/residue: 2.3741 time to fit residues: 96.8076 Evaluate side-chains 41 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.0770 chunk 4 optimal weight: 5.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.129784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.117609 restraints weight = 6794.765| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.80 r_work: 0.3770 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.230 Angle : 1.024 10.937 2520 Z= 0.519 Chirality : 0.255 1.429 285 Planarity : 0.005 0.039 318 Dihedral : 5.837 19.791 252 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.31 % Allowed : 17.59 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.38), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.63 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.001 TYR C 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7999 (tmtm) cc_final: 0.7220 (mmtp) REVERT: E 311 LYS cc_start: 0.8145 (mtpt) cc_final: 0.7763 (mttp) outliers start: 5 outliers final: 5 residues processed: 41 average time/residue: 2.2309 time to fit residues: 93.3735 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 0.0050 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.130251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.118170 restraints weight = 6724.120| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.78 r_work: 0.3781 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1884 Z= 0.231 Angle : 1.020 10.934 2520 Z= 0.516 Chirality : 0.254 1.426 285 Planarity : 0.005 0.039 318 Dihedral : 5.698 19.632 252 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.78 % Allowed : 17.59 % Favored : 79.63 % 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: -3.43 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.29), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.004 0.001 PHE E 346 TYR 0.009 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8003 (tmtm) cc_final: 0.7224 (mmtp) REVERT: A 341 SER cc_start: 0.8601 (t) cc_final: 0.8208 (p) REVERT: C 316 SER cc_start: 0.8627 (m) cc_final: 0.8197 (t) REVERT: E 311 LYS cc_start: 0.8122 (mtpt) cc_final: 0.7748 (mttp) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 2.2333 time to fit residues: 91.1011 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.129969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.118061 restraints weight = 6720.031| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 1.78 r_work: 0.3782 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1884 Z= 0.228 Angle : 1.013 10.922 2520 Z= 0.513 Chirality : 0.254 1.427 285 Planarity : 0.005 0.039 318 Dihedral : 5.642 19.274 252 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.31 % Allowed : 18.06 % Favored : 79.63 % 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: -3.39 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.58 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.004 0.001 PHE E 346 TYR 0.010 0.001 TYR C 310 ARG 0.002 0.001 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8027 (tmtm) cc_final: 0.7257 (mmtm) REVERT: A 341 SER cc_start: 0.8600 (t) cc_final: 0.8199 (p) REVERT: C 316 SER cc_start: 0.8627 (m) cc_final: 0.8174 (t) REVERT: E 311 LYS cc_start: 0.8106 (mtpt) cc_final: 0.7730 (mttp) outliers start: 5 outliers final: 4 residues processed: 39 average time/residue: 2.3233 time to fit residues: 92.4592 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.133083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.120228 restraints weight = 6753.865| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.85 r_work: 0.3838 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3753 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.232 Angle : 1.019 10.911 2520 Z= 0.515 Chirality : 0.255 1.431 285 Planarity : 0.005 0.046 318 Dihedral : 5.571 19.206 252 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.78 % Allowed : 19.44 % Favored : 77.78 % 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: -3.43 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.007 0.001 PHE E 346 TYR 0.010 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.7986 (tmtm) cc_final: 0.7198 (mmtm) REVERT: A 341 SER cc_start: 0.8554 (t) cc_final: 0.8146 (p) REVERT: C 316 SER cc_start: 0.8620 (m) cc_final: 0.8160 (t) REVERT: E 311 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7723 (mttp) outliers start: 6 outliers final: 5 residues processed: 39 average time/residue: 2.2555 time to fit residues: 89.8921 Evaluate side-chains 42 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 17 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.128768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.116434 restraints weight = 6965.971| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 1.83 r_work: 0.3731 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3639 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 1884 Z= 0.230 Angle : 1.012 10.917 2520 Z= 0.513 Chirality : 0.254 1.424 285 Planarity : 0.005 0.043 318 Dihedral : 5.612 19.524 252 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.31 % Allowed : 20.37 % Favored : 77.31 % 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: -3.44 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.005 0.001 PHE E 346 TYR 0.010 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 474 Ramachandran restraints generated. 237 Oldfield, 0 Emsley, 237 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 LYS cc_start: 0.8038 (tmtm) cc_final: 0.7378 (mptm) REVERT: A 341 SER cc_start: 0.8565 (t) cc_final: 0.8218 (p) REVERT: C 316 SER cc_start: 0.8622 (m) cc_final: 0.8154 (t) REVERT: E 311 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7735 (mttp) outliers start: 5 outliers final: 5 residues processed: 40 average time/residue: 2.3065 time to fit residues: 94.1872 Evaluate side-chains 43 residues out of total 216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 352 SER Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.128224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.115871 restraints weight = 6915.965| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 1.83 r_work: 0.3728 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1884 Z= 0.230 Angle : 1.016 10.898 2520 Z= 0.514 Chirality : 0.254 1.421 285 Planarity : 0.005 0.045 318 Dihedral : 5.601 19.519 252 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.31 % Allowed : 20.37 % Favored : 77.31 % 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: -3.47 (0.39), residues: 237 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS F 330 PHE 0.005 0.001 PHE E 346 TYR 0.010 0.001 TYR C 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4162.33 seconds wall clock time: 73 minutes 49.19 seconds (4429.19 seconds total)