Starting phenix.real_space_refine on Tue Mar 3 19:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9upb_64390/03_2026/9upb_64390.cif Found real_map, /net/cci-nas-00/data/ceres_data/9upb_64390/03_2026/9upb_64390.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9upb_64390/03_2026/9upb_64390.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9upb_64390/03_2026/9upb_64390.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9upb_64390/03_2026/9upb_64390.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9upb_64390/03_2026/9upb_64390.map" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 65 5.16 5 C 5256 2.51 5 N 1413 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8266 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2836 Classifications: {'peptide': 355} Link IDs: {'PTRANS': 16, 'TRANS': 338} Chain: "B" Number of atoms: 3140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3140 Classifications: {'peptide': 387} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 374} Chain breaks: 2 Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 451 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 1, 'TRANS': 51} Chain: "D" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1808 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.83, per 1000 atoms: 0.22 Number of scatterers: 8266 At special positions: 0 Unit cell: (72.98, 100.86, 110.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 3 15.00 O 1529 8.00 N 1413 7.00 C 5256 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: 0.82 Conformation dependent library (CDL) restraints added in 454.1 milliseconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1966 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 64.3% alpha, 2.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 642 through 653 Processing helix chain 'A' and resid 687 through 691 Processing helix chain 'A' and resid 693 through 708 Processing helix chain 'A' and resid 715 through 738 Processing helix chain 'A' and resid 741 through 762 Processing helix chain 'A' and resid 763 through 765 No H-bonds generated for 'chain 'A' and resid 763 through 765' Processing helix chain 'A' and resid 771 through 795 Processing helix chain 'A' and resid 802 through 814 Processing helix chain 'A' and resid 819 through 827 removed outlier: 3.531A pdb=" N GLU A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 851 through 862 Processing helix chain 'A' and resid 863 through 872 removed outlier: 3.780A pdb=" N CYS A 872 " --> pdb=" O CYS A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 890 removed outlier: 3.675A pdb=" N THR A 890 " --> pdb=" O ASN A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 912 through 923 removed outlier: 3.517A pdb=" N ALA A 916 " --> pdb=" O ASP A 912 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N HIS A 923 " --> pdb=" O PHE A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 939 removed outlier: 3.987A pdb=" N PHE A 939 " --> pdb=" O ARG A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 957 Processing helix chain 'A' and resid 961 through 968 Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 21 through 30 removed outlier: 3.533A pdb=" N CYS B 25 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 57 through 72 removed outlier: 4.015A pdb=" N MET B 61 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 98 Processing helix chain 'B' and resid 104 through 127 removed outlier: 3.781A pdb=" N LEU B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLN B 124 " --> pdb=" O ASN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 155 removed outlier: 3.995A pdb=" N ASP B 155 " --> pdb=" O VAL B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.504A pdb=" N LEU B 171 " --> pdb=" O GLY B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 187 through 198 removed outlier: 3.919A pdb=" N LEU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 223 Processing helix chain 'B' and resid 225 through 240 Processing helix chain 'B' and resid 244 through 261 removed outlier: 3.855A pdb=" N TYR B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) Proline residue: B 257 - end of helix Processing helix chain 'B' and resid 267 through 274 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 290 through 301 Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 315 Processing helix chain 'B' and resid 317 through 334 