Starting phenix.real_space_refine on Tue Mar 3 13:19:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qkm_14047/03_2026/7qkm_14047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qkm_14047/03_2026/7qkm_14047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qkm_14047/03_2026/7qkm_14047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qkm_14047/03_2026/7qkm_14047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qkm_14047/03_2026/7qkm_14047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qkm_14047/03_2026/7qkm_14047.map" } resolution = 2.66 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 1524 2.51 5 N 438 2.21 5 O 462 1.98 5 H 2634 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5070 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "A" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "D" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "F" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 845 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Time building chain proxies: 0.70, per 1000 atoms: 0.14 Number of scatterers: 5070 At special positions: 0 Unit cell: (93.112, 83.224, 35.432, 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 462 8.00 N 438 7.00 C 1524 6.00 H 2634 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: 0.24 Conformation dependent library (CDL) restraints added in 192.8 milliseconds 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 41.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 275 through 288 removed outlier: 6.456A pdb=" N GLN B 276 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ASN A 279 " --> pdb=" O GLN B 276 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE B 278 " --> pdb=" O ASN A 279 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS A 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N LYS B 280 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ASP A 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N LEU B 282 " --> pdb=" O ASP A 283 " (cutoff:3.500A) removed outlier: 10.181A pdb=" N SER A 285 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N LEU B 284 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 10.384A pdb=" N VAL A 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N ASN B 286 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU C 282 " --> pdb=" O LYS B 281 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP B 283 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU C 284 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N SER B 285 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN C 286 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 287 " --> pdb=" O ASN C 286 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN C 288 " --> pdb=" O VAL B 287 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 293 through 294 removed outlier: 6.500A pdb=" N SER B 293 " --> pdb=" O LYS C 294 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.635A pdb=" N VAL B 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL C 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE B 308 " --> pdb=" O VAL C 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.905A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 317 through 319 removed outlier: 6.496A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 325 removed outlier: 6.146A pdb=" N GLY B 323 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 275 through 288 removed outlier: 6.949A pdb=" N GLN E 276 " --> pdb=" O VAL D 275 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE D 277 " --> pdb=" O GLN E 276 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE E 278 " --> pdb=" O ILE D 277 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ASN D 279 " --> pdb=" O ILE E 278 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS E 280 " --> pdb=" O ASN D 279 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LYS D 281 " --> pdb=" O LYS E 280 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU F 282 " --> pdb=" O LYS D 281 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ASP D 283 " --> pdb=" O LEU F 282 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU F 284 " --> pdb=" O ASP D 283 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER D 285 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN F 286 " --> pdb=" O SER D 285 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL D 287 " --> pdb=" O ASN F 286 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN F 288 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 293 through 294 removed outlier: 6.528A pdb=" N SER D 293 " --> pdb=" O LYS F 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.535A pdb=" N VAL D 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL F 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE D 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.920A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 317 through 319 Processing sheet with id=AB3, first strand: chain 'E' and resid 323 through 325 removed outlier: 6.016A pdb=" N GLY D 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) 41 hydrogen bonds defined for protein. 123 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: 0.35 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: 2622 1.12 - 1.30: 408 1.30 - 1.47: 772 1.47 - 1.64: 1274 1.64 - 1.82: 12 Bond restraints: 5088 Sorted by residual: bond pdb=" N ILE A 278 " pdb=" H ILE A 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N GLY B 326 " pdb=" H GLY B 326 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N LYS B 280 " pdb=" H LYS B 280 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N VAL A 306 " pdb=" H VAL A 306 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N ILE F 278 " pdb=" H ILE F 278 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 5083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 8008 2.83 - 5.65: 1063 5.65 - 8.48: 235 8.48 - 11.30: 1 11.30 - 14.13: 11 Bond angle restraints: 9318 Sorted by residual: angle pdb=" CA LYS C 311 " pdb=" C LYS C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 118.16 121.81 -3.65 7.00e-01 2.04e+00 2.72e+01 angle pdb=" CB HIS D 299 " pdb=" CG HIS D 299 " pdb=" CD2 HIS D 299 " ideal