Starting phenix.real_space_refine on Wed Sep 17 07:36:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr6_62520/09_2025/9kr6_62520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr6_62520/09_2025/9kr6_62520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kr6_62520/09_2025/9kr6_62520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr6_62520/09_2025/9kr6_62520.map" model { file = "/net/cci-nas-00/data/ceres_data/9kr6_62520/09_2025/9kr6_62520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr6_62520/09_2025/9kr6_62520.cif" } resolution = 2.77 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= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 4372 2.51 5 N 1098 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.01s 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: 6760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3334 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 10, 'TRANS': 398} Chain breaks: 1 Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 46 Classifications: {'peptide': 6} Link IDs: {'TRANS': 5} Restraints were copied for chains: B, D Time building chain proxies: 2.44, per 1000 atoms: 0.36 Number of scatterers: 6760 At special positions: 0 Unit cell: (123.82, 66.42, 85.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1240 8.00 N 1098 7.00 C 4372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 62 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 62 " distance=2.04 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: 0.54 Conformation dependent library (CDL) restraints added in 404.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 48.2% alpha, 8.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 16 through 28 removed outlier: 3.516A pdb=" N LEU A 20 " --> pdb=" O GLY A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 39 removed outlier: 3.547A pdb=" N LYS A 38 " --> pdb=" O ASP A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.604A pdb=" N GLN A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR A 100 " --> pdb=" O LEU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 107 removed outlier: 3.584A pdb=" N VAL A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 170 through 183 removed outlier: 3.744A pdb=" N ILE A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 180 " --> pdb=" O ASN A 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 226 Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.518A pdb=" N PHE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.669A pdb=" N ASP A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.968A pdb=" N PHE A 331 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 removed outlier: 3.807A pdb=" N VAL A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 372 removed outlier: 3.877A pdb=" N SER A 370 " --> pdb=" O THR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 416 Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 16 through 28 removed outlier: 3.516A pdb=" N LEU B 20 " --> pdb=" O GLY B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.547A pdb=" N LYS B 38 " --> pdb=" O ASP B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 64 through 73 Processing helix chain 'B' and resid 84 through 100 removed outlier: 3.603A pdb=" N GLN B 88 " --> pdb=" O ASP B 84 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.584A pdb=" N VAL B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 170 through 183 removed outlier: 3.744A pdb=" N ILE B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 180 " --> pdb=" O ASN B 176 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 226 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.519A pdb=" N PHE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 309 removed outlier: 3.669A pdb=" N ASP B 299 " --> pdb=" O ASN B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 342 removed outlier: 3.968A pdb=" N PHE B 331 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 removed outlier: 3.807A pdb=" N VAL B 353 " --> pdb=" O SER B 349 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 372 removed outlier: 3.877A pdb=" N SER B 370 " --> pdb=" O THR