Starting phenix.real_space_refine on Wed Sep 17 05:02:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkw_14055/09_2025/7qkw_14055.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkw_14055/09_2025/7qkw_14055.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qkw_14055/09_2025/7qkw_14055.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkw_14055/09_2025/7qkw_14055.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qkw_14055/09_2025/7qkw_14055.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkw_14055/09_2025/7qkw_14055.map" } resolution = 2.32 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= 0.000 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 12 5.16 5 C 1419 2.51 5 N 405 2.21 5 O 432 1.98 5 H 2439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4707 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 746 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "E" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 746 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "F" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 746 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Time building chain proxies: 1.00, per 1000 atoms: 0.21 Number of scatterers: 4707 At special positions: 0 Unit cell: (84.872, 84.048, 31.312, 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 12 16.00 O 432 8.00 N 405 7.00 C 1419 6.00 H 2439 1.00 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: 0.41 Conformation dependent library (CDL) restraints added in 112.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 43.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 276 through 283 removed outlier: 6.502A pdb=" N GLN B 276 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASN C 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 291 removed outlier: 6.895A pdb=" N SER B 289 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 290 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N CYS B 291 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LYS C 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER B 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.428A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.240A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 314 removed outlier: 7.191A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 322 removed outlier: 6.452A pdb=" N LYS B 317 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N SER A 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N THR B 319 " --> pdb=" O SER A 320 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N CYS A 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS B 321 " --> pdb=" O CYS A 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 276 through 283 removed outlier: 6.437A pdb=" N ILE D 277 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LYS E 280 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN D 279 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LEU E 282 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LYS D 281 " --> pdb=" O LEU E 282 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N GLN D 276 " --> pdb=" O ILE F 277 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ASN F 279 " --> pdb=" O GLN D 276 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE D 278 " --> pdb=" O ASN F 279 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N LYS F 281 " --> pdb=" O ILE D 278 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS D 280 " --> pdb=" O LYS F 281 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ASP F 283 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU D 282 " --> pdb=" O ASP F 283 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 286 through 291 removed outlier: 6.955A pdb=" N VAL E 287 " --> pdb=" O ASN D 286 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLN D 288 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL D 287 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LYS F 290 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N SER D 289 " --> pdb=" O LYS F 290 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 297 through 298 removed outlier: 6.545A pdb=" N ILE D 297 " --> pdb=" O LYS F 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'E' and resid 313 through 314 removed outlier: 7.114A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 317 through 321 removed outlier: 6.559A pdb=" N VAL D 318 " --> pdb=" O THR F 319 " (cutoff:3.500A) 37 hydrogen bonds defined for protein. 111 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: 0.98 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 2427 1.12 - 1.30: 381 1.30 - 1.47: 731 1.47 - 1.64: 1174 1.64 - 1.82: 12 Bond restraints: 4725 Sorted by residual: bond pdb=" N VAL A 275 " pdb=" H VAL A 275 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NE2 GLN A 276 " pdb="HE21 GLN A 276 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LYS A 317 " pdb=" H LYS A 317 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ASP E 295 " pdb=" H ASP E 295 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 GLN C 276 " pdb="HE22 GLN C 276 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 4720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 7100 2.46 - 4.93: 1196 4.93 - 7.39: 331 7.39 - 9.85: 11 9.85 - 12.31: 11 Bond angle restraints: 