Starting phenix.real_space_refine on Wed Mar 12 04:24:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vyb_43655/03_2025/8vyb_43655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vyb_43655/03_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_43655/03_2025/8vyb_43655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vyb_43655/03_2025/8vyb_43655.map" model { file = "/net/cci-nas-00/data/ceres_data/8vyb_43655/03_2025/8vyb_43655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vyb_43655/03_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-5624/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: 9.73, 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: 1.70 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: 0.88 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: 2.18 Time building geometry restraints manager: 2.06 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: 11.160 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: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.610 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.310 ------------------------------------------------------------------------------- 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 : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2568 time to fit residues: 50.2339 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 : 0.827 ------------------------------------------------------------------------------- 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: 0.6980 chunk 43 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 overall best weight: 0.4876 ------------------------------------------------------------------------------- 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 A 860 GLN B 243 ASN ** B 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.140357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.109468 restraints weight = 16243.578| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 4.24 r_work: 0.3727 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2421 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= 0.203 Angle : 0.638 10.531 10078 Z= 0.321 Chirality : 0.044 0.208 1123 Planarity : 0.005 0.051 1300 Dihedral : 3.917 16.212 978 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.12 % Allowed : 22.72 % 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: 0.87 (0.35), residues: 206 sheet: 0.54 (0.32), residues: 274 loop : -1.51 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 256 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.002 PHE A 67 TYR 0.015 0.002 TYR B 168 ARG 0.012 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: 17 poor density : 85 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8383 (t80) cc_final: 0.7904 (t80) REVERT: A 77 HIS cc_start: 0.7910 (OUTLIER) cc_final: 0.7680 (m90) REVERT: A 180 GLU cc_start: 0.7751 (tt0) cc_final: 0.7423 (tt0) REVERT: A 959 MET cc_start: 0.8457 (tpp) cc_final: 0.8105 (ttt) REVERT: B 10 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6730 (t80) outliers start: 17 outliers final: 8 residues processed: 94 average time/residue: 0.1806 time to fit residues: 23.6945 Evaluate side-chains 77 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 36 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.106180 restraints weight = 16555.016| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 4.34 r_work: 0.3677 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7424 Z= 0.204 Angle : 0.586 8.857 10078 Z= 0.298 Chirality : 0.044 0.155 1123 Planarity : 0.004 0.046 1300 Dihedral : 3.914 16.625 978 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.12 % Allowed : 21.97 % Favored : 74.91 % 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: -0.34 (0.28), residues: 904 helix: 1.05 (0.35), residues: 209 sheet: 0.69 (0.32), residues: 275 loop : -1.56 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 256 HIS 0.009 0.001 HIS A 77 PHE 0.015 0.001 PHE A 67 TYR 0.015 0.001 TYR B 168 ARG 0.012 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 96 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 71 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8409 (t80) cc_final: 0.8002 (t80) REVERT: A 180 GLU cc_start: 0.7911 (tt0) cc_final: 0.7418 (tt0) REVERT: A 879 GLU cc_start: 0.8157 (pm20) cc_final: 0.7957 (pm20) REVERT: B 10 TYR cc_start: 0.7516 (OUTLIER) cc_final: 0.7023 (t80) REVERT: B 207 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7239 (mt-10) outliers start: 25 outliers final: 13 residues processed: 87 average time/residue: 0.1621 time to fit residues: 20.4062 Evaluate side-chains 78 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 261 ILE Chi-restraints excluded: chain B residue 282 LYS 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: 0.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.128916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.099267 restraints weight = 16854.081| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 4.02 r_work: 0.3566 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 7424 Z= 0.420 Angle : 0.709 10.006 10078 Z= 0.370 Chirality : 0.047 0.205 1123 Planarity : 0.005 0.055 1300 Dihedral : 4.757 20.461 978 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 4.99 % Allowed : 19.35 % 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: -0.61 (0.27), residues: 904 helix: 0.74 (0.33), residues: 213 sheet: 0.39 (0.31), residues: 280 loop : -1.62 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 285 HIS 0.006 0.002 HIS B 198 PHE 0.036 0.002 PHE A 67 TYR 0.020 0.002 TYR B 168 ARG 0.014 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 108 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.775 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8597 (t80) cc_final: 0.8337 (t80) REVERT: A 31 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 77 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7777 (m90) REVERT: A 180 GLU cc_start: 0.8018 (tt0) cc_final: 0.7721 (tt0) REVERT: B 244 GLU cc_start: -0.3969 (OUTLIER) cc_final: -0.4432 (tp30) REVERT: B 463 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7674 (mt0) outliers start: 40 outliers final: 25 residues processed: 99 average time/residue: 0.1851 time to fit residues: 25.2049 Evaluate side-chains 85 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 56 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 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 