B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 416 Processing sheet with id=AA1, first strand: chain 'A' and resid 187 through 194 removed outlier: 6.492A pdb=" N ASP A 188 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY A 235 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N ILE A 190 " --> pdb=" O GLY A 235 " (cutoff:3.500A) removed outlier: 12.055A pdb=" N CYS A 237 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N GLN A 192 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 253 " --> pdb=" O ASP A 248 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A 317 " --> pdb=" O PHE A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 187 through 194 removed outlier: 6.492A pdb=" N ASP B 188 " --> pdb=" O MET B 233 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N GLY B 235 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE B 190 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 12.054A pdb=" N CYS B 237 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 10.554A pdb=" N GLN B 192 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 253 " --> pdb=" O ASP B 248 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN B 317 " --> pdb=" O PHE B 256 " (cutoff:3.500A) 276 hydrogen bonds defined for protein. 792 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: 1.12 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1716 1.33 - 1.45: 1362 1.45 - 1.57: 3762 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6914 Sorted by residual: bond pdb=" C GLY C 10 " pdb=" O GLY C 10 " ideal model delta sigma weight residual 1.231 1.401 -0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" C GLY D 10 " pdb=" O GLY D 10 " ideal model delta sigma weight residual 1.231 1.401 -0.170 2.00e-02 2.50e+03 7.21e+01 bond pdb=" CA ALA C 8 " pdb=" CB ALA C 8 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.65e-02 3.67e+03 1.43e+01 bond pdb=" CA ALA D 8 " pdb=" CB ALA D 8 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.65e-02 3.67e+03 1.43e+01 bond pdb=" CG LEU B 334 " pdb=" CD1 LEU B 334 " ideal model delta sigma weight residual 1.521 1.452 0.069 3.30e-02 9.18e+02 4.32e+00 ... (remaining 6909 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 9094 2.49 - 4.98: 174 4.98 - 7.47: 26 7.47 - 9.96: 4 9.96 - 12.44: 6 Bond angle restraints: 9304 Sorted by residual: angle pdb=" O ALA D 8 " pdb=" C ALA D 8 " pdb=" N GLY D 10 " ideal model delta sigma weight residual 123.56 111.53 12.03 1.06e+00 8.90e-01 1.29e+02 angle pdb=" O ALA C 8 " pdb=" C ALA C 8 " pdb=" N GLY C 10 " ideal model delta sigma weight residual 123.56 111.53 12.03 1.06e+00 8.90e-01 1.29e+02 angle pdb=" C ALA C 8 " pdb=" N GLY C 10 " pdb=" CA GLY C 10 " ideal model delta sigma weight residual 121.70 110.43 11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" C ALA D 8 " pdb=" N GLY D 10 " pdb=" CA GLY D 10 " ideal model delta sigma weight residual 121.70 110.43 11.27 1.80e+00 3.09e-01 3.92e+01 angle pdb=" CA GLY C 10 " pdb=" C GLY C 10 " pdb=" O GLY C 10 " ideal model delta sigma weight residual 120.80 108.36 12.44 2.10e+00 2.27e-01 3.51e+01 ... (remaining 9299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 3612 15.87 - 31.74: 422 31.74 - 47.60: 74 47.60 - 63.47: 16 63.47 - 79.34: 10 Dihedral angle restraints: 4134 sinusoidal: 1688 harmonic: 2446 Sorted by residual: dihedral pdb=" CA ILE B 12 " pdb=" C ILE B 12 " pdb=" N PRO B 13 " pdb=" CA PRO B 13 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ILE A 12 " pdb=" C ILE A 12 " pdb=" N PRO A 13 " pdb=" CA PRO A 13 " ideal model delta harmonic sigma weight residual -180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA ARG B 196 " pdb=" C ARG B 196 " pdb=" N PHE B 197 " pdb=" CA PHE B 197 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 4131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 547 0.043 - 0.087: 381 0.087 - 0.130: 74 0.130 - 0.174: 16 0.174 - 0.217: 8 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA PRO B 13 " pdb=" N PRO B 13 " pdb=" C PRO B 13 " pdb=" CB PRO B 13 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA PRO A 13 " pdb=" N PRO A 13 " pdb=" C PRO A 13 " pdb=" CB PRO A 13 " both_signs ideal model delta sigma weight residual False 2.72 2.50 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU B 411 " pdb=" CB LEU B 411 " pdb=" CD1 LEU B 411 " pdb=" CD2 LEU B 411 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1023 not shown) Planarity restraints: 1160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA C 8 " 0.053 2.00e-02 2.50e+03 9.64e-02 9.29e+01 pdb=" C ALA C 8 " -0.167 2.00e-02 2.50e+03 pdb=" O ALA C 8 " 0.061 2.00e-02 2.50e+03 pdb=" N GLY C 10 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 8 " -0.053 2.00e-02 2.50e+03 9.63e-02 9.28e+01 pdb=" C ALA D 8 " 0.167 2.00e-02 2.50e+03 pdb=" O ALA D 8 " -0.061 2.00e-02 2.50e+03 pdb=" N GLY D 10 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 12 " -0.044 5.00e-02 4.00e+02 6.65e-02 7.08e+00 pdb=" N PRO B 13 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 13 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 13 " -0.037 5.00e-02 4.00e+02 ... (remaining 1157 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 16 2.42 - 3.04: 4022 3.04 - 3.66: 9145 3.66 - 4.28: 16044 4.28 - 4.90: 26609 Nonbonded interactions: 55836 Sorted by model distance: nonbonded pdb=" SG CYS A 328 " pdb=" C GLY C 10 " model vdw 1.801 3.630 nonbonded pdb=" SG CYS B 328 " pdb=" C GLY D 10 " model vdw 1.802 3.630 nonbonded pdb=" O PRO B 13 " pdb=" N LEU B 15 " model vdw 2.187 3.120 nonbonded pdb=" O PRO A 13 " pdb=" N LEU A 15 " model vdw 2.187 3.120 nonbonded pdb=" O LEU B 198 " pdb=" NZ LYS B 206 " model vdw 2.210 3.120 ... (remaining 55831 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 9.060 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:7.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 0.011 0.170 6916 Z= 0.461 Angle : 0.929 12.444 9308 Z= 0.529 Chirality : 0.056 0.217 1026 Planarity : 0.007 0.096 1160 Dihedral : 14.329 79.340 2544 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.49 % Allowed : 7.58 % Favored : 91.93 % Rotamer: Outliers : 0.78 % Allowed : 8.98 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.24), residues: 818 helix: -2.00 (0.24), residues: 352 sheet: -0.03 (0.63), residues: 70 loop : -2.38 (0.24), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 341 TYR 0.022 0.003 TYR A 257 PHE 0.025 0.003 PHE B 282 TRP 0.020 0.004 TRP B 242 HIS 0.006 0.002 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.01112 ( 6914) covalent geometry : angle 0.92816 ( 9304) SS BOND : bond 0.00520 ( 2) SS BOND : angle 1.72791 ( 4) hydrogen bonds : bond 0.17794 ( 276) hydrogen bonds : angle 6.68472 ( 792) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 126 time to evaluate : 0.263 Fit side-chains REVERT: A 67 MET cc_start: 0.8007 (mmt) cc_final: 0.7298 (mmt) REVERT: A 223 LYS cc_start: 0.7951 (mttm) cc_final: 0.7750 (mttp) REVERT: A 336 MET cc_start: 0.8896 (mtm) cc_final: 0.8563 (mtm) REVERT: A 409 ASP cc_start: 0.7558 (m-30) cc_final: 0.7318 (m-30) REVERT: B 67 MET cc_start: 0.7991 (mmt) cc_final: 0.7290 (mmt) REVERT: B 223 LYS cc_start: 0.7946 (mttm) cc_final: 0.7742 (mttp) REVERT: B 336 MET cc_start: 0.8904 (mtm) cc_final: 0.8574 (mtm) REVERT: B 409 ASP cc_start: 0.7542 (m-30) cc_final: 0.7307 (m-30) outliers start: 6 outliers final: 0 residues processed: 132 average time/residue: 0.6851 time to fit residues: 94.4401 Evaluate side-chains 89 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 214 HIS A 286 HIS B 88 GLN B 214 HIS B 286 HIS B 322 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.192153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.158022 restraints weight = 6646.845| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.53 r_work: 0.3652 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6916 Z= 0.124 Angle : 0.603 8.381 9308 Z= 0.330 Chirality : 0.040 0.139 1026 Planarity : 0.004 0.053 1160 Dihedral : 5.028 18.988 890 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 2.86 % Allowed : 13.93 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (0.27), residues: 818 helix: -0.16 (0.27), residues: 366 sheet: 0.09 (0.59), residues: 70 loop : -1.77 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 287 TYR 0.011 0.001 