Processing helix chain 'B' and resid 340 through 350 Processing helix chain 'B' and resid 356 through 370 Processing helix chain 'C' and resid 50 through 63 Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.739A pdb=" N LEU D 51 " --> pdb=" O ARG D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 69 through 82 Proline residue: D 77 - end of helix Processing helix chain 'D' and resid 94 through 106 Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 153 through 163 removed outlier: 3.506A pdb=" N ASP D 157 " --> pdb=" O SER D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 182 Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.834A pdb=" N MET D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D 204 " --> pdb=" O LYS D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 218 Processing helix chain 'D' and resid 234 through 241 removed outlier: 4.195A pdb=" N VAL D 238 " --> pdb=" O GLU D 234 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 897 through 900 Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 266 removed outlier: 3.501A pdb=" N MET B 265 " --> pdb=" O GLU C 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AA4, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.539A pdb=" N CYS D 87 " --> pdb=" O SER D 228 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 116 through 118 Processing sheet with id=AA6, first strand: chain 'D' and resid 147 through 148 437 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2709 1.34 - 1.46: 1475 1.46 - 1.58: 4154 1.58 - 1.69: 3 1.69 - 1.81: 100 Bond restraints: 8441 Sorted by residual: bond pdb=" N CYS D 63 " pdb=" CA CYS D 63 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.33e-02 5.65e+03 5.22e+00 bond pdb=" N GLU D 66 " pdb=" CA GLU D 66 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.38e+00 bond pdb=" CA PHE D 65 " pdb=" C PHE D 65 " ideal model delta sigma weight residual 1.523 1.501 0.022 1.30e-02 5.92e+03 2.91e+00 bond pdb=" N GLY D 64 " pdb=" CA GLY D 64 " ideal model delta sigma weight residual 1.453 1.477 -0.024 1.50e-02 4.44e+03 2.59e+00 bond pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta sigma weight residual 1.462 1.478 -0.016 1.27e-02 6.20e+03 1.68e+00 ... (remaining 8436 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 10821 1.04 - 2.07: 450 2.07 - 3.11: 97 3.11 - 4.14: 26 4.14 - 5.18: 4 Bond angle restraints: 11398 Sorted by residual: angle pdb=" N CYS D 63 " pdb=" CA CYS D 63 " pdb=" C CYS D 63 " ideal model delta sigma weight residual 113.28 109.15 4.13 1.22e+00 6.72e-01 1.14e+01 angle pdb=" C GLU D 248 " pdb=" CA GLU D 248 " pdb=" CB GLU D 248 " ideal model delta sigma weight residual 111.82 108.24 3.58 1.28e+00 6.10e-01 7.84e+00 angle pdb=" CA ASN B 183 " pdb=" CB ASN B 183 " pdb=" CG ASN B 183 " ideal model delta sigma weight residual 112.60 115.07 -2.47 1.00e+00 1.00e+00 6.10e+00 angle pdb=" O GLY D 64 " pdb=" C GLY D 64 " pdb=" N PHE D 65 " ideal model delta sigma weight residual 122.54 124.76 -2.22 1.02e+00 9.61e-01 4.72e+00 angle pdb=" CA GLU D 248 " pdb=" C GLU D 248 " pdb=" N ILE D 249 " ideal model delta sigma weight residual 115.83 118.34 -2.51 1.18e+00 7.18e-01 4.54e+00 ... (remaining 11393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 4557 17.71 - 35.41: 447 35.41 - 53.12: 117 53.12 - 70.82: 22 70.82 - 88.53: 7 Dihedral angle restraints: 5150 sinusoidal: 2138 harmonic: 3012 Sorted by residual: dihedral pdb=" CB GLU B 60 " pdb=" CG GLU B 60 " pdb=" CD GLU B 60 " pdb=" OE1 GLU B 60 " ideal model delta sinusoidal sigma weight residual 0.00 88.53 -88.53 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CA ASP D 62 " pdb=" CB ASP D 62 " pdb=" CG ASP D 62 " pdb=" OD1 ASP D 62 " ideal model delta sinusoidal sigma weight residual -30.00 -83.04 53.04 1 2.00e+01 2.50e-03 9.57e+00 dihedral pdb=" N ASN A 776 " pdb=" CA ASN A 776 " pdb=" CB ASN A 776 " pdb=" CG ASN A 776 " ideal model delta sinusoidal sigma weight residual -180.00 -121.15 -58.85 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 783 0.027 - 0.055: 323 0.055 - 0.082: 98 0.082 - 0.110: 44 0.110 - 0.137: 12 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ILE D 168 " pdb=" N ILE D 168 " pdb=" C ILE D 168 " pdb=" CB ILE D 168 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE D 190 " pdb=" N ILE D 190 " pdb=" C ILE D 190 " pdb=" CB ILE D 190 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA VAL A 974 " pdb=" N VAL A 974 " pdb=" C VAL A 974 " pdb=" CB VAL A 974 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 1257 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 33 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO B 34 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 34 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 34 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 822 " 0.151 9.50e-02 1.11e+02 6.80e-02 3.12e+00 pdb=" NE ARG A 822 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 822 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 822 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 822 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 183 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C ASN B 183 " -0.028 2.00e-02 2.50e+03 pdb=" O ASN B 183 " 0.010 2.00e-02 2.50e+03 pdb=" N LYS B 184 " 0.009 2.00e-02 2.50e+03 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 248 2.71 - 3.26: 9493 3.26 - 3.80: 13656 3.80 - 4.35: 17344 4.35 - 4.90: 28574 Nonbonded interactions: 69315 Sorted by model distance: nonbonded pdb=" O ASN B 183 " pdb=" OD1 ASN B 183 " model vdw 2.162 3.040 nonbonded pdb=" O GLN A 711 " pdb=" OE1 GLN A 711 " model vdw 2.455 3.040 nonbonded pdb=" O GLU A 915 " pdb=" OD1 ASP A 918 " model vdw 2.464 3.040 nonbonded pdb=" OE2 GLU D 132 " pdb=" O3' ANP D 501 " model vdw 2.475 3.040 nonbonded pdb=" O ALA B 280 " pdb=" OG1 THR B 283 " model vdw 2.484 3.040 ... (remaining 69310 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: 1.080 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.050 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 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 : 0.003 0.030 8441 Z= 0.141 Angle : 0.515 5.176 11398 Z= 0.284 Chirality : 0.036 0.137 1260 Planarity : 0.004 0.068 1464 Dihedral : 15.547 88.529 3184 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 2.51 % Allowed : 15.94 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.27), residues: 1007 helix: 0.54 (0.21), residues: 612 sheet: -2.97 (0.82), residues: 32 loop : -1.42 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 822 TYR 0.017 0.001 TYR B 376 PHE 0.019 0.001 PHE A 754 TRP 0.005 0.001 TRP A 719 HIS 0.003 0.001 HIS A 760 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8441) covalent geometry : angle 0.51535 (11398) hydrogen bonds : bond 0.13060 ( 437) hydrogen bonds : angle 6.26331 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.336 Fit side-chains revert: symmetry clash REVERT: A 639 ASP cc_start: 0.8115 (t70) cc_final: 0.7538 (t0) REVERT: A 709 MET cc_start: 0.8184 (ttm) cc_final: 0.7894 (mtt) REVERT: A 711 GLN cc_start: 0.7992 (tm-30) cc_final: 0.7174 (tm-30) REVERT: A 940 LEU cc_start: 0.9151 (tp) cc_final: 0.8692 (pp) REVERT: B 14 TYR cc_start: 0.8044 (t80) cc_final: 0.7763 (t80) REVERT: B 61 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.7200 (tmm) REVERT: B 67 ARG cc_start: 0.8615 (ttm170) cc_final: 0.8377 (mmt90) REVERT: B 146 MET cc_start: 0.8069 (tpp) cc_final: 0.7607 (mmt) REVERT: B 223 ASP cc_start: 0.8305 (t70) cc_final: 0.7841 (t0) REVERT: B 278 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7280 (mt0) REVERT: B 308 CYS cc_start: 0.8581 (m) cc_final: 0.8278 (m) REVERT: B 336 HIS cc_start: 0.7245 (m90) cc_final: 0.6967 (m170) REVERT: C 40 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: D 55 GLU cc_start: 0.7771 (pm20) cc_final: 0.7316 (mm-30) REVERT: D 154 ILE cc_start: 0.8001 (mp) cc_final: 0.7569 (tt) REVERT: D 159 GLU cc_start: 0.8440 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 168 ILE cc_start: 0.8689 (mp) cc_final: 0.8435 (mm) REVERT: D 183 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7650 (tttt) REVERT: D 186 ASN cc_start: 0.7988 (t0) cc_final: 0.7213 (p0) outliers start: 23 outliers final: 18 residues processed: 209 average time/residue: 0.0791 time to fit residues: 24.2712 Evaluate side-chains 202 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 721 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.0670 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 366 ASN B 379 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.153302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.123729 restraints weight = 12475.251| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.20 r_work: 0.3577 