Starting phenix.real_space_refine on Mon Apr 28 00:26:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kr6_62520/04_2025/9kr6_62520.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kr6_62520/04_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_62520/04_2025/9kr6_62520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kr6_62520/04_2025/9kr6_62520.map" model { file = "/net/cci-nas-00/data/ceres_data/9kr6_62520/04_2025/9kr6_62520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kr6_62520/04_2025/9kr6_62520.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.136 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: D, B Time building chain proxies: 5.87, per 1000 atoms: 0.87 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: 1.55 Conformation dependent library (CDL) restraints added in 895.0 milliseconds 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: 0.67 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: 2.01 Time building geometry restraints manager: 1.86 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.730 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.150 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.310 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (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 TRP 0.020 0.004 TRP B 242 HIS 0.006 0.002 HIS B 269 PHE 0.025 0.003 PHE B 282 TYR 0.022 0.003 TYR A 257 ARG 0.003 0.001 ARG A 341 Details of bonding type rmsd hydrogen bonds : bond 0.17794 ( 276) hydrogen bonds : angle 6.68472 ( 792) SS BOND : bond 0.00520 ( 2) SS BOND : angle 1.72791 ( 4) covalent geometry : bond 0.01112 ( 6914) covalent geometry : angle 0.92816 ( 9304) *********************** 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 : 0.783 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: 1.3361 time to fit residues: 184.5924 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 : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.191173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.154288 restraints weight = 6585.895| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.64 r_work: 0.3635 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6916 Z= 0.140 Angle : 0.614 8.333 9308 Z= 0.334 Chirality : 0.041 0.136 1026 Planarity : 0.004 0.055 1160 Dihedral : 5.078 19.298 890 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.65 % Favored : 95.11 % Rotamer: Outliers : 2.86 % Allowed : 13.28 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.27), residues: 818 helix: -0.29 (0.27), residues: 368 sheet: 0.14 (0.60), residues: 70 loop : -1.76 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 242 HIS 0.002 0.001 HIS A 268 PHE 0.013 0.001 PHE A 133 TYR 0.011 0.001 TYR A 257 ARG 0.003 0.001 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.05056 ( 276) hydrogen bonds : angle 4.53333 ( 792) SS BOND : bond 0.00204 ( 2) SS BOND : angle 1.32589 ( 4) covalent geometry : bond 0.00300 ( 6914) covalent geometry : angle 0.61366 ( 9304) *********************** 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 122 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.800 Fit side-chains REVERT: A 49 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: A 251 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.6642 (mp10) REVERT: A 287 ARG cc_start: 0.6760 (ttp80) cc_final: 0.6533 (ttt-90) REVERT: A 384 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6530 (tm-30) REVERT: A 409 ASP cc_start: 0.7781 (m-30) cc_final: 0.7518 (m-30) REVERT: B 49 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: B 67 MET cc_start: 0.7740 (mmt) cc_final: 0.7165 (mmt) REVERT: B 251 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.6627 (mp10) REVERT: B 287 ARG cc_start: 0.6786 (ttp80) cc_final: 0.6545 (ttt-90) REVERT: B 384 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: B 409 ASP cc_start: 0.7744 (m-30) cc_final: 0.7476 (m-30) outliers start: 22 outliers final: 8 residues processed: 108 average time/residue: 1.0966 time to fit residues: 125.6035 Evaluate side-chains 98 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 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 251 GLN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 411 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.0070 chunk 29 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 = 0.4133 r_free = 0.4133 target = 0.193171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.156899 restraints weight = 6724.063| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 1.59 r_work: 0.3643 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2183 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= 0.125 Angle : 0.587 7.756 9308 Z= 0.319 Chirality : 0.041 0.142 1026 Planarity : 0.004 0.046 1160 Dihedral : 4.882 18.344 890 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.13 % Favored : 94.62 % Rotamer: Outliers : 3.26 % Allowed : 14.58 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.28), residues: 818 helix: 0.54 (0.28), residues: 366 sheet: 0.29 (0.61), residues: 70 loop : -1.48 (0.28), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 242 HIS 0.002 0.000 HIS A 269 PHE 0.010 0.001 PHE A 133 TYR 0.010 0.001 TYR B 257 ARG 0.002 0.000 ARG B 287 Details of bonding type