8649 Sorted by residual: angle pdb=" C VAL F 300 " pdb=" N PRO F 301 " pdb=" CA PRO F 301 " ideal model delta sigma weight residual 119.24 125.09 -5.85 1.04e+00 9.25e-01 3.16e+01 angle pdb=" C VAL D 300 " pdb=" N PRO D 301 " pdb=" CA PRO D 301 " ideal model delta sigma weight residual 119.24 125.00 -5.76 1.04e+00 9.25e-01 3.06e+01 angle pdb=" CB HIS D 299 " pdb=" CG HIS D 299 " pdb=" CD2 HIS D 299 " ideal model delta sigma weight residual 131.20 125.22 5.98 1.30e+00 5.92e-01 2.12e+01 angle pdb=" C ASP F 314 " pdb=" N LEU F 315 " pdb=" CA LEU F 315 " ideal model delta sigma weight residual 122.37 129.43 -7.06 1.54e+00 4.22e-01 2.10e+01 angle pdb=" CA LYS E 311 " pdb=" C LYS E 311 " pdb=" N PRO E 312 " ideal model delta sigma weight residual 118.16 121.36 -3.20 7.00e-01 2.04e+00 2.09e+01 ... (remaining 8644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.91: 1859 14.91 - 29.83: 162 29.83 - 44.74: 37 44.74 - 59.65: 71 59.65 - 74.56: 46 Dihedral angle restraints: 2175 sinusoidal: 1275 harmonic: 900 Sorted by residual: dihedral pdb=" CA ILE E 297 " pdb=" C ILE E 297 " pdb=" N LYS E 298 " pdb=" CA LYS E 298 " ideal model delta harmonic sigma weight residual 180.00 -151.92 -28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE D 297 " pdb=" C ILE D 297 " pdb=" N LYS D 298 " pdb=" CA LYS D 298 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA SER C 285 " pdb=" C SER C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 2172 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 216 0.071 - 0.142: 99 0.142 - 0.214: 43 0.214 - 0.285: 11 0.285 - 0.356: 3 Chirality restraints: 372 Sorted by residual: chirality pdb=" CA GLN A 288 " pdb=" N GLN A 288 " pdb=" C GLN A 288 " pdb=" CB GLN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.16e+00 chirality pdb=" CA PRO F 301 " pdb=" N PRO F 301 " pdb=" C PRO F 301 " pdb=" CB PRO F 301 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ASN B 296 " pdb=" N ASN B 296 " pdb=" C ASN B 296 " pdb=" CB ASN B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.21e+00 ... (remaining 369 not shown) Planarity restraints: 669 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 299 " -0.099 2.00e-02 2.50e+03 5.35e-02 6.44e+01 pdb=" CG HIS A 299 " 0.033 2.00e-02 2.50e+03 pdb=" ND1 HIS A 299 " 0.054 2.00e-02 2.50e+03 pdb=" CD2 HIS A 299 " 0.044 2.00e-02 2.50e+03 pdb=" CE1 HIS A 299 " 0.021 2.00e-02 2.50e+03 pdb=" NE2 HIS A 299 " -0.025 2.00e-02 2.50e+03 pdb=" HD2 HIS A 299 " 0.057 2.00e-02 2.50e+03 pdb=" HE1 HIS A 299 " -0.008 2.00e-02 2.50e+03 pdb=" HE2 HIS A 299 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 288 " 0.062 2.00e-02 2.50e+03 5.92e-02 5.25e+01 pdb=" CD GLN C 288 " -0.018 2.00e-02 2.50e+03 pdb=" OE1 GLN C 288 " -0.057 2.00e-02 2.50e+03 pdb=" NE2 GLN C 288 " 0.016 2.00e-02 2.50e+03 pdb="HE21 GLN C 288 " -0.082 2.00e-02 2.50e+03 pdb="HE22 GLN C 288 " 0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 288 " 0.062 2.00e-02 2.50e+03 5.72e-02 4.91e+01 pdb=" CD GLN B 288 " -0.015 2.00e-02 2.50e+03 pdb=" OE1 GLN B 288 " -0.054 2.00e-02 2.50e+03 pdb=" NE2 GLN B 288 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 288 " -0.075 2.00e-02 2.50e+03 pdb="HE22 GLN B 288 " 0.084 2.00e-02 2.50e+03 ... (remaining 666 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 396 2.18 - 2.79: 8449 2.79 - 3.39: 12554 3.39 - 4.00: 17045 4.00 - 4.60: 23633 Nonbonded interactions: 62077 Sorted by model distance: nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.576 2.450 nonbonded pdb=" OD1 ASP F 283 " pdb=" HG SER F 285 " model vdw 1.589 2.450 nonbonded pdb=" OD1 ASP E 283 " pdb=" HG SER E 285 " model vdw 1.600 2.450 nonbonded pdb=" OD1 ASP D 283 " pdb=" HG SER D 285 " model vdw 1.612 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.612 2.450 ... (remaining 62072 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' and resid 275 through 322) selection = (chain 'B' and resid 275 through 322) selection = (chain 'C' and resid 275 through 322) selection = chain 'D' selection = chain 'E' 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.050 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.780 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 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:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 : 0.010 0.032 2286 Z= 0.648 Angle : 1.934 7.092 3063 Z= 1.278 Chirality : 0.098 0.356 372 Planarity : 0.010 0.059 381 Dihedral : 13.527 74.563 885 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.36 % 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: -2.79 (0.37), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.29), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.050 0.015 TYR D 310 HIS 0.024 0.009 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.01050 ( 2286) covalent geometry : angle 1.93393 ( 3063) hydrogen bonds : bond 0.08803 ( 37) hydrogen bonds : angle 8.09619 ( 111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 ASP cc_start: 0.7772 (t0) cc_final: 0.7438 (t70) REVERT: A 317 LYS cc_start: 0.7443 (tptm) cc_final: 0.6787 (pmtt) REVERT: E 321 LYS cc_start: 0.7596 (mtmm) cc_final: 0.7197 (pmtt) REVERT: F 321 LYS cc_start: 0.7052 (mtmt) cc_final: 0.6581 (mmtt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 1.2771 time to fit residues: 102.8151 Evaluate side-chains 35 