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8441 Z= 0.155 Angle : 0.558 5.906 11398 Z= 0.296 Chirality : 0.041 0.145 1260 Planarity : 0.004 0.042 1464 Dihedral : 7.489 58.303 1167 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.82 % Allowed : 16.16 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 1007 helix: 0.93 (0.21), residues: 620 sheet: -3.42 (0.65), residues: 53 loop : -1.03 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 822 TYR 0.015 0.001 TYR D 13 PHE 0.024 0.002 PHE A 806 TRP 0.006 0.001 TRP B 103 HIS 0.005 0.001 HIS A 738 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8441) covalent geometry : angle 0.55764 (11398) hydrogen bonds : bond 0.04325 ( 437) hydrogen bonds : angle 4.77697 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 940 LEU cc_start: 0.9112 (tp) cc_final: 0.8592 (pp) REVERT: B 14 TYR cc_start: 0.8238 (t80) cc_final: 0.7974 (t80) REVERT: B 61 MET cc_start: 0.7795 (ptm) cc_final: 0.7293 (tmm) REVERT: B 67 ARG cc_start: 0.8653 (ttm170) cc_final: 0.8428 (mmt90) REVERT: B 116 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7809 (ttp80) REVERT: B 146 MET cc_start: 0.7911 (tpp) cc_final: 0.7445 (mmt) REVERT: B 223 ASP cc_start: 0.8438 (t70) cc_final: 0.7995 (t0) REVERT: B 308 CYS cc_start: 0.8629 (m) cc_final: 0.8153 (m) REVERT: B 310 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7395 (pp) REVERT: B 336 HIS cc_start: 0.7264 (m90) cc_final: 0.7018 (m170) REVERT: D 55 GLU cc_start: 0.7927 (pm20) cc_final: 0.7227 (mm-30) REVERT: D 154 ILE cc_start: 0.8013 (mp) cc_final: 0.7591 (tt) REVERT: D 183 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7728 (tttt) REVERT: D 186 ASN cc_start: 0.8060 (t0) cc_final: 0.7282 (p0) REVERT: D 226 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7383 (ptm) outliers start: 35 outliers final: 19 residues processed: 226 average time/residue: 0.0756 time to fit residues: 25.2863 Evaluate side-chains 198 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 176 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.0470 chunk 76 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 4 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 42 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 90 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 HIS ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 361 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.124393 restraints weight = 12318.740| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 3.19 r_work: 0.3588 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8441 Z= 0.143 Angle : 0.531 5.332 11398 Z= 0.282 Chirality : 0.041 0.181 1260 Planarity : 0.004 0.040 1464 Dihedral : 6.724 59.009 1148 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.37 % Allowed : 17.58 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.27), residues: 1007 helix: 1.04 (0.21), residues: 623 sheet: -3.27 (0.67), residues: 53 loop : -0.98 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 822 TYR 0.011 0.001 TYR B 109 PHE 0.013 0.002 PHE A 754 TRP 0.007 0.001 TRP A 719 HIS 0.006 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8441) covalent geometry : angle 0.53137 (11398) hydrogen bonds : bond 0.03950 ( 437) hydrogen bonds : angle 4.50495 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8184 (tm-30) cc_final: 0.7345 (tm-30) REVERT: A 940 LEU cc_start: 0.9099 (tp) cc_final: 0.8583 (pp) REVERT: B 14 TYR cc_start: 0.8178 (t80) cc_final: 0.7926 (t80) REVERT: B 61 MET cc_start: 0.7924 (ptm) cc_final: 0.7330 (tmm) REVERT: B 67 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8418 (mmt90) REVERT: B 136 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: B 146 MET cc_start: 0.7848 (tpp) cc_final: 0.7352 (mmt) REVERT: B 223 ASP cc_start: 0.8406 (t70) cc_final: 0.7969 (t0) REVERT: B 308 CYS cc_start: 0.8685 (m) cc_final: 0.8209 (m) REVERT: B 310 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7443 (pp) REVERT: D 55 GLU cc_start: 0.7904 (pm20) cc_final: 0.7189 (mm-30) REVERT: D 121 HIS cc_start: 0.8024 (t-170) cc_final: 0.7574 (t-170) REVERT: D 127 PHE cc_start: 0.8366 (m-80) cc_final: 0.8066 (m-80) REVERT: D 154 ILE cc_start: 0.8033 (mp) cc_final: 0.7648 (tt) REVERT: D 183 LYS cc_start: 0.8276 (ttmt) cc_final: 0.7737 (tttt) REVERT: D 186 ASN cc_start: 0.8027 (t0) cc_final: 0.7251 (p0) outliers start: 40 outliers final: 23 residues processed: 218 average