rmsd hydrogen bonds : bond 0.04883 ( 276) hydrogen bonds : angle 4.27282 ( 792) SS BOND : bond 0.00353 ( 2) SS BOND : angle 2.48577 ( 4) covalent geometry : bond 0.00275 ( 6914) covalent geometry : angle 0.58499 ( 9304) *********************** 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 124 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.762 Fit side-chains REVERT: A 49 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6959 (mp0) REVERT: A 73 GLU cc_start: 0.7261 (mp0) cc_final: 0.6873 (mp0) REVERT: A 251 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6789 (mp10) REVERT: A 384 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6513 (tm-30) REVERT: A 409 ASP cc_start: 0.7730 (m-30) cc_final: 0.7490 (m-30) REVERT: B 49 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: B 73 GLU cc_start: 0.7249 (mp0) cc_final: 0.6822 (mp0) REVERT: B 251 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.6776 (mp10) REVERT: B 384 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: B 409 ASP cc_start: 0.7733 (m-30) cc_final: 0.7488 (m-30) outliers start: 25 outliers final: 14 residues processed: 112 average time/residue: 1.0251 time to fit residues: 121.9896 Evaluate side-chains 107 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 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 251 GLN 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 411 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 38 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.3980 chunk 42 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.4140 r_free = 0.4140 target = 0.193696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160263 restraints weight = 6784.793| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.46 r_work: 0.3660 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2414 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= 0.130 Angle : 0.579 7.194 9308 Z= 0.313 Chirality : 0.041 0.131 1026 Planarity : 0.004 0.041 1160 Dihedral : 4.808 18.013 890 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.89 % Favored : 94.87 % Rotamer: Outliers : 3.39 % Allowed : 15.89 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.29), residues: 818 helix: 0.73 (0.28), residues: 370 sheet: 0.32 (0.61), residues: 70 loop : -1.39 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 242 HIS 0.002 0.001 HIS B 269 PHE 0.013 0.001 PHE B 133 TYR 0.010 0.001 TYR A 257 ARG 0.001 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.04955 ( 276) hydrogen bonds : angle 4.21656 ( 792) SS BOND : bond 0.00433 ( 2) SS BOND : angle 2.59984 ( 4) covalent geometry : bond 0.00289 ( 6914) covalent geometry : angle 0.57680 ( 9304) *********************** 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 121 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.714 Fit side-chains REVERT: A 49 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6858 (mp0) REVERT: A 73 GLU cc_start: 0.7343 (mp0) cc_final: 0.7113 (mp0) REVERT: A 251 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6780 (mp10) REVERT: A 384 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6480 (tm-30) REVERT: A 409 ASP cc_start: 0.7740 (m-30) cc_final: 0.7503 (m-30) REVERT: B 49 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6854 (mp0) REVERT: B 73 GLU cc_start: 0.7358 (mp0) cc_final: 0.7139 (mp0) REVERT: B 251 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.6812 (mp10) REVERT: B 384 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6447 (tm-30) REVERT: B 409 ASP cc_start: 0.7703 (m-30) cc_final: 0.7458 (m-30) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 1.0851 time to fit residues: 125.1932 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 : 0.785 ------------------------------------------------------------------------------- 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 240 SER Chi-restraints excluded: chain A residue 251 GLN 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 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 240 SER Chi-restraints excluded: chain B residue 251 GLN 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 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.190448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154214 restraints weight = 6637.580| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.53 r_work: 0.3584 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6916 Z= 0.187 Angle : 0.643 7.084 9308 Z= 0.347 Chirality : 0.044 0.137 1026 Planarity : 0.004 0.040 1160 Dihedral : 5.047 19.167 890 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.13 % Favored : 94.62 % Rotamer: Outliers : 5.08 % Allowed : 15.62 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.29), residues: 818 helix: 0.51 (0.28), residues: 370 sheet: 0.31 (0.63), residues: 70 loop : -1.37 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 242 HIS 0.003 0.001 HIS B 269 PHE 0.017 0.002 PHE A 133 TYR 0.013 0.002 TYR A 257 ARG 0.002 0.000 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.06068 ( 276) hydrogen bonds : angle 4.37900 ( 792) SS BOND : bond 0.00089 ( 2) SS BOND : angle 3.35938 ( 4) covalent geometry : bond 0.00443 ( 6914) covalent geometry : angle 0.63963 ( 9304) *********************** 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 131 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.718 Fit side-chains REVERT: A 49 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: A 73 GLU cc_start: 0.7420 (mp0) cc_final: 0.6881 (mp0) REVERT: A 384 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: A 395 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7550 (ptp-110) REVERT: A 409 ASP cc_start: 0.7951 (m-30) cc_final: 0.7704 (m-30) REVERT: B 49 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: B 73 GLU cc_start: 0.7455 (mp0) cc_final: 0.7157 (mp0) REVERT: B 384 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6536 (tm-30) REVERT: B 395 ARG cc_start: 0.7887 (OUTLIER) cc_final: 0.7546 (ptp-110) REVERT: B 409 ASP cc_start: 0.7924 (m-30) cc_final: 0.7675 (m-30) outliers start: 39 outliers final: 20 residues processed: 111 average time/residue: 1.1251 time to fit residues: 131.9636 Evaluate side-chains 114 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 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 395 ARG 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 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 395 ARG 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 20 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 48 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.4980 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 B 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.194370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.156522 restraints weight = 6581.124| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.56 r_work: 0.3622 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2609 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= 0.121 Angle : 0.561 6.614 9308 Z= 0.307 Chirality : 0.040 0.128 1026 Planarity : 0.003 0.038 1160 Dihedral : 4.764 17.973 890 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.77 % Favored : 94.99 % Rotamer: Outliers : 4.17 % Allowed : 16.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.29), residues: 818 helix: 0.63 (0.28), residues: 382 sheet: 0.42 (0.62), residues: 70 loop : -1.27 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 242 HIS 0.002 0.000 HIS A 269 PHE 0.012 0.001 PHE B 133 TYR 0.010 0.001 TYR A 257 ARG 0.001 0.000 ARG B 230 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 276) hydrogen bonds : angle 4.14346 ( 792) SS BOND : bond 0.00109 ( 2) SS BOND : angle 1.75589 ( 4) covalent geometry : bond 0.00265 ( 6914) covalent geometry : angle 0.55961 ( 9304) *********************** 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 123 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.760 Fit side-chains REVERT: A 49 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6675 (mp0) REVERT: A 73 GLU cc_start: 0.7396 (mp0) cc_final: 0.6835 (mp0) REVERT: A 287 ARG cc_start: 0.7218 (ttt-90) cc_final: 0.6870 (ttp-170) REVERT: A 384 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6274 (tm-30) REVERT: A 395 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7419 (ptp-110) REVERT: A 409 ASP cc_start: 0.7604 (m-30) cc_final: 0.7347 (m-30) REVERT: B 49 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6699 (mp0) REVERT: B 73 GLU cc_start: 0.7443 (mp0) cc_final: 0.6877 (mp0) REVERT: B 384 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6262 (tm-30) REVERT: B 395 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7397 (ptp-110) REVERT: B 409 ASP cc_start: 0.7565 (m-30) cc_final: 0.7303 (m-30) outliers start: 32 outliers final: 18 residues processed: 112 average time/residue: 1.0971 time to fit residues: 130.2798 Evaluate side-chains 110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 370 SER 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 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 370 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 B 251 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.189756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153193 restraints weight = 6767.482| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.68 r_work: 0.3546 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 6916 Z= 0.283 Angle : 0.753 7.445 9308 Z= 0.401 Chirality : 0.049 0.144 1026 Planarity : 0.004 0.037 1160 Dihedral : 5.335 18.497 890 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.62 % Favored : 94.13 % Rotamer: Outliers : 4.30 % Allowed : 16.54 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.28), residues: 818 helix: 0.28 (0.27), residues: 362 sheet: 0.21 (0.63), residues: 70 loop : -1.33 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 242 HIS 0.004 0.001 HIS A 269 PHE 0.020 0.003 PHE B 133 TYR 0.018 0.002 TYR B 257 ARG 0.004 0.001 ARG A 230 Details of bonding type rmsd hydrogen bonds : bond 0.07258 ( 276) hydrogen bonds : angle 4.56702 ( 792) SS BOND : bond 0.00260 ( 2) SS BOND : angle 4.42244 ( 4) covalent geometry : bond 0.00693 ( 6914) covalent geometry : angle 0.74774 ( 9304) *********************** 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 120 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.738 Fit side-chains REVERT: A 49 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: A 73 GLU cc_start: 0.7518 (mp0) cc_final: 0.7187 (mp0) REVERT: A 287 ARG cc_start: 0.7442 (ttt-90) cc_final: 0.7090 (ttp-170) REVERT: A 384 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6515 (tm-30) REVERT: A 395 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7660 (ptp-110) REVERT: A 409 ASP cc_start: 0.8013 (m-30) cc_final: 0.7774 (m-30) REVERT: B 49 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: B 73 GLU cc_start: 0.7550 (mp0) cc_final: 0.7226 (mp0) REVERT: B 384 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: B 395 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7609 (ptp-110) REVERT: B 409 ASP cc_start: 0.7999 (m-30) cc_final: 0.7761 (m-30) outliers start: 33 outliers final: 18 residues processed: 107 average time/residue: 1.1000 time to fit residues: 124.7516 Evaluate side-chains 110 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 395 ARG 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 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 9 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 27 optimal weight: 0.0670 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.193906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.155836 restraints weight = 6668.109| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.58 r_work: 0.3623 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2700 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= 0.117 Angle : 0.554 5.519 9308 Z= 0.305 Chirality : 0.040 0.131 1026 Planarity : 0.003 0.036 1160 Dihedral : 4.807 19.710 890 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.43 % Allowed : 16.28 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.29), residues: 818 helix: 0.56 (0.27), residues: 382 sheet: 0.40 (0.62), residues: 70 loop : -1.26 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 242 HIS 0.002 0.000 HIS A 269 PHE 0.013 0.001 PHE B 133 TYR 0.009 0.001 TYR B 257 ARG 0.001 0.000 ARG B 99 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 276) hydrogen bonds : angle 4.17380 ( 792) SS BOND : bond 0.00174 ( 2) SS BOND : angle 1.39329 ( 4) covalent geometry : bond 0.00257 ( 6914) covalent geometry : angle 0.55293 ( 9304) *********************** 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 128 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 94 time to evaluate : 0.716 Fit side-chains REVERT: A 73 GLU cc_start: 0.7432 (mp0) cc_final: 0.6825 (mp0) REVERT: A 79 ARG cc_start: 0.8409 (ttm170) cc_final: 0.8125 (mtt-85) REVERT: A 377 ASP cc_start: 0.7778 (m-30) cc_final: 0.7544 (m-30) REVERT: A 384 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6227 (tm-30) REVERT: A 395 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7412 (ptp-110) REVERT: A 409 ASP cc_start: 0.7742 (m-30) cc_final: 0.7481 (m-30) REVERT: B 73 GLU cc_start: 0.7440 (mp0) cc_final: 0.7118 (mp0) REVERT: B 91 GLU cc_start: 0.7832 (tt0) cc_final: 0.7623 (pt0) REVERT: B 377 ASP cc_start: 0.7808 (m-30) cc_final: 0.7526 (m-30) REVERT: B 384 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6235 (tm-30) REVERT: B 395 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7365 (ptp-110) REVERT: B 409 ASP cc_start: 0.7683 (m-30) cc_final: 0.7415 (m-30) outliers start: 34 outliers final: 22 residues processed: 117 average time/residue: 1.0894 time to fit residues: 134.7484 Evaluate side-chains 113 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 87 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 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 348 LYS 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 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 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 348 LYS 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 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 44 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.193558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155906 restraints weight = 6688.326| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.56 r_work: 0.3610 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2733 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 5.463 9308 Z= 0.310 Chirality : 0.041 0.131 1026 Planarity : 0.003 0.035 1160 Dihedral : 4.775 18.908 890 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.78 % Allowed : 17.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.29), residues: 818 helix: 0.58 (0.27), residues: 382 sheet: 0.36 (0.62), residues: 70 loop : -1.20 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 242 HIS 0.002 0.001 HIS A 269 PHE 0.019 0.002 PHE B 133 TYR 0.010 0.001 TYR A 257 ARG 0.001 0.000 ARG A 99 Details of bonding type rmsd hydrogen bonds : bond 0.05097 ( 276) hydrogen bonds : angle 4.16763 ( 792) SS BOND : bond 0.00276 ( 2) SS BOND : angle 2.26603 ( 4) covalent geometry : bond 0.00308 ( 6914) covalent geometry : angle 0.56761 ( 9304) *********************** 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 119 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.793 Fit side-chains REVERT: A 73 GLU cc_start: 0.7424 (mp0) cc_final: 0.6817 (mp0) REVERT: A 79 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8099 (mtt-85) REVERT: A 377 ASP cc_start: 0.7792 (m-30) cc_final: 0.7569 (m-30) REVERT: A 384 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6219 (tm-30) REVERT: A 395 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7390 (ptp-110) REVERT: A 409 ASP cc_start: 0.7757 (m-30) cc_final: 0.7490 (m-30) REVERT: B 73 GLU cc_start: 0.7468 (mp0) cc_final: 0.7148 (mp0) REVERT: B 91 GLU cc_start: 0.7811 (tt0) cc_final: 0.7597 (pt0) REVERT: B 377 ASP cc_start: 0.7830 (m-30) cc_final: 0.7546 (m-30) REVERT: B 384 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6240 (tm-30) REVERT: B 395 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7381 (ptp-110) REVERT: B 409 ASP cc_start: 0.7680 (m-30) cc_final: 0.7406 (m-30) outliers start: 29 outliers final: 22 residues processed: 108 average time/residue: 1.1103 time to fit residues: 126.9397 Evaluate side-chains 114 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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 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 348 LYS 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 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 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 348 LYS 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 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 57 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 51 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.0070 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.196984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.158394 restraints weight = 6724.831| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.63 r_work: 0.3657 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6916 Z= 0.101 Angle : 0.525 6.707 9308 Z= 0.285 Chirality : 0.039 0.130 1026 Planarity : 0.003 0.032 1160 Dihedral : 4.543 19.194 890 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.39 % Allowed : 17.84 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.29), residues: 818 helix: 0.87 (0.28), residues: 380 sheet: 0.37 (0.61), residues: 70 loop : -1.08 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 242 HIS 0.001 0.000 HIS A 269 PHE 0.013 0.001 PHE B 133 TYR 0.008 0.001 TYR A 276 ARG 0.003 0.000 ARG B 196 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 276) hydrogen bonds : angle 4.01683 ( 792) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.98416 ( 4) covalent geometry : bond 0.00213 ( 6914) covalent geometry : angle 0.52441 ( 9304) ********************** 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 121 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.701 Fit side-chains REVERT: A 73 GLU cc_start: 0.7394 (mp0) cc_final: 0.7038 (mp0) REVERT: A 377 ASP cc_start: 0.7730 (m-30) cc_final: 0.7513 (m-30) REVERT: A 384 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6163 (tm-30) REVERT: A 395 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7397 (ptp-110) REVERT: A 409 ASP cc_start: 0.7568 (m-30) cc_final: 0.7275 (m-30) REVERT: B 73 GLU cc_start: 0.7445 (mp0) cc_final: 0.7110 (mp0) REVERT: B 91 GLU cc_start: 0.7789 (tt0) cc_final: 0.7556 (pt0) REVERT: B 251 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.6579 (mp-120) REVERT: B 287 ARG cc_start: 0.7115 (OUTLIER) cc_final: 0.6891 (ttt-90) REVERT: B 377 ASP cc_start: 0.7794 (m-30) cc_final: 0.7517 (m-30) REVERT: B 384 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6133 (tm-30) REVERT: B 395 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.7359 (ptp-110) REVERT: B 409 ASP cc_start: 0.7558 (m-30) cc_final: 0.7269 (m-30) outliers start: 26 outliers final: 16 residues processed: 113 average time/residue: 1.0664 time to fit residues: 127.6146 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 : 0.707 ------------------------------------------------------------------------------- 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 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 251 GLN Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 287 ARG 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 36 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.0010 chunk 72 optimal weight: 0.7980 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.197759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160866 restraints weight = 6777.668| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.53 r_work: 0.3649 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2897 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= 0.115 Angle : 0.545 6.630 9308 Z= 0.293 Chirality : 0.040 0.147 1026 Planarity : 0.003 0.032 1160 Dihedral : 4.545 17.988 890 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.86 % Allowed : 17.97 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.29), residues: 818 helix: 0.87 (0.28), residues: 380 sheet: 0.25 (0.61), residues: 70 loop : -1.03 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 242 HIS 0.002 0.000 HIS B 269 PHE 0.023 0.002 PHE A 197 TYR 0.009 0.001 TYR A 257 ARG 0.001 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04503 ( 276) hydrogen bonds : angle 4.04648 ( 792) SS BOND : bond 0.00146 ( 2) SS BOND : angle 1.66605 ( 4) covalent geometry : bond 0.00256 ( 6914) covalent geometry : angle 0.54398 ( 9304) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5347.68 seconds wall clock time: 91 minutes 57.54 seconds (5517.54 seconds total)