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 ASN A 286 ASN C 286 ASN D 279 ASN D 286 ASN E 279 ASN E 286 ASN F 279 ASN F 286 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.133963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.123354 restraints weight = 9385.432| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 1.59 r_work: 0.4056 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3988 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2286 Z= 0.176 Angle : 0.720 4.647 3063 Z= 0.388 Chirality : 0.056 0.173 372 Planarity : 0.004 0.044 381 Dihedral : 8.213 26.944 306 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.99 % Allowed : 12.68 % 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 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: -2.89 (0.36), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.28), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR E 310 HIS 0.002 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 2286) covalent geometry : angle 0.72023 ( 3063) hydrogen bonds : bond 0.03423 ( 37) hydrogen bonds : angle 6.42162 ( 111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.145 Fit side-chains REVERT: B 314 ASP cc_start: 0.8118 (t0) cc_final: 0.7800 (t70) REVERT: A 317 LYS cc_start: 0.7467 (tptm) cc_final: 0.6699 (pmtt) REVERT: D 295 ASP cc_start: 0.8024 (m-30) cc_final: 0.7544 (m-30) REVERT: E 321 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7199 (pmtt) REVERT: F 321 LYS cc_start: 0.7607 (mtmt) cc_final: 0.6737 (mmtt) outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.7996 time to fit residues: 35.4698 Evaluate side-chains 37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.132879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.122145 restraints weight = 9252.284| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 1.58 r_work: 0.4044 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3978 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2286 Z= 0.204 Angle : 0.670 4.867 3063 Z= 0.360 Chirality : 0.056 0.162 372 Planarity : 0.005 0.048 381 Dihedral : 7.595 24.506 306 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.71 % Allowed : 11.96 % 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 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: -2.97 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR F 310 HIS 0.003 0.001 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 2286) covalent geometry : angle 0.66960 ( 3063) hydrogen bonds : bond 0.02627 ( 37) hydrogen bonds : angle 5.66852 ( 111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.156 Fit side-chains REVERT: B 314 ASP cc_start: 0.8199 (t0) cc_final: 0.7933 (t70) REVERT: A 317 LYS cc_start: 0.7662 (tptm) cc_final: 0.6956 (pmtt) REVERT: E 321 LYS cc_start: 0.8062 (mtmm) cc_final: 0.7336 (pmtt) REVERT: F 321 LYS cc_start: 0.7523 (mtmt) cc_final: 0.6718 (mmtt) outliers start: 13 outliers final: 9 residues processed: 40 average time/residue: 0.7964 time to fit residues: 32.9238 Evaluate side-chains 39 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 276 GLN E 276 GLN F 276 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.135050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.124387 restraints weight = 9287.885| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.61 r_work: 0.4078 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2286 Z= 0.125 Angle : 0.561 4.081 3063 Z= 0.299 Chirality : 0.054 0.163 372 Planarity : 0.004 0.046 381 Dihedral : 6.991 22.402 306 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.62 % Allowed : 13.41 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.00 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 310 HIS 0.001 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2286) covalent geometry : angle 0.56125 ( 3063) hydrogen bonds : bond 0.02202 ( 37) hydrogen bonds : angle 5.20508 ( 111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.150 Fit side-chains REVERT: B 314 ASP cc_start: 0.8185 (t0) cc_final: 0.7943 (t70) REVERT: A 317 LYS cc_start: 0.7595 (tptm) cc_final: 0.6907 (pmtt) REVERT: D 282 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8031 (mp) REVERT: E 282 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8140 (tt) REVERT: E 321 LYS cc_start: 0.8037 (mtmm) cc_final: 0.7300 (pmtt) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.9292 time to fit residues: 38.2615 Evaluate side-chains 36 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4186 r_free = 0.4186 target = 0.131122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.120549 restraints weight = 9311.100| |-----------------------------------------------------------------------------| r_work (start): 0.4076 rms_B_bonded: 1.55 r_work: 0.4027 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3959 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 2286 Z= 0.207 Angle : 0.631 4.830 3063 Z= 0.337 Chirality : 0.054 0.158 372 Planarity : 0.005 0.046 381 Dihedral : 7.118 23.828 306 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.35 % Allowed : 15.22 % Favored : 80.43 % 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: -3.12 (0.34), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.26), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR F 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 2286) covalent geometry : angle 0.63120 ( 3063) hydrogen bonds : bond 0.02388 ( 37) hydrogen bonds : angle 5.29445 ( 111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 28 time to evaluate : 0.175 Fit side-chains REVERT: B 314 ASP cc_start: 0.8163 (t0) cc_final: 0.7926 (t70) REVERT: A 317 LYS cc_start: 0.7755 (tptm) cc_final: 0.7069 (pmtt) REVERT: D 282 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7887 (mt) REVERT: E 281 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8342 (tptp) REVERT: E 321 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7271 (pmtt) outliers start: 12 outliers final: 8 residues processed: 36 average time/residue: 0.7360 time to fit residues: 27.5253 Evaluate side-chains 37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 27 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.0170 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 0.0470 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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 = 0.4233 r_free = 0.4233 target = 0.134730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.124146 restraints weight = 9448.264| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.59 r_work: 0.4081 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2286 Z= 0.097 Angle : 0.534 3.947 3063 Z= 0.280 Chirality : 0.054 0.156 372 Planarity : 0.004 0.043 381 Dihedral : 6.663 21.400 306 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.62 % Allowed : 15.22 % Favored : 81.16 % 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: -3.04 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR C 310 HIS 0.002 0.000 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 2286) covalent geometry : angle 0.53366 ( 3063) hydrogen bonds : bond 0.01998 ( 37) hydrogen bonds : angle 4.96992 ( 111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.108 Fit side-chains REVERT: B 282 LEU cc_start: 0.8301 (mp) cc_final: 0.8039 (mm) REVERT: B 314 ASP cc_start: 0.8179 (t0) cc_final: 0.7921 (t70) REVERT: A 317 LYS cc_start: 0.7692 (tptm) cc_final: 0.7007 (pmtt) REVERT: D 282 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7883 (mt) REVERT: E 321 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7217 (pmtt) outliers start: 10 outliers final: 8 residues processed: 34 average time/residue: 0.7654 time to fit residues: 27.0216 Evaluate side-chains 37 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 22 optimal weight: 0.0170 chunk 16 optimal weight: 8.9990 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 0.0670 chunk 6 optimal weight: 3.9990 overall best weight: 0.9158 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.143780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.132678 restraints weight = 8226.880| |-----------------------------------------------------------------------------| r_work (start): 0.4148 rms_B_bonded: 1.56 r_work: 0.4101 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4033 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2286 Z= 0.087 Angle : 0.494 3.931 3063 Z= 0.257 Chirality : 0.054 0.151 372 Planarity : 0.004 0.042 381 Dihedral : 6.064 18.182 306 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.99 % Allowed : 15.22 % Favored : 80.80 % 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: -2.97 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR F 310 HIS 0.002 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 2286) covalent geometry : angle 0.49408 ( 3063) hydrogen bonds : bond 0.01657 ( 37) hydrogen bonds : angle 4.64288 ( 111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.156 Fit side-chains REVERT: B 282 LEU cc_start: 0.8297 (mp) cc_final: 0.8054 (mm) REVERT: B 314 ASP cc_start: 0.8215 (t0) cc_final: 0.7989 (t70) REVERT: A 317 LYS cc_start: 0.7593 (tptm) cc_final: 0.6897 (pmtt) REVERT: D 282 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7921 (mt) REVERT: E 281 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8282 (tptp) REVERT: E 321 LYS cc_start: 0.8001 (mtmm) cc_final: 0.7202 (pmtt) outliers start: 11 outliers final: 8 residues processed: 38 average time/residue: 0.7594 time to fit residues: 29.8591 Evaluate side-chains 40 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 281 LYS Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 10 optimal weight: 0.0270 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 overall best weight: 1.0640 ------------------------------------------------------------------------------- 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 = 0.4265 r_free = 0.4265 target = 0.143507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.132379 restraints weight = 8352.514| |-----------------------------------------------------------------------------| r_work (start): 0.4149 rms_B_bonded: 1.57 r_work: 0.4102 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.4034 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.4034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2286 Z= 0.085 Angle : 0.494 4.041 3063 Z= 0.257 Chirality : 0.054 0.147 372 Planarity : 0.004 0.042 381 Dihedral : 5.984 18.072 306 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.99 % Allowed : 15.22 % Favored : 80.80 % 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: -2.90 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR F 310 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 2286) covalent geometry : angle 0.49369 ( 3063) hydrogen bonds : bond 0.01572 ( 37) hydrogen bonds : angle 4.48927 ( 111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.158 Fit side-chains REVERT: B 282 LEU cc_start: 0.8292 (mp) cc_final: 0.8054 (mm) REVERT: B 314 ASP cc_start: 0.8189 (t0) cc_final: 0.7978 (t70) REVERT: A 290 LYS cc_start: 0.8732 (tttm) cc_final: 0.8370 (ttmt) REVERT: A 317 LYS cc_start: 0.7600 (tptm) cc_final: 0.6925 (pmtt) REVERT: D 282 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7909 (mt) REVERT: E 281 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8278 (tptp) REVERT: E 321 LYS cc_start: 0.7998 (mtmm) cc_final: 0.7206 (pmtt) outliers start: 11 outliers final: 6 residues processed: 40 average time/residue: 0.7872 time to fit residues: 32.5585 Evaluate side-chains 41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.143773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.133394 restraints weight = 8878.124| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.60 r_work: 0.4109 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.4044 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2286 Z= 0.079 Angle : 0.493 4.491 3063 Z= 0.252 Chirality : 0.054 0.146 372 Planarity : 0.004 0.041 381 Dihedral : 5.848 17.379 306 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.26 % Allowed : 15.94 % Favored : 80.80 % 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: -2.90 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR F 310 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 2286) covalent geometry : angle 0.49309 ( 3063) hydrogen bonds : bond 0.01512 ( 37) hydrogen bonds : angle 4.25233 ( 111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.155 Fit side-chains REVERT: B 282 LEU cc_start: 0.8310 (mp) cc_final: 0.8080 (mm) REVERT: A 290 LYS cc_start: 0.8721 (tttm) cc_final: 0.8341 (ttmt) REVERT: A 317 LYS cc_start: 0.7569 (tptm) cc_final: 0.6904 (pmtt) REVERT: D 282 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7910 (mt) REVERT: E 281 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8240 (tptp) REVERT: E 321 LYS cc_start: 0.7981 (mtmm) cc_final: 0.7188 (pmtt) outliers start: 9 outliers final: 6 residues processed: 40 average time/residue: 0.8776 time to fit residues: 36.1210 Evaluate side-chains 41 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain E residue 281 LYS Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.131219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.120756 restraints weight = 9389.383| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 1.60 r_work: 0.4031 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3964 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2286 Z= 0.231 Angle : 0.626 4.639 3063 Z= 0.332 Chirality : 0.054 0.144 372 Planarity : 0.004 0.045 381 Dihedral : 6.572 21.735 306 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.90 % Allowed : 16.30 % Favored : 80.80 % 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: -3.05 (0.34), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.26), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR F 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00544 ( 2286) covalent geometry : angle 0.62562 ( 3063) hydrogen bonds : bond 0.02051 ( 37) hydrogen bonds : angle 4.80066 ( 111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 588 Ramachandran restraints generated. 294 Oldfield, 0 Emsley, 294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.158 Fit side-chains REVERT: A 317 LYS cc_start: 0.7828 (tptm) cc_final: 0.7125 (pmtt) REVERT: D 282 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7908 (mt) REVERT: E 321 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7207 (pmtt) outliers start: 8 outliers final: 5 residues processed: 35 average time/residue: 0.6885 time to fit residues: 25.1448 Evaluate side-chains 34 residues out of total 276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 SER Chi-restraints excluded: chain A residue 324 SER Chi-restraints excluded: chain C residue 324 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain F residue 320 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4234 r_free = 0.4234 target = 0.134509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.124147 restraints weight = 9415.115| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.56 r_work: 0.4085 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4019 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.4019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2286 Z= 0.103 Angle : 0.527 4.241 3063 Z= 0.273 Chirality : 0.054 0.148 372 Planarity : 0.004 0.041 381 Dihedral : 6.282 19.789 306 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.26 % Allowed : 16.30 % Favored : 80.43 % 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: -2.96 (0.35), residues: 294 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR F 310 HIS 0.001 0.000 HIS C 299 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 2286) covalent geometry : angle 0.52693 ( 3063) hydrogen bonds : bond 0.01797 ( 37) hydrogen bonds : angle 4.58009 ( 111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.00 seconds wall clock time: 43 minutes 32.05 seconds (2612.05 seconds total)