TYR A 257 PHE 0.013 0.001 PHE A 133 TRP 0.011 0.002 TRP A 242 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 6914) covalent geometry : angle 0.60246 ( 9304) SS BOND : bond 0.00106 ( 2) SS BOND : angle 1.37710 ( 4) hydrogen bonds : bond 0.04730 ( 276) hydrogen bonds : angle 4.46228 ( 792) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.269 Fit side-chains REVERT: A 49 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6958 (mp0) REVERT: A 251 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.6666 (mp10) REVERT: A 287 ARG cc_start: 0.6789 (ttp80) cc_final: 0.6553 (ttt-90) REVERT: A 384 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6575 (tm-30) REVERT: A 409 ASP cc_start: 0.7801 (m-30) cc_final: 0.7539 (m-30) REVERT: B 49 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.6987 (mp0) REVERT: B 67 MET cc_start: 0.7785 (mmt) cc_final: 0.7205 (mmt) REVERT: B 223 LYS cc_start: 0.7904 (mttm) cc_final: 0.7693 (mttt) REVERT: B 251 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.6688 (mp10) REVERT: B 287 ARG cc_start: 0.6830 (ttp80) cc_final: 0.6584 (ttt-90) REVERT: B 384 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: B 409 ASP cc_start: 0.7764 (m-30) cc_final: 0.7498 (m-30) outliers start: 22 outliers final: 6 residues processed: 117 average time/residue: 0.5471 time to fit residues: 67.5035 Evaluate side-chains 100 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 251 GLN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 384 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.188320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.153790 restraints weight = 6690.986| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.51 r_work: 0.3554 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 6916 Z= 0.231 Angle : 0.722 7.835 9308 Z= 0.386 Chirality : 0.046 0.158 1026 Planarity : 0.004 0.050 1160 Dihedral : 5.371 21.055 890 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % Rotamer: Outliers : 4.43 % Allowed : 14.58 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.28), residues: 818 helix: 0.01 (0.27), residues: 370 sheet: 0.33 (0.65), residues: 70 loop : -1.63 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 230 TYR 0.015 0.002 TYR A 257 PHE 0.017 0.002 PHE A 133 TRP 0.015 0.002 TRP B 242 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 6914) covalent geometry : angle 0.71540 ( 9304) SS BOND : bond 0.00669 ( 2) SS BOND : angle 4.64439 ( 4) hydrogen bonds : bond 0.06892 ( 276) hydrogen bonds : angle 4.60135 ( 792) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.316 Fit side-chains REVERT: A 49 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7110 (mp0) REVERT: A 73 GLU cc_start: 0.7309 (mp0) cc_final: 0.6906 (mp0) REVERT: A 287 ARG cc_start: 0.6939 (ttp80) cc_final: 0.6736 (ttt-90) REVERT: A 384 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: A 409 ASP cc_start: 0.8040 (m-30) cc_final: 0.7800 (m-30) REVERT: B 49 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7075 (mp0) REVERT: B 73 GLU cc_start: 0.7343 (mp0) cc_final: 0.6928 (mp0) REVERT: B 223 LYS cc_start: 0.8049 (mttm) cc_final: 0.7837 (mttt) REVERT: B 287 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6738 (ttt-90) REVERT: B 384 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: B 409 ASP cc_start: 0.8033 (m-30) cc_final: 0.7807 (m-30) outliers start: 34 outliers final: 16 residues processed: 114 average time/residue: 0.6008 time to fit residues: 72.0657 Evaluate side-chains 116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 MET Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 11 optimal weight: 0.0270 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.188516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.153933 restraints weight = 6316.727| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.51 r_work: 0.3483 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6916 Z= 0.111 Angle : 0.564 7.240 9308 Z= 0.308 Chirality : 0.040 0.141 1026 Planarity : 0.004 0.044 1160 Dihedral : 4.821 18.217 890 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.40 % Favored : 95.35 % Rotamer: Outliers : 3.65 % Allowed : 15.49 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.29), residues: 818 helix: 0.73 (0.28), residues: 366 sheet: 0.36 (0.61), residues: 70 loop : -1.34 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 287 TYR 0.009 0.001 TYR A 257 PHE 0.011 0.001 PHE B 234 TRP 0.010 0.001 TRP B 242 HIS 0.002 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 6914) covalent geometry : angle 0.56322 ( 9304) SS BOND : bond 0.00089 ( 2) SS BOND : angle 1.71957 ( 4) hydrogen bonds : bond 0.04407 ( 276) hydrogen bonds : angle 4.18145 ( 792) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.275 Fit side-chains REVERT: A 49 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: A 73 GLU cc_start: 0.7264 (mp0) cc_final: 0.6980 (mp0) REVERT: A 91 GLU cc_start: 0.7694 (tt0) cc_final: 0.7477 (pt0) REVERT: A 384 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6249 (tm-30) REVERT: A 409 ASP cc_start: 0.7611 (m-30) cc_final: 0.7351 (m-30) REVERT: B 49 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6487 (mp0) REVERT: B 73 GLU cc_start: 0.7357 (mp0) cc_final: 0.7087 (mp0) REVERT: B 91 GLU cc_start: 0.7767 (tt0) cc_final: 0.7501 (pt0) REVERT: B 384 GLU cc_start: 0.7021 (OUTLIER) cc_final: 0.6266 (tm-30) REVERT: B 409 ASP cc_start: 0.7591 (m-30) cc_final: 0.7334 (m-30) outliers start: 28 outliers final: 16 residues processed: 121 average time/residue: 0.5635 time to fit residues: 71.9800 Evaluate side-chains 111 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 3 optimal weight: 0.0770 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.185197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.150274 restraints weight = 6326.184| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.56 r_work: 0.3473 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6916 Z= 0.159 Angle : 0.614 6.990 9308 Z= 0.332 Chirality : 0.042 0.132 1026 Planarity : 0.004 0.040 1160 Dihedral : 4.939 18.191 890 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.13 % Rotamer: Outliers : 4.69 % Allowed : 15.36 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.29), residues: 818 helix: 0.56 (0.28), residues: 370 sheet: 0.18 (0.61), residues: 70 loop : -1.34 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 395 TYR 0.012 0.001 TYR B 257 PHE 0.014 0.002 PHE A 133 TRP 0.014 0.002 TRP A 242 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 6914) covalent geometry : angle 0.61134 ( 9304) SS BOND : bond 0.00088 ( 2) SS BOND : angle 2.97910 ( 4) hydrogen bonds : bond 0.05614 ( 276) hydrogen bonds : angle 4.31544 ( 792) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.272 Fit side-chains REVERT: A 49 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: A 73 GLU cc_start: 0.7444 (mp0) cc_final: 0.6866 (mp0) REVERT: A 91 GLU cc_start: 0.7760 (tt0) cc_final: 0.7536 (pt0) REVERT: A 108 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7452 (mm-30) REVERT: A 384 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6377 (tm-30) REVERT: A 409 ASP cc_start: 0.7778 (m-30) cc_final: 0.7518 (m-30) REVERT: B 49 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: B 73 GLU cc_start: 0.7464 (mp0) cc_final: 0.7131 (mp0) REVERT: B 91 GLU cc_start: 0.7800 (tt0) cc_final: 0.7530 (pt0) REVERT: B 384 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6383 (tm-30) REVERT: B 409 ASP cc_start: 0.7761 (m-30) cc_final: 0.7503 (m-30) outliers start: 36 outliers final: 20 residues processed: 115 average time/residue: 0.5478 time to fit residues: 66.4704 Evaluate side-chains 112 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 240 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 HIS B 214 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.181546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.146625 restraints weight = 6359.421| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.51 r_work: 0.3403 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 6916 Z= 0.268 Angle : 0.744 6.723 9308 Z= 0.399 Chirality : 0.048 0.144 1026 Planarity : 0.004 0.040 1160 Dihedral : 5.366 19.494 890 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.38 % Favored : 94.38 % Rotamer: Outliers : 4.82 % Allowed : 16.28 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.80 (0.28), residues: 818 helix: 0.20 (0.27), residues: 362 sheet: 0.19 (0.64), residues: 70 loop : -1.36 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 230 TYR 0.017 0.002 TYR A 257 PHE 0.020 0.003 PHE A 133 TRP 0.015 0.003 TRP A 242 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00653 ( 6914) covalent geometry : angle 0.73871 ( 9304) SS BOND : bond 0.00074 ( 2) SS BOND : angle 4.19902 ( 4) hydrogen bonds : bond 0.07178 ( 276) hydrogen bonds : angle 4.58742 ( 792) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.277 Fit side-chains REVERT: A 49 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: A 73 GLU cc_start: 0.7529 (mp0) cc_final: 0.7209 (mp0) REVERT: A 91 GLU cc_start: 0.7872 (tt0) cc_final: 0.7622 (pt0) REVERT: A 108 GLU cc_start: 0.7724 (mt-10) cc_final: 0.7488 (mm-30) REVERT: A 384 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6358 (tm-30) REVERT: A 409 ASP cc_start: 0.7961 (m-30) cc_final: 0.7704 (m-30) REVERT: B 49 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6752 (mp0) REVERT: B 73 GLU cc_start: 0.7558 (mp0) cc_final: 0.7247 (mp0) REVERT: B 91 GLU cc_start: 0.7961 (tt0) cc_final: 0.7731 (pt0) REVERT: B 108 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7476 (mm-30) REVERT: B 384 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6371 (tm-30) REVERT: B 409 ASP cc_start: 0.7969 (m-30) cc_final: 0.7711 (m-30) outliers start: 37 outliers final: 18 residues processed: 109 average time/residue: 0.5438 time to fit residues: 62.6849 Evaluate side-chains 111 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 89 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 49 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.187259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.152796 restraints weight = 6297.238| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.61 r_work: 0.3502 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6916 Z= 0.119 Angle : 0.554 5.552 9308 Z= 0.305 Chirality : 0.040 0.132 1026 Planarity : 0.003 0.037 1160 Dihedral : 4.837 19.495 890 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.91 % Allowed : 16.41 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.29), residues: 818 helix: 0.51 (0.27), residues: 382 sheet: 0.30 (0.61), residues: 70 loop : -1.33 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 303 TYR 0.010 0.001 TYR B 257 PHE 0.014 0.001 PHE A 133 TRP 0.011 0.001 TRP A 242 HIS 0.002 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 6914) covalent geometry : angle 0.55284 ( 9304) SS BOND : bond 0.00369 ( 2) SS BOND : angle 1.42820 ( 4) hydrogen bonds : bond 0.04754 ( 276) hydrogen bonds : angle 4.18595 ( 792) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.248 Fit side-chains REVERT: A 73 GLU cc_start: 0.7447 (mp0) cc_final: 0.7109 (mp0) REVERT: A 91 GLU cc_start: 0.7839 (tt0) cc_final: 0.7592 (pt0) REVERT: A 108 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7428 (mm-30) REVERT: A 377 ASP cc_start: 0.7771 (m-30) cc_final: 0.7568 (m-30) REVERT: A 384 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6194 (tm-30) REVERT: A 395 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7336 (ptp-110) REVERT: A 409 ASP cc_start: 0.7791 (m-30) cc_final: 0.7528 (m-30) REVERT: B 73 GLU cc_start: 0.7490 (mp0) cc_final: 0.7158 (mp0) REVERT: B 91 GLU cc_start: 0.7839 (tt0) cc_final: 0.7635 (pt0) REVERT: B 108 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7428 (mm-30) REVERT: B 377 ASP cc_start: 0.7754 (m-30) cc_final: 0.7507 (m-30) REVERT: B 384 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6216 (tm-30) REVERT: B 395 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7316 (ptp-110) REVERT: B 409 ASP cc_start: 0.7783 (m-30) cc_final: 0.7515 (m-30) outliers start: 30 outliers final: 18 residues processed: 120 average time/residue: 0.5362 time to fit residues: 67.8966 Evaluate side-chains 107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 18 optimal weight: 0.0270 chunk 24 optimal weight: 0.0970 