880 VAL 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 173 VAL Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 267 HIS 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 433 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 80 optimal weight: 0.0270 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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 = 0.4214 r_free = 0.4214 target = 0.132052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.101499 restraints weight = 16875.699| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 4.27 r_work: 0.3592 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7424 Z= 0.235 Angle : 0.609 10.845 10078 Z= 0.311 Chirality : 0.044 0.201 1123 Planarity : 0.005 0.050 1300 Dihedral : 4.448 19.667 978 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.00 % Allowed : 20.72 % 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: -0.44 (0.28), residues: 904 helix: 0.97 (0.34), residues: 214 sheet: 0.51 (0.31), residues: 278 loop : -1.58 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 478 HIS 0.009 0.001 HIS A 76 PHE 0.022 0.002 PHE A 332 TYR 0.015 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 97 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8552 (t80) cc_final: 0.8346 (t80) REVERT: A 31 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: A 77 HIS cc_start: 0.7943 (OUTLIER) cc_final: 0.7693 (m90) REVERT: A 180 GLU cc_start: 0.7961 (tt0) cc_final: 0.7556 (tt0) REVERT: B 244 GLU cc_start: -0.4023 (OUTLIER) cc_final: -0.4475 (tp30) outliers start: 32 outliers final: 22 residues processed: 86 average time/residue: 0.1822 time to fit residues: 22.0224 Evaluate side-chains 86 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 292 ILE Chi-restraints excluded: chain A residue 311 SER Chi-restraints excluded: chain A residue 784 VAL Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 880 VAL 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 244 GLU Chi-restraints excluded: chain B residue 261 ILE Chi-restraints excluded: chain B residue 287 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 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: 5.9990 chunk 51 optimal weight: 2.9990 chunk 83 optimal weight: 0.2980 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4219 r_free = 0.4219 target = 0.132439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.100717 restraints weight = 16865.202| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 4.43 r_work: 0.3597 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4184 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= 0.200 Angle : 0.602 10.836 10078 Z= 0.300 Chirality : 0.045 0.269 1123 Planarity : 0.004 0.047 1300 Dihedral : 4.315 18.968 978 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.12 % Allowed : 20.47 % Favored : 75.41 % 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: -0.31 (0.28), residues: 904 helix: 1.12 (0.34), residues: 214 sheet: 0.63 (0.31), residues: 278 loop : -1.55 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 478 HIS 0.009 0.001 HIS A 77 PHE 0.015 0.001 PHE A 67 TYR 0.014 0.001 TYR B 168 ARG 0.010 0.001 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 99 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 26 PHE cc_start: 0.8517 (t80) cc_final: 0.8309 (t80) REVERT: A 31 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: A 180 GLU cc_start: 0.7919 (tt0) cc_final: 0.7468 (tt0) REVERT: B 244 GLU cc_start: -0.4110 (OUTLIER) cc_final: -0.4590 (tp30) REVERT: B 463 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7740 (mt0) outliers start: 33 outliers final: 20 residues processed: 90 average time/residue: 0.1830 time to fit residues: 22.8110 Evaluate side-chains 82 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 233 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 880 VAL 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 195 ILE Chi-restraints excluded: chain B residue 244 GLU Chi-restraints excluded: chain B residue 261 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 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: 2.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 7 optimal weight: 0.0670 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 chunk 89 optimal weight: 1.9990 overall best weight: 0.5332 ------------------------------------------------------------------------------- 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 = 0.4248 r_free = 0.4248 target = 0.132143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.102213 restraints weight = 16848.029| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 4.21 r_work: 0.3654 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7424 Z= 0.177 Angle : 0.584 10.941 10078 Z= 0.290 Chirality : 0.044 0.208 1123 Planarity : 0.004 0.050 1300 Dihedral : 4.081 17.786 978 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.00 % Allowed : 22.10 % Favored : 74.91 % 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: 1.21 (0.35), residues: 215 sheet: 0.75 (0.32), residues: 278 loop : -1.52 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 478 HIS 0.003 0.001 HIS A 76 PHE 0.022 0.001 PHE B 22 TYR 0.013 0.001 TYR B 168 ARG 0.009 0.000 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 86 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.961 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 180 GLU cc_start: 0.7771 (tt0) cc_final: 0.7341 (tt0) REVERT: B 463 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7683 (mt0) outliers start: 24 outliers final: 19 residues processed: 81 average time/residue: 0.2484 time to fit residues: 28.0311 Evaluate side-chains 80 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 311 SER Chi-restraints excluded: chain A residue 803 SER Chi-restraints excluded: chain A residue 894 ILE Chi-restraints excluded: chain B residue 10 TYR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 18 optimal weight: 0.4980 chunk 68 optimal weight: 0.3980 chunk 76 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 0.0050 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 0.0050 overall best weight: 0.3608 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.133037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.103195 restraints weight = 17067.556| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 4.20 r_work: 0.3672 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7424 