time/residue: 0.0755 time to fit residues: 24.1428 Evaluate side-chains 203 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 58 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 11 optimal weight: 0.0570 chunk 93 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 778 ASN A 828 HIS ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 366 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.156695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.126780 restraints weight = 12512.185| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.25 r_work: 0.3600 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8441 Z= 0.131 Angle : 0.541 5.057 11398 Z= 0.286 Chirality : 0.041 0.192 1260 Planarity : 0.004 0.048 1464 Dihedral : 6.533 62.586 1143 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.69 % Allowed : 16.70 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.27), residues: 1007 helix: 1.13 (0.21), residues: 629 sheet: -3.20 (0.73), residues: 43 loop : -0.97 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 822 TYR 0.012 0.001 TYR B 109 PHE 0.027 0.002 PHE A 806 TRP 0.007 0.001 TRP A 719 HIS 0.010 0.001 HIS A 828 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8441) covalent geometry : angle 0.54096 (11398) hydrogen bonds : bond 0.03732 ( 437) hydrogen bonds : angle 4.36539 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 201 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 806 PHE cc_start: 0.8798 (m-80) cc_final: 0.8473 (m-80) REVERT: A 940 LEU cc_start: 0.9105 (tp) cc_final: 0.8592 (pp) REVERT: A 959 THR cc_start: 0.8664 (p) cc_final: 0.8397 (t) REVERT: B 14 TYR cc_start: 0.8190 (t80) cc_final: 0.7942 (t80) REVERT: B 61 MET cc_start: 0.7964 (ptm) cc_final: 0.7427 (tmm) REVERT: B 67 ARG cc_start: 0.8645 (ttm170) cc_final: 0.8418 (mmt90) REVERT: B 136 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7149 (m-30) REVERT: B 146 MET cc_start: 0.7817 (tpp) cc_final: 0.7364 (mmt) REVERT: B 221 MET cc_start: 0.8831 (ttp) cc_final: 0.8542 (ttp) REVERT: B 223 ASP cc_start: 0.8365 (t70) cc_final: 0.7945 (t0) REVERT: B 307 ARG cc_start: 0.7531 (ptt90) cc_final: 0.7112 (ptp-170) REVERT: B 308 CYS cc_start: 0.8659 (m) cc_final: 0.8225 (m) REVERT: B 310 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7448 (pp) REVERT: D 55 GLU cc_start: 0.7943 (pm20) cc_final: 0.7255 (mm-30) REVERT: D 121 HIS cc_start: 0.7988 (t-170) cc_final: 0.7682 (t-170) REVERT: D 154 ILE cc_start: 0.8029 (mp) cc_final: 0.7644 (tt) REVERT: D 183 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7684 (tttt) REVERT: D 186 ASN cc_start: 0.7988 (t0) cc_final: 0.7231 (p0) outliers start: 43 outliers final: 32 residues processed: 221 average time/residue: 0.0808 time to fit residues: 25.5873 Evaluate side-chains 216 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 65 PHE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 73 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 HIS ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.126420 restraints weight = 12453.826| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.22 r_work: 0.3584 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8441 Z= 0.139 Angle : 0.533 5.089 11398 Z= 0.281 Chirality : 0.041 0.183 1260 Planarity : 0.004 0.052 1464 Dihedral : 6.542 69.234 1143 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.48 % Allowed : 18.45 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.27), residues: 1007 helix: 1.08 (0.21), residues: 628 sheet: -2.87 (0.72), residues: 53 loop : -0.85 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 822 TYR 0.011 0.001 TYR B 109 PHE 0.025 0.002 PHE A 754 TRP 0.009 0.001 TRP A 719 HIS 0.005 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 8441) covalent geometry : angle 0.53328 (11398) hydrogen bonds : bond 0.03670 ( 437) hydrogen bonds : angle 4.35523 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8127 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 806 PHE cc_start: 0.8809 (m-80) cc_final: 0.8416 (m-80) REVERT: A 940 LEU cc_start: 0.9124 (tp) cc_final: 0.8614 (pp) REVERT: A 959 THR cc_start: 0.8641 (p) cc_final: 0.8390 (t) REVERT: B 14 TYR cc_start: 0.8176 (t80) cc_final: 0.7925 (t80) REVERT: B 61 MET cc_start: 0.7942 (ptm) cc_final: 0.7413 (tmm) REVERT: B 67 ARG cc_start: 0.8657 (ttm170) cc_final: 0.8412 (mmt90) REVERT: B 146 MET cc_start: 0.7832 (tpp) cc_final: 