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.187054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.150724 restraints weight = 6327.178| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.71 r_work: 0.3476 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6916 Z= 0.124 Angle : 0.559 5.436 9308 Z= 0.305 Chirality : 0.040 0.128 1026 Planarity : 0.003 0.036 1160 Dihedral : 4.735 18.965 890 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.52 % Allowed : 17.06 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.29), residues: 818 helix: 0.61 (0.28), residues: 382 sheet: 0.40 (0.62), residues: 70 loop : -1.22 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.009 0.001 TYR A 257 PHE 0.015 0.002 PHE A 133 TRP 0.011 0.001 TRP B 242 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6914) covalent geometry : angle 0.55771 ( 9304) SS BOND : bond 0.00321 ( 2) SS BOND : angle 1.91829 ( 4) hydrogen bonds : bond 0.04851 ( 276) hydrogen bonds : angle 4.12259 ( 792) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.295 Fit side-chains REVERT: A 73 GLU cc_start: 0.7410 (mp0) cc_final: 0.7047 (mp0) REVERT: A 91 GLU cc_start: 0.7842 (tt0) cc_final: 0.7547 (pt0) REVERT: A 108 GLU cc_start: 0.7694 (mt-10) cc_final: 0.7382 (mm-30) REVERT: A 312 LYS cc_start: 0.8168 (OUTLIER) cc_final: 0.7525 (mttm) REVERT: A 377 ASP cc_start: 0.7768 (m-30) cc_final: 0.7544 (m-30) REVERT: A 384 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6191 (tm-30) REVERT: A 395 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7318 (ptp-110) REVERT: A 409 ASP cc_start: 0.7750 (m-30) cc_final: 0.7487 (m-30) REVERT: B 73 GLU cc_start: 0.7452 (mp0) cc_final: 0.7107 (mp0) REVERT: B 91 GLU cc_start: 0.7839 (tt0) cc_final: 0.7618 (pt0) REVERT: B 108 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7382 (mm-30) REVERT: B 377 ASP cc_start: 0.7750 (m-30) cc_final: 0.7528 (m-30) REVERT: B 384 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.6202 (tm-30) REVERT: B 395 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7303 (ptp-110) REVERT: B 409 ASP cc_start: 0.7739 (m-30) cc_final: 0.7470 (m-30) outliers start: 27 outliers final: 18 residues processed: 113 average time/residue: 0.5467 time to fit residues: 65.1598 Evaluate side-chains 116 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 59 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.187935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.152251 restraints weight = 6383.419| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 1.77 r_work: 0.3501 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6916 Z= 0.116 Angle : 0.546 6.518 9308 Z= 0.296 Chirality : 0.040 0.127 1026 Planarity : 0.003 0.034 1160 Dihedral : 4.626 18.870 890 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.99 % Allowed : 17.19 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.29), residues: 818 helix: 0.71 (0.28), residues: 382 sheet: 0.41 (0.62), residues: 70 loop : -1.09 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.009 0.001 TYR A 257 PHE 0.020 0.001 PHE A 197 TRP 0.011 0.001 TRP B 242 HIS 0.002 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 6914) covalent geometry : angle 0.54467 ( 9304) SS BOND : bond 0.00187 ( 2) SS BOND : angle 1.55036 ( 4) hydrogen bonds : bond 0.04609 ( 276) hydrogen bonds : angle 4.08863 ( 792) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.286 Fit side-chains REVERT: A 73 GLU cc_start: 0.7410 (mp0) cc_final: 0.7058 (mp0) REVERT: A 91 GLU cc_start: 0.7854 (tt0) cc_final: 0.7605 (pt0) REVERT: A 108 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7422 (mm-30) REVERT: A 312 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7488 (mttm) REVERT: A 377 ASP cc_start: 0.7794 (m-30) cc_final: 0.7579 (m-30) REVERT: A 384 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6149 (tm-30) REVERT: A 395 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7320 (ptp-110) REVERT: A 409 ASP cc_start: 0.7719 (m-30) cc_final: 0.7465 (m-30) REVERT: B 73 GLU cc_start: 0.7449 (mp0) cc_final: 0.7118 (mp0) REVERT: B 91 GLU cc_start: 0.7844 (tt0) cc_final: 0.7639 (pt0) REVERT: B 108 GLU cc_start: 0.7717 (mt-10) cc_final: 0.7420 (mm-30) REVERT: B 377 ASP cc_start: 0.7782 (m-30) cc_final: 0.7560 (m-30) REVERT: B 384 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6159 (tm-30) REVERT: B 395 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7310 (ptp-110) REVERT: B 409 ASP cc_start: 0.7717 (m-30) cc_final: 0.7454 (m-30) outliers start: 23 outliers final: 16 residues processed: 120 average time/residue: 0.5448 time to fit residues: 69.1130 Evaluate side-chains 113 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 3 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.4041 r_free = 0.4041 target = 0.185833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.150316 restraints weight = 6330.679| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 1.59 r_work: 0.3479 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6916 Z= 0.135 Angle : 0.569 6.322 9308 Z= 0.309 Chirality : 0.041 0.129 1026 Planarity : 0.003 0.035 1160 Dihedral : 4.688 18.616 890 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.12 % Allowed : 17.84 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.29), residues: 818 helix: 0.67 (0.27), residues: 382 sheet: 0.33 (0.62), residues: 70 loop : -1.05 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 196 TYR 0.010 0.001 TYR B 257 PHE 0.017 0.002 PHE A 133 TRP 0.012 0.002 TRP B 242 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 6914) covalent geometry : angle 0.56718 ( 9304) SS BOND : bond 0.00093 ( 2) SS BOND : angle 2.16668 ( 4) hydrogen bonds : bond 0.05072 ( 276) hydrogen bonds : angle 4.15386 ( 792) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.298 Fit side-chains REVERT: A 73 GLU cc_start: 0.7425 (mp0) cc_final: 0.7072 (mp0) REVERT: A 91 GLU cc_start: 0.7854 (tt0) cc_final: 0.7577 (pt0) REVERT: A 312 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7488 (mttm) REVERT: A 377 ASP cc_start: 0.7776 (m-30) cc_final: 0.7569 (m-30) REVERT: A 384 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.6203 (tm-30) REVERT: A 395 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7371 (ptp-110) REVERT: A 409 ASP cc_start: 0.7786 (m-30) cc_final: 0.7528 (m-30) REVERT: B 73 GLU cc_start: 0.7473 (mp0) cc_final: 0.7136 (mp0) REVERT: B 91 GLU cc_start: 0.7844 (tt0) cc_final: 0.7625 (pt0) REVERT: B 108 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7401 (mm-30) REVERT: B 377 ASP cc_start: 0.7757 (m-30) cc_final: 0.7536 (m-30) REVERT: B 384 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6218 (tm-30) REVERT: B 395 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7364 (ptp-110) REVERT: B 409 ASP cc_start: 0.7777 (m-30) cc_final: 0.7519 (m-30) outliers start: 24 outliers final: 16 residues processed: 111 average time/residue: 0.5568 time to fit residues: 65.2165 Evaluate side-chains 113 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 395 ARG Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 395 ARG Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 77 optimal weight: 0.0970 chunk 71 optimal weight: 0.0070 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.189751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.154598 restraints weight = 6371.279| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.51 r_work: 0.3538 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6916 Z= 0.105 Angle : 0.537 6.329 9308 Z= 0.291 Chirality : 0.040 0.135 1026 Planarity : 0.003 0.033 1160 Dihedral : 4.491 18.471 890 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.86 % Allowed : 18.62 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.29), residues: 818 helix: 0.90 (0.28), residues: 382 sheet: 0.32 (0.62), residues: 70 loop : -0.88 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 196 TYR 0.009 0.001 TYR B 276 PHE 0.012 0.001 PHE A 133 TRP 0.009 0.001 TRP A 242 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 6914) covalent geometry : angle 0.53610 ( 9304) SS BOND : bond 0.00268 ( 2) SS BOND : angle 1.24367 ( 4) hydrogen bonds : bond 0.04115 ( 276) hydrogen bonds : angle 3.99036 ( 792) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2736.57 seconds wall clock time: 47 minutes 31.05 seconds (2851.05 seconds total)