model delta sigma weight residual 131.20 124.77 6.43 1.30e+00 5.92e-01 2.45e+01 angle pdb=" CB HIS E 299 " pdb=" CG HIS E 299 " pdb=" CD2 HIS E 299 " ideal model delta sigma weight residual 131.20 124.84 6.36 1.30e+00 5.92e-01 2.39e+01 angle pdb=" CA LYS F 311 " pdb=" C LYS F 311 " pdb=" N PRO F 312 " ideal model delta sigma weight residual 118.16 121.52 -3.36 7.00e-01 2.04e+00 2.30e+01 angle pdb=" CB HIS A 299 " pdb=" CG HIS A 299 " pdb=" CD2 HIS A 299 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 ... (remaining 9313 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2124 17.84 - 35.68: 120 35.68 - 53.52: 31 53.52 - 71.37: 53 71.37 - 89.21: 6 Dihedral angle restraints: 2334 sinusoidal: 1374 harmonic: 960 Sorted by residual: dihedral pdb=" CA SER B 305 " pdb=" C SER B 305 " pdb=" N VAL B 306 " pdb=" CA VAL B 306 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C SER B 289 " pdb=" N SER B 289 " pdb=" CA SER B 289 " pdb=" CB SER B 289 " ideal model delta harmonic sigma weight residual -122.60 -132.43 9.83 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" CA SER A 305 " pdb=" C SER A 305 " pdb=" N VAL A 306 " pdb=" CA VAL A 306 " ideal model delta harmonic sigma weight residual 180.00 160.53 19.47 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 2331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 228 0.077 - 0.154: 108 0.154 - 0.231: 44 0.231 - 0.308: 9 0.308 - 0.385: 7 Chirality restraints: 396 Sorted by residual: chirality pdb=" CA SER B 289 " pdb=" N SER B 289 " pdb=" C SER B 289 " pdb=" CB SER B 289 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA SER D 289 " pdb=" N SER D 289 " pdb=" C SER D 289 " pdb=" CB SER D 289 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA GLN B 307 " pdb=" N GLN B 307 " pdb=" C GLN B 307 " pdb=" CB GLN B 307 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.17e+00 ... (remaining 393 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " -0.036 2.00e-02 2.50e+03 4.39e-02 2.89e+01 pdb=" CG ASN C 327 " -0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " 0.048 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.034 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " 0.069 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 296 " -0.003 2.00e-02 2.50e+03 4.18e-02 2.62e+01 pdb=" CG ASN D 296 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN D 296 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN D 296 " 0.083 2.00e-02 2.50e+03 pdb="HD21 ASN D 296 " -0.048 2.00e-02 2.50e+03 pdb="HD22 ASN D 296 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 296 " 0.036 2.00e-02 2.50e+03 3.94e-02 2.33e+01 pdb=" CG ASN E 296 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN E 296 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN E 296 " 0.032 2.00e-02 2.50e+03 pdb="HD21 ASN E 296 " -0.062 2.00e-02 2.50e+03 pdb="HD22 ASN E 296 " 0.040 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 458 2.19 - 2.79: 8995 2.79 - 3.40: 13459 3.40 - 4.00: 17923 4.00 - 4.60: 25111 Nonbonded interactions: 65946 Sorted by model distance: nonbonded pdb=" OD1 ASP F 314 " pdb=" HG SER F 316 " model vdw 1.591 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.603 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.608 2.450 nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.618 2.450 nonbonded pdb=" OD1 ASP D 314 " pdb=" HG SER D 316 " model vdw 1.620 2.450 ... (remaining 65941 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 'B' selection = chain 'C' 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: 4.750 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: 0.020 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.060 Find NCS groups from input model: 0.050 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:8.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 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 0.034 2454 Z= 0.632 Angle : 1.886 6.687 3282 Z= 1.229 Chirality : 0.109 0.385 396 Planarity : 0.008 0.023 408 Dihedral : 12.518 89.206 954 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Cbeta Deviations : 0.34 % 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 are not related in a simple way. whole: -1.95 (0.37), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (0.28), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.033 0.007 TYR D 310 HIS 0.010 0.004 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.01027 ( 2454) covalent geometry : angle 1.88622 ( 3282) hydrogen bonds : bond 0.10325 ( 41) hydrogen bonds : angle 8.04383 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 311 LYS cc_start: 0.8346 (mttt) cc_final: 0.8134 (mttm) outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.3512 time to fit residues: 127.8824 Evaluate side-chains 50 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN E 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.164888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.153337 restraints weight = 8913.948| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 2.00 r_work: 0.4262 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4170 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2454 Z= 0.140 Angle : 0.694 3.993 3282 Z= 0.357 Chirality : 0.057 0.155 396 Planarity : 0.002 0.013 408 Dihedral : 6.152 17.758 330 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.70 % Allowed : 18.71 % Favored : 79.59 % 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 are not related in a simple way. whole: -1.38 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.04 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR B 310 HIS 0.003 0.001 HIS E 299 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2454) covalent geometry : angle 0.69397 ( 3282) hydrogen bonds : bond 0.03367 ( 41) hydrogen bonds : angle 5.73165 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8481 (tttm) cc_final: 0.7254 (pmtt) REVERT: C 295 ASP cc_start: 0.8510 (t70) cc_final: 0.8175 (t0) REVERT: E 294 LYS cc_start: 0.8464 (tttm) cc_final: 0.7143 (pmtt) outliers start: 5 outliers final: 1 residues processed: 54 average time/residue: 1.4709 time to fit residues: 80.7677 Evaluate side-chains 41 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 