0.7359 (mmt) REVERT: B 221 MET cc_start: 0.8787 (ttp) cc_final: 0.8520 (ttp) REVERT: B 223 ASP cc_start: 0.8393 (t70) cc_final: 0.7978 (t0) REVERT: B 307 ARG cc_start: 0.7484 (ptt90) cc_final: 0.7079 (ptp-170) REVERT: B 310 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7439 (pp) REVERT: D 55 GLU cc_start: 0.7972 (pm20) cc_final: 0.7313 (mm-30) REVERT: D 121 HIS cc_start: 0.8018 (t-170) cc_final: 0.7718 (t-170) REVERT: D 154 ILE cc_start: 0.8093 (mp) cc_final: 0.7716 (tt) REVERT: D 183 LYS cc_start: 0.8211 (ttmt) cc_final: 0.7658 (tttt) REVERT: D 186 ASN cc_start: 0.8009 (t0) cc_final: 0.7248 (p0) outliers start: 41 outliers final: 29 residues processed: 211 average time/residue: 0.0826 time to fit residues: 24.9837 Evaluate side-chains 205 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 20 optimal weight: 0.0270 chunk 60 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 33 optimal weight: 0.0570 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.158194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.128949 restraints weight = 12274.270| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.21 r_work: 0.3619 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8441 Z= 0.119 Angle : 0.537 10.310 11398 Z= 0.281 Chirality : 0.040 0.177 1260 Planarity : 0.004 0.045 1464 Dihedral : 6.404 77.117 1143 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.48 % Allowed : 19.43 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.27), residues: 1007 helix: 1.19 (0.21), residues: 628 sheet: -2.54 (0.77), residues: 49 loop : -0.86 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 822 TYR 0.014 0.001 TYR B 109 PHE 0.025 0.002 PHE B 95 TRP 0.009 0.001 TRP A 719 HIS 0.006 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 8441) covalent geometry : angle 0.53668 (11398) hydrogen bonds : bond 0.03450 ( 437) hydrogen bonds : angle 4.24825 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 183 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7195 (tm-30) REVERT: A 784 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 806 PHE cc_start: 0.8761 (m-80) cc_final: 0.8368 (m-80) REVERT: A 940 LEU cc_start: 0.9115 (tp) cc_final: 0.8618 (pp) REVERT: A 959 THR cc_start: 0.8591 (p) cc_final: 0.8365 (t) REVERT: B 14 TYR cc_start: 0.8154 (t80) cc_final: 0.7899 (t80) REVERT: B 61 MET cc_start: 0.7983 (ptm) cc_final: 0.7416 (tmm) REVERT: B 67 ARG cc_start: 0.8687 (ttm170) cc_final: 0.8415 (mmt90) REVERT: B 116 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7584 (mtp-110) REVERT: B 146 MET cc_start: 0.7749 (tpp) cc_final: 0.7234 (mmt) REVERT: B 221 MET cc_start: 0.8796 (ttp) cc_final: 0.8534 (ttp) REVERT: B 223 ASP cc_start: 0.8349 (t70) cc_final: 0.7964 (t0) REVERT: B 307 ARG cc_start: 0.7411 (ptt90) cc_final: 0.7047 (ptp-170) REVERT: B 310 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7462 (pp) REVERT: D 55 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7316 (mm-30) REVERT: D 121 HIS cc_start: 0.7968 (t-170) cc_final: 0.7655 (t-170) REVERT: D 154 ILE cc_start: 0.8144 (mp) cc_final: 0.7782 (tt) REVERT: D 183 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7636 (tttt) REVERT: D 186 ASN cc_start: 0.7998 (t0) cc_final: 0.7267 (p0) REVERT: D 221 GLU cc_start: 0.8136 (pp20) cc_final: 0.7870 (pt0) outliers start: 41 outliers final: 32 residues processed: 205 average time/residue: 0.0753 time to fit residues: 22.6131 Evaluate side-chains 211 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 176 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125139 restraints weight = 12521.052| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 3.22 r_work: 0.3590 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8441 Z= 0.167 Angle : 0.564 8.399 11398 Z= 0.294 Chirality : 0.041 0.190 1260 Planarity : 0.004 0.046 1464 Dihedral : 6.460 78.171 1143 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.04 % Allowed : 19.87 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.27), residues: 1007 helix: 1.14 (0.21), residues: 628 sheet: -2.64 (0.75), residues: 49 loop : -0.81 (0.35), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 822 TYR 0.016 0.001 TYR D 13 PHE 0.023 0.002 PHE A 754 TRP 0.011 0.001 TRP A 719 HIS 0.005 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8441) covalent geometry : angle 0.56355 (11398) hydrogen bonds : bond 0.03639 ( 437) hydