Starting phenix.real_space_refine on Wed Feb 12 04:48:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyb_43655/02_2025/8vyb_43655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyb_43655/02_2025/8vyb_43655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vyb_43655/02_2025/8vyb_43655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyb_43655/02_2025/8vyb_43655.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyb_43655/02_2025/8vyb_43655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyb_43655/02_2025/8vyb_43655.cif" } resolution = 3.37 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= 0.019 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 35 5.16 5 C 4637 2.51 5 N 1238 2.21 5 O 1339 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 7249 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 3700 Classifications: {'peptide': 464} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 434} Chain breaks: 3 Chain: "B" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3549 Classifications: {'peptide': 456} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 426} Chain breaks: 3 Time building chain proxies: 9.74, per 1000 atoms: 1.34 Number of scatterers: 7249 At special positions: 0 Unit cell: (84.37, 97.35, 149.86, 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 35 16.00 O 1339 8.00 N 1238 7.00 C 4637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 10 sheets defined 26.6% alpha, 26.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 21 through 37 removed outlier: 3.962A pdb=" N TRP A 37 " --> pdb=" O VAL A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 98 through 104 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 141 through 160 Processing helix chain 'A' and resid 199 through 203 removed outlier: 3.852A pdb=" N THR A 203 " --> pdb=" O ASN A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 217 removed outlier: 3.508A pdb=" N LEU A 208 " --> pdb=" O HIS A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 307 Processing helix chain 'A' and resid 323 through 328 removed outlier: 3.710A pdb=" N PHE A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 323 through 328' Processing helix chain 'A' and resid 329 through 332 Processing helix chain 'A' and resid 782 through 782 No H-bonds generated for 'chain 'A' and resid 782 through 782' Processing helix chain 'A' and resid 783 through 800 removed outlier: 3.810A pdb=" N ALA A 787 " --> pdb=" O CYS A 783 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 788 " --> pdb=" O VAL A 784 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 790 " --> pdb=" O HIS A 786 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 793 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU A 798 " --> pdb=" O GLU A 794 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 817 removed outlier: 4.350A pdb=" N LYS A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 854 removed outlier: 4.418A pdb=" N LEU A 829 " --> pdb=" O GLU A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 871 removed outlier: 3.549A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 901 removed outlier: 4.212A pdb=" N ILE A 894 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 221 through 241 removed outlier: 3.932A pdb=" N ARG B 229 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA B 230 " --> pdb=" O GLN B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 288 Processing helix chain 'B' and resid 508 through 515 removed outlier: 3.533A pdb=" N GLN B 513 " --> pdb=" O ASN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 544 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 61 removed outlier: 4.280A pdb=" N MET A 176 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N TYR A 177 " --> pdb=" O MET A 192 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N MET A 192 " --> pdb=" O TYR A 177 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 975 " --> pdb=" O PRO A 956 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY A 936 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 278 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS A 309 " --> pdb=" O THR A 284 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 4 through 10 removed outlier: 6.677A pdb=" N VAL B 532 " --> pdb=" O PHE B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 79 through 82 removed outlier: 3.595A pdb=" N GLY B 122 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 101 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N VAL B 118 " --> pdb=" O VAL B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 106 Processing sheet with id=AA6, first strand: chain 'B' and resid 132 through 139 removed outlier: 6.536A pdb=" N GLY B 159 " --> pdb=" O THR B 133 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ALA B 135 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 157 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N CYS B 137 " --> pdb=" O CYS B 155 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N CYS B 155 " --> pdb=" O CYS B 137 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 164 " --> pdb=" O PHE B 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.602A pdb=" N GLN B 187 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS B 254 " --> pdb=" O THR B 218 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS B 255 