285 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.162646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.151287 restraints weight = 8235.234| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.98 r_work: 0.4268 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.4172 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2454 Z= 0.141 Angle : 0.578 4.078 3282 Z= 0.294 Chirality : 0.055 0.145 396 Planarity : 0.002 0.008 408 Dihedral : 5.604 15.796 330 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.70 % Allowed : 18.03 % Favored : 80.27 % 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 are not related in a simple way. whole: -1.40 (0.42), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.06 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2454) covalent geometry : angle 0.57796 ( 3282) hydrogen bonds : bond 0.02395 ( 41) hydrogen bonds : angle 5.03986 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8466 (tttm) cc_final: 0.7124 (pmtt) REVERT: C 295 ASP cc_start: 0.8531 (t70) cc_final: 0.8236 (t0) REVERT: E 294 LYS cc_start: 0.8540 (tttm) cc_final: 0.7094 (pmtt) REVERT: E 311 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8773 (ttmt) outliers start: 5 outliers final: 4 residues processed: 44 average time/residue: 1.3492 time to fit residues: 60.5025 Evaluate side-chains 45 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 13 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 2.6986 ------------------------------------------------------------------------------- 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 = 0.4451 r_free = 0.4451 target = 0.158599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.147291 restraints weight = 8400.318| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 1.98 r_work: 0.4226 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.4129 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2454 Z= 0.187 Angle : 0.576 4.082 3282 Z= 0.297 Chirality : 0.056 0.150 396 Planarity : 0.002 0.007 408 Dihedral : 5.431 14.633 330 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.72 % Allowed : 14.97 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.40), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR A 310 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 2454) covalent geometry : angle 0.57562 ( 3282) hydrogen bonds : bond 0.02097 ( 41) hydrogen bonds : angle 4.63501 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 ASP cc_start: 0.8532 (t70) cc_final: 0.8223 (t0) REVERT: E 311 LYS cc_start: 0.9032 (mtpp) cc_final: 0.8772 (ttmt) outliers start: 8 outliers final: 6 residues processed: 47 average time/residue: 1.3329 time to fit residues: 63.8778 Evaluate side-chains 49 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.162093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.150797 restraints weight = 8171.080| |-----------------------------------------------------------------------------| r_work (start): 0.4353 rms_B_bonded: 1.95 r_work: 0.4269 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4171 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2454 Z= 0.110 Angle : 0.528 4.034 3282 Z= 0.267 Chirality : 0.054 0.141 396 Planarity : 0.001 0.010 408 Dihedral : 5.220 14.760 330 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.06 % Allowed : 14.97 % Favored : 81.97 % 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 are not related in a simple way. whole: -1.66 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR A 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2454) covalent geometry : angle 0.52775 ( 3282) hydrogen bonds : bond 0.01931 ( 41) hydrogen bonds : angle 4.41264 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 LYS cc_start: 0.8556 (tttm) cc_final: 0.7158 (pmtt) REVERT: C 295 ASP cc_start: 0.8503 (t70) cc_final: 0.8223 (t0) REVERT: E 285 SER cc_start: 0.9251 (OUTLIER) cc_final: 0.8937 (t) REVERT: E 311 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8764 (ttmt) outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 1.3204 time to fit residues: 63.2812 Evaluate side-chains 49 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 GLN Chi-restraints excluded: chain D residue 307 GLN Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.162392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.151028 restraints weight = 8285.794| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.96 r_work: 0.4272 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4177 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2454 Z= 0.120 Angle : 0.523 4.349 3282 Z= 0.265 Chirality : 0.055 0.139 396 Planarity : 0.001 0.010 408 Dihedral : 5.030 14.047 330 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.72 % Allowed : 15.31 % Favored : 81.97 % 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 are not related in a simple way. whole: -1.62 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.000 TYR A 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2454) covalent geometry : angle 0.52348 ( 3282) hydrogen bonds : bond 0.01832 ( 41) hydrogen bonds : angle 4.24195 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 ASP cc_start: 0.8549 (t70) cc_final: 0.8234 (t0) REVERT: E 285 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.8950 (t) REVERT: E 311 LYS cc_start: 0.9048 (mtpp) cc_final: 0.8827 (mtmm) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.3355 time to fit residues: 65.3260 Evaluate side-chains 48 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 307 GLN Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.163814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.152408 restraints weight = 8113.721| |-----------------------------------------------------------------------------| r_work (start): 0.4369 rms_B_bonded: 1.93 r_work: 0.4287 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4192 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2454 Z= 0.105 Angle : 0.516 5.228 3282 Z= 0.259 Chirality : 0.054 0.137 396 Planarity : 0.001 0.010 408 Dihedral : 4.949 13.984 330 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.38 % Allowed : 15.99 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR E 310 HIS 0.001 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 2454) covalent geometry : angle 0.51644 ( 3282) hydrogen bonds : bond 0.01798 ( 41) hydrogen bonds : angle 4.13199 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 ASP cc_start: 0.8532 (t70) cc_final: 0.8253 (t0) REVERT: E 285 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8923 (t) REVERT: E 311 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8822 (mtmm) outliers start: 7 outliers final: 4 residues processed: 46 average time/residue: 1.3090 time to fit residues: 61.3629 Evaluate side-chains 46 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 18 optimal weight: 0.0770 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN A 307 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.163118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.151594 restraints weight = 8205.294| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 1.95 r_work: 0.4279 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.4186 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.4186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2454 Z= 0.122 Angle : 0.524 5.559 3282 Z= 0.262 Chirality : 0.054 0.142 396 Planarity : 0.001 0.010 408 Dihedral : 4.917 13.819 330 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.04 % Allowed : 16.33 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR A 310 HIS 0.002 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2454) covalent geometry : angle 0.52367 ( 3282) hydrogen bonds : bond 0.01831 ( 41) hydrogen bonds : angle 4.07697 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 ASP cc_start: 0.8541 (t70) cc_final: 0.8253 (t0) REVERT: E 285 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8945 (t) REVERT: E 311 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8828 (mtmm) outliers start: 6 outliers final: 4 residues processed: 44 average time/residue: 1.2237 time to fit residues: 54.9782 Evaluate side-chains 45 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain C residue 307 GLN Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain E residue 285 SER Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 327 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4541 r_free = 0.4541 target = 0.166085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.154430 restraints weight = 8053.652| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 1.93 r_work: 0.4316 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4224 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2454 Z= 0.084 Angle : 0.518 6.535 3282 Z= 0.256 Chirality : 0.054 0.136 396 Planarity : 0.002 0.011 408 Dihedral : 4.790 13.708 330 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.68 % Allowed : 17.69 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.26 (0.29), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR E 310 HIS 0.001 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 2454) covalent geometry : angle 0.51825 ( 3282) hydrogen bonds : bond 0.01647 ( 41) hydrogen bonds : angle 3.93419 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 ASP cc_start: 0.8559 (t70) cc_final: 0.8305 (t0) REVERT: E 285 SER cc_start: 0.9216 (p) cc_final: 0.8942 (t) REVERT: E 294 LYS cc_start: 0.8555 (tttm) cc_final: 0.7107 (pmtt) REVERT: E 311 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8820 (mtmm) REVERT: F 311 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8641 (mttm) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 1.3286 time to fit residues: 58.2017 Evaluate side-chains 42 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 8 optimal weight: 0.0870 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.168257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.156347 restraints weight = 8000.692| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.93 r_work: 0.4334 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.4242 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2454 Z= 0.081 Angle : 0.503 5.937 3282 Z= 0.248 Chirality : 0.054 0.135 396 Planarity : 0.002 0.012 408 Dihedral : 4.660 13.388 330 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.68 % Allowed : 17.69 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR E 310 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 2454) covalent geometry : angle 0.50316 ( 3282) hydrogen bonds : bond 0.01542 ( 41) hydrogen bonds : angle 3.82662 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 636 Ramachandran restraints generated. 318 Oldfield, 0 Emsley, 318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 295 ASP cc_start: 0.8538 (t70) cc_final: 0.8317 (t0) REVERT: E 285 SER cc_start: 0.9183 (p) cc_final: 0.8928 (t) REVERT: E 311 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8819 (mtmm) REVERT: F 311 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8629 (mttm) outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 1.4005 time to fit residues: 65.6187 Evaluate side-chains 43 residues out of total 294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 283 ASP Chi-restraints excluded: chain F residue 311 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.165911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.154056 restraints weight = 8029.880| |-----------------------------------------------------------------------------| r_work (start): 0.4392 rms_B_bonded: 1.93 r_work: 0.4308 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2454 Z= 0.111 Angle : 0.531 5.499 3282 Z= 0.262 Chirality : 0.054 0.142 396 Planarity : 0.002 0.012 408 Dihedral : 4.684 13.298 330 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.02 % Allowed : 18.37 % Favored : 80.61 % 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 are not related in a simple way. whole: -1.62 (0.39), residues: 318 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.001 0.000 TYR E 310 HIS 0.001 0.000 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2454) covalent geometry : angle 0.53081 ( 3282) hydrogen bonds : bond 0.01624 ( 41) hydrogen bonds : angle 3.84821 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2682.56 seconds wall clock time: 46 minutes 10.34 seconds (2770.34 seconds total)