Z= 0.154 Angle : 0.567 10.562 10078 Z= 0.282 Chirality : 0.043 0.202 1123 Planarity : 0.004 0.055 1300 Dihedral : 3.938 16.214 978 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.24 % Allowed : 21.10 % 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: -0.06 (0.28), residues: 904 helix: 1.31 (0.35), residues: 215 sheet: 0.84 (0.32), residues: 280 loop : -1.47 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 478 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.001 PHE A 26 TYR 0.011 0.001 TYR B 168 ARG 0.011 0.001 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 99 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7400 (tm-30) REVERT: A 180 GLU cc_start: 0.7692 (tt0) cc_final: 0.6988 (tt0) REVERT: B 93 ARG cc_start: 0.6595 (tmm-80) cc_final: 0.6163 (tmm-80) REVERT: B 244 GLU cc_start: -0.3591 (OUTLIER) cc_final: -0.3865 (mm-30) REVERT: B 463 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7663 (mt0) outliers start: 34 outliers final: 24 residues processed: 91 average time/residue: 0.2662 time to fit residues: 34.3141 Evaluate side-chains 89 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 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 A residue 930 ASP 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 173 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 244 GLU 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: 3.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.131004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.100957 restraints weight = 17232.697| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 4.24 r_work: 0.3634 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7424 Z= 0.225 Angle : 0.624 12.631 10078 Z= 0.306 Chirality : 0.044 0.202 1123 Planarity : 0.005 0.054 1300 Dihedral : 4.090 17.288 978 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.75 % Allowed : 21.60 % 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: -0.14 (0.28), residues: 904 helix: 1.17 (0.35), residues: 214 sheet: 0.80 (0.32), residues: 280 loop : -1.47 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 74 HIS 0.003 0.001 HIS B 198 PHE 0.016 0.002 PHE A 26 TYR 0.015 0.001 TYR B 168 ARG 0.013 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 93 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7503 (mp0) REVERT: A 180 GLU cc_start: 0.7779 (tt0) cc_final: 0.7276 (tt0) REVERT: A 879 GLU cc_start: 0.8289 (pm20) cc_final: 0.8086 (pm20) REVERT: B 93 ARG cc_start: 0.6873 (tmm-80) cc_final: 0.6490 (tmm-80) REVERT: B 244 GLU cc_start: -0.3524 (OUTLIER) cc_final: -0.3801 (mm-30) REVERT: B 463 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: B 471 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.6530 (mtm180) outliers start: 30 outliers final: 24 residues processed: 87 average time/residue: 0.2028 time to fit residues: 24.4266 Evaluate side-chains 87 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 233 THR 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 A residue 930 ASP 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 173 VAL Chi-restraints excluded: chain B residue 244 GLU 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 471 ARG 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: 0.0040 chunk 77 optimal weight: 0.8980 chunk 7 optimal weight: 0.0970 chunk 9 optimal weight: 0.0370 chunk 32 optimal weight: 0.0970 chunk 29 optimal weight: 0.0030 chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 overall best weight: 0.0476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.134916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.105085 restraints weight = 16750.193| |-----------------------------------------------------------------------------| r_work (start): 0.3825 rms_B_bonded: 4.16 r_work: 0.3686 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7424 Z= 0.149 Angle : 0.588 10.092 10078 Z= 0.287 Chirality : 0.043 0.197 1123 Planarity : 0.004 0.043 1300 Dihedral : 3.768 13.916 978 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.00 % Allowed : 23.60 % Favored : 74.41 % 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: 0.18 (0.29), residues: 904 helix: 1.39 (0.36), residues: 209 sheet: 1.11 (0.33), residues: 279 loop : -1.30 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 478 HIS 0.005 0.001 HIS A 76 PHE 0.022 0.001 PHE A 26 TYR 0.008 0.001 TYR B 168 ARG 0.009 0.001 ARG B 471 ********************** 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 89 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 ARG cc_start: 0.6793 (tmm-80) cc_final: 0.6444 (tmm-80) REVERT: B 244 GLU cc_start: -0.3186 (OUTLIER) cc_final: -0.3439 (mm-30) REVERT: B 471 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6345 (mtm180) outliers start: 16 outliers final: 13 residues processed: 83 average time/residue: 0.2450 time to fit residues: 27.8726 Evaluate side-chains 78 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 HIS Chi-restraints excluded: chain A residue 193 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 244 GLU 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 421 MET Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 471 ARG Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 495 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 72 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.0670 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 81 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.4254 r_free = 0.4254 target = 0.133522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.103478 restraints weight = 16696.832| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 4.21 r_work: 0.3662 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.4770 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= 0.173 Angle : 0.619 15.976 10078 Z= 0.300 Chirality : 0.043 0.193 1123 Planarity : 0.004 0.050 1300 Dihedral : 3.771 13.857 978 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.25 % Allowed : 24.34 % Favored : 73.41 % 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: 0.13 (0.28), residues: 904 helix: 1.20 (0.35), residues: 211 sheet: 1.05 (0.32), residues: 280 loop : -1.23 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 74 HIS 0.004 0.001 HIS A 76 PHE 0.024 0.001 PHE B 22 TYR 0.012 0.001 TYR B 168 ARG 0.011 0.001 ARG A 869 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5443.73 seconds wall clock time: 97 minutes 18.10 seconds (5838.10 seconds total)