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU B 374 " --> pdb=" O LYS B 255 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLY B 257 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 263 through 271 removed outlier: 6.922A pdb=" N VAL B 307 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N HIS B 267 " --> pdb=" O ILE B 305 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE B 305 " --> pdb=" O HIS B 267 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N SER B 269 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N GLN B 303 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLY B 271 " --> pdb=" O MET B 301 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N MET B 301 " --> pdb=" O GLY B 271 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 313 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE B 378 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 387 through 392 removed outlier: 6.556A pdb=" N THR B 402 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE B 390 " --> pdb=" O ALA B 400 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 400 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 392 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 398 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ARG B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 408 " --> pdb=" O MET B 421 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 421 " --> pdb=" O VAL B 408 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N LEU B 410 " --> pdb=" O ILE B 419 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 429 through 435 309 hydrogen bonds defined for protein. 852 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: 2.20 Time building geometry restraints manager: 2.04 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: 1760 1.33 - 1.45: 1435 1.45 - 1.57: 4182 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 7424 Sorted by residual: bond pdb=" N SER A 62 " pdb=" CA SER A 62 " ideal model delta sigma weight residual 1.452 1.500 -0.048 1.22e-02 6.72e+03 1.54e+01 bond pdb=" N VAL A 945 " pdb=" CA VAL A 945 " ideal model delta sigma weight residual 1.462 1.495 -0.033 8.70e-03 1.32e+04 1.43e+01 bond pdb=" N ASN A 319 " pdb=" CA ASN A 319 " ideal model delta sigma weight residual 1.458 1.484 -0.026 7.40e-03 1.83e+04 1.28e+01 bond pdb=" N ILE B 5 " pdb=" CA ILE B 5 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.17e-02 7.31e+03 1.27e+01 bond pdb=" C HIS A 170 " pdb=" N HIS A 171 " ideal model delta sigma weight residual 1.332 1.285 0.047 1.41e-02 5.03e+03 1.10e+01 ... (remaining 7419 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 8835 1.62 - 3.25: 1102 3.25 - 4.87: 122 4.87 - 6.49: 14 6.49 - 8.12: 5 Bond angle restraints: 10078 Sorted by residual: angle pdb=" C ARG A 947 " pdb=" CA ARG A 947 " pdb=" CB ARG A 947 " ideal model delta sigma weight residual 108.86 116.98 -8.12 1.44e+00 4.82e-01 3.18e+01 angle pdb=" N ARG A 947 " pdb=" CA ARG A 947 " pdb=" CB ARG A 947 " ideal model delta sigma weight residual 110.03 103.37 6.66 1.21e+00 6.83e-01 3.03e+01 angle pdb=" CA ARG A 947 " pdb=" C ARG A 947 " pdb=" O ARG A 947 " ideal model delta sigma weight residual 120.60 116.85 3.75 9.00e-01 1.23e+00 1.73e+01 angle pdb=" CA LEU B 258 " pdb=" C LEU B 258 " pdb=" O LEU B 258 " ideal model delta sigma weight residual 121.87 117.53 4.34 1.10e+00 8.26e-01 1.55e+01 angle pdb=" C HIS A 170 " pdb=" CA HIS A 170 " pdb=" CB HIS A 170 " ideal model delta sigma weight residual 116.63 112.10 4.53 1.16e+00 7.43e-01 1.52e+01 ... (remaining 10073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 3920 17.11 - 34.22: 395 34.22 - 51.34: 115 51.34 - 68.45: 20 68.45 - 85.56: 8 Dihedral angle restraints: 4458 sinusoidal: 1800 harmonic: 2658 Sorted by residual: dihedral pdb=" N ARG B 229 " pdb=" C ARG B 229 " pdb=" CA ARG B 229 " pdb=" CB ARG B 229 " ideal model delta harmonic sigma weight residual 122.80 113.81 8.99 0 2.50e+00 1.60e-01 1.29e+01 dihedral pdb=" CA ASP B 13 " pdb=" CB ASP B 13 " pdb=" CG ASP B 13 " pdb=" OD1 ASP B 13 " ideal model delta sinusoidal sigma weight residual -30.00 -85.70 55.70 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU A 142 " pdb=" CG GLU A 142 " pdb=" CD GLU A 142 " pdb=" OE1 GLU A 142 " ideal model delta sinusoidal sigma weight residual 0.00 -85.56 85.56 1 3.00e+01 1.11e-03 9.84e+00 ... (remaining 4455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 678 0.052 - 0.103: 251 0.103 - 0.155: 144 0.155 - 0.206: 41 0.206 - 0.258: 9 Chirality restraints: 1123 Sorted by residual: chirality pdb=" CA ARG B 229 " pdb=" N ARG B 229 " pdb=" C ARG B 229 " pdb=" CB ARG B 229 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 535 " pdb=" N VAL B 535 " pdb=" C VAL B 535 " pdb=" CB VAL B 535 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CA LEU A 941 " pdb=" N LEU A 941 " pdb=" C LEU A 941 " pdb=" CB LEU A 941 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1120 not shown) Planarity restraints: 1300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 61 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C LYS A 61 " -0.068 2.00e-02 2.50e+03 pdb=" O LYS A 61 " 0.025 2.00e-02 2.50e+03 pdb=" N SER A 62 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 171 " 0.017 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" C HIS A 171 " -0.061 2.00e-02 2.50e+03 pdb=" O HIS A 171 " 0.022 2.00e-02 2.50e+03 pdb=" N LYS A 172 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 191 " -0.264 9.50e-02 1.11e+02 1.18e-01 8.56e+00 pdb=" NE ARG B 191 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG B 191 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 191 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 191 " -0.009 2.00e-02 2.50e+03 ... (remaining 1297 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2405 2.85 - 3.37: 6346 3.37 - 3.88: 11516 3.88 - 4.39: 12644 4.39 - 4.90: 22156 Nonbonded interactions: 55067 Sorted by model distance: nonbonded pdb=" OG SER A 66 " pdb=" O PHE A 70 " model vdw 2.344 3.040 nonbonded pdb=" O HIS A 135 " pdb=" OG SER A 136 " model vdw 2.358 3.040 nonbonded pdb=" OE1 GLU A 191 " pdb=" NZ LYS B 282 " model vdw 2.365 3.120 nonbonded pdb=" N LEU A 205 " pdb=" OD2 ASP A 295 " model vdw 2.379 3.120 nonbonded pdb=" N GLU B 369 " pdb=" OE1 GLU B 369 " model vdw 2.439 3.120 ... (remaining 55062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 17.000 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: 0.360 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.830 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6253 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 : 0.008 0.048 7424 Z= 0.547 Angle : 1.054 8.118 10078 Z= 0.756 Chirality : 0.073 0.258 1123 Planarity : 0.009 0.118 1300 Dihedral : 15.537 85.562 2734 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 19.85 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -1.28 (0.27), residues: 904 helix: -0.06 (0.36), residues: 204 sheet: 0.06 (0.31), residues: 276 loop : -1.89 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 422 HIS 0.006 0.001 HIS A 171 PHE 0.012 0.001 PHE B 22 TYR 0.026 0.002 TYR B 425 ARG 0.018 0.001 ARG B 471 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2643 time to fit residues: 51.5563 Evaluate side-chains 73 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 0.0170 chunk 27 optimal weight: 0.0770 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 109 ASN B 243 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.141316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.110507 restraints weight = 16211.481| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 4.24 r_work: 0.3745 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7424 Z= 0.189 Angle : 0.630 10.137 10078 Z= 0.319 Chirality : 0.044 0.209 1123 Planarity : 0.005 0.045 1300 Dihedral : 3.859 16.128 978 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.25 % Allowed : 22.60 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.46 (0.28), residues: 904 helix: 0.90 (0.35), residues: 206 sheet: 0.53 (0.32), residues: 274 loop : -1.52 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 256 HIS 0.004 0.001 HIS A 76 PHE 0.014 0.001 PHE A 72 TYR 0.014 0.001 TYR B 168 ARG 0.014 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8400 (t80) cc_final: 0.7918 (t80) REVERT: A 77 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7650 (m90) REVERT: A 180 GLU cc_start: 0.7725 (tt0) cc_final: 0.7377 (tt0) REVERT: B 10 TYR cc_start: 0.7206 (OUTLIER) cc_final: 0.6666 (t80) REVERT: B 244 GLU cc_start: -0.4236 (OUTLIER) cc_final: -0.4714 (tp30) outliers start: 18 outliers final: 8 residues processed: 94 average time/residue: 0.1959 time to fit residues: 25.5293 Evaluate side-chains 79 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 80 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 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 860 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.136895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.105879 restraints weight = 16525.978| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.25 r_work: 0.3673 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7424 Z= 0.215 Angle : 0.591 9.233 10078 Z= 0.301 Chirality : 0.044 0.182 1123 Planarity : 0.005 0.048 1300 Dihedral : 3.941 16.935 978 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.12 % Allowed : 22.22 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.37 (0.28), residues: 904 helix: 1.01 (0.35), residues: 209 sheet: 0.66 (0.32), residues: 275 loop : -1.57 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 256 HIS 0.011 0.001 HIS A 77 PHE 0.016 0.001 PHE A 67 TYR 0.015 0.001 TYR B 168 ARG 0.013 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.800 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8409 (t80) cc_final: 0.8028 (t80) REVERT: A 180 GLU cc_start: 0.7887 (tt0) cc_final: 0.7478 (tt0) REVERT: A 959 MET cc_start: 0.8465 (tpp) cc_final: 0.8253 (ttt) REVERT: B 10 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.7033 (t80) REVERT: B 207 GLU cc_start: 0.7451 (mt-10) cc_final: 0.7212 (mt-10) outliers start: 25 outliers final: 13 residues processed: 87 average time/residue: 0.1643 time to fit residues: 20.6670 Evaluate side-chains 76 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.134006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.102840 restraints weight = 16750.439| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 4.30 r_work: 0.3592 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7424 Z= 0.337 Angle : 0.639 10.399 10078 Z= 0.331 Chirality : 0.045 0.222 1123 Planarity : 0.005 0.052 1300 Dihedral : 4.311 18.196 978 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.24 % Allowed : 20.10 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.43 (0.27), residues: 904 helix: 0.94 (0.33), residues: 214 sheet: 0.56 (0.31), residues: 278 loop : -1.60 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 256 HIS 0.006 0.001 HIS A 77 PHE 0.025 0.002 PHE A 67 TYR 0.018 0.002 TYR B 168 ARG 0.006 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 0.883 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7396 (mp0) REVERT: A 195 LEU cc_start: 0.9205 (tp) cc_final: 0.8963 (tt) REVERT: A 834 HIS cc_start: 0.9358 (OUTLIER) cc_final: 0.9014 (t-170) REVERT: B 207 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7363 (mt-10) outliers start: 34 outliers final: 23 residues processed: 90 average time/residue: 0.2042 time to fit residues: 25.7018 Evaluate side-chains 80 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.9990 chunk 38 optimal weight: 0.0570 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.135234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.104148 restraints weight = 16650.226| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 4.34 r_work: 0.3635 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7424 Z= 0.177 Angle : 0.570 10.547 10078 Z= 0.289 Chirality : 0.043 0.213 1123 Planarity : 0.004 0.044 1300 Dihedral : 4.029 17.024 978 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.87 % Allowed : 21.10 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.15 (0.28), residues: 904 helix: 1.26 (0.34), residues: 215 sheet: 0.71 (0.31), residues: 278 loop : -1.46 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 478 HIS 0.003 0.001 HIS B 198 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR B 168 ARG 0.009 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8355 (t80) cc_final: 0.8074 (t80) REVERT: A 31 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7226 (tm-30) REVERT: A 77 HIS cc_start: 0.7959 (OUTLIER) cc_final: 0.7737 (m90) REVERT: A 195 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8949 (tt) REVERT: B 207 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7399 (mt-10) REVERT: B 244 GLU cc_start: -0.4052 (OUTLIER) cc_final: -0.4514 (tp30) REVERT: B 463 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7682 (mt0) outliers start: 31 outliers final: 19 residues processed: 85 average time/residue: 0.1670 time to fit residues: 20.7320 Evaluate side-chains 83 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 77 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 75 optimal weight: 0.0770 chunk 51 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 74 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.135895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.105033 restraints weight = 16705.732| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 4.36 r_work: 0.3641 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7424 Z= 0.163 Angle : 0.559 10.901 10078 Z= 0.278 Chirality : 0.043 0.272 1123 Planarity : 0.004 0.044 1300 Dihedral : 3.940 16.247 978 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.87 % Allowed : 20.85 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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 (0.28), residues: 904 helix: 1.33 (0.34), residues: 215 sheet: 0.78 (0.32), residues: 278 loop : -1.43 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 478 HIS 0.008 0.001 HIS A 77 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR B 168 ARG 0.007 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.846 Fit side-chains REVERT: A 26 PHE cc_start: 0.8380 (t80) cc_final: 0.8117 (t80) REVERT: A 31 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: B 207 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7327 (mt-10) REVERT: B 244 GLU cc_start: -0.4054 (OUTLIER) cc_final: -0.4550 (tp30) REVERT: B 463 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7686 (mt0) outliers start: 31 outliers final: 21 residues processed: 89 average time/residue: 0.1799 time to fit residues: 22.7559 Evaluate side-chains 86 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 30 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.131629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.101412 restraints weight = 16595.863| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.20 r_work: 0.3588 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7424 Z= 0.272 Angle : 0.615 9.982 10078 Z= 0.313 Chirality : 0.044 0.175 1123 Planarity : 0.004 0.048 1300 Dihedral : 4.226 18.957 978 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.25 % Allowed : 21.47 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.19 (0.28), residues: 904 helix: 1.17 (0.34), residues: 215 sheet: 0.62 (0.31), residues: 280 loop : -1.40 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 285 HIS 0.004 0.001 HIS B 198 PHE 0.025 0.002 PHE A 67 TYR 0.017 0.002 TYR B 168 ARG 0.010 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8518 (t80) cc_final: 0.8302 (t80) REVERT: A 31 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: A 195 LEU cc_start: 0.9153 (tp) cc_final: 0.8941 (tt) REVERT: B 207 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7436 (mt-10) REVERT: B 463 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7717 (mt0) outliers start: 26 outliers final: 18 residues processed: 84 average time/residue: 0.1907 time to fit residues: 22.3732 Evaluate side-chains 80 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 60 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.131679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.102677 restraints weight = 16674.499| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.08 r_work: 0.3659 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7424 Z= 0.189 Angle : 0.570 10.691 10078 Z= 0.285 Chirality : 0.044 0.225 1123 Planarity : 0.004 0.047 1300 Dihedral : 3.990 18.277 978 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.50 % Allowed : 20.85 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.04 (0.28), residues: 904 helix: 1.39 (0.35), residues: 215 sheet: 0.69 (0.32), residues: 280 loop : -1.35 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 478 HIS 0.004 0.001 HIS A 76 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.001 TYR B 168 ARG 0.010 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8456 (t80) cc_final: 0.8245 (t80) REVERT: A 31 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7421 (mp0) REVERT: B 463 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7703 (mt0) outliers start: 28 outliers final: 22 residues processed: 85 average time/residue: 0.1878 time to fit residues: 22.2445 Evaluate side-chains 84 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 834 HIS Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.130388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.100548 restraints weight = 17205.216| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 4.18 r_work: 0.3627 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7424 Z= 0.246 Angle : 0.617 15.954 10078 Z= 0.305 Chirality : 0.045 0.211 1123 Planarity : 0.005 0.064 1300 Dihedral : 4.134 18.901 978 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.50 % Allowed : 21.35 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.14 (0.28), residues: 904 helix: 1.22 (0.34), residues: 215 sheet: 0.64 (0.32), residues: 280 loop : -1.37 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 58 HIS 0.004 0.001 HIS B 198 PHE 0.019 0.001 PHE A 67 TYR 0.016 0.001 TYR B 168 ARG 0.017 0.001 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: B 463 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7730 (mt0) outliers start: 28 outliers final: 21 residues processed: 83 average time/residue: 0.1891 time to fit residues: 21.9953 Evaluate side-chains 83 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 384 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 417 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 27 optimal weight: 0.0980 chunk 77 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 32 optimal weight: 0.0470 chunk 29 optimal weight: 0.0040 chunk 47 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 overall best weight: 0.2090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.133614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103216 restraints weight = 16876.797| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 4.33 r_work: 0.3645 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.4574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7424 Z= 0.149 Angle : 0.593 16.131 10078 Z= 0.286 Chirality : 0.044 0.209 1123 Planarity : 0.004 0.046 1300 Dihedral : 3.869 16.268 978 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.50 % Allowed : 22.35 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.09 (0.29), residues: 904 helix: 1.35 (0.35), residues: 215 sheet: 0.97 (0.32), residues: 277 loop : -1.33 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 58 HIS 0.005 0.001 HIS A 76 PHE 0.021 0.001 PHE A 26 TYR 0.010 0.001 TYR B 168 ARG 0.012 0.001 ARG B 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7450 (tm-30) REVERT: B 463 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7682 (mt0) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.2069 time to fit residues: 22.9101 Evaluate side-chains 79 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 802 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 463 GLN Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Chi-restraints excluded: chain B residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 61 optimal weight: 0.0030 chunk 88 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 0.0070 chunk 45 optimal weight: 3.9990 overall best weight: 0.5408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.132242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.102093 restraints weight = 16785.970| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 4.17 r_work: 0.3633 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7424 Z= 0.182 Angle : 0.602 15.416 10078 Z= 0.295 Chirality : 0.043 0.230 1123 Planarity : 0.005 0.076 1300 Dihedral : 3.892 16.159 978 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.37 % Allowed : 22.85 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.01 (0.28), residues: 904 helix: 1.14 (0.35), residues: 216 sheet: 0.90 (0.32), residues: 280 loop : -1.33 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 58 HIS 0.004 0.001 HIS A 76 PHE 0.014 0.001 PHE B 22 TYR 0.014 0.001 TYR B 168 ARG 0.020 0.001 ARG B 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4774.45 seconds wall clock time: 86 minutes 16.76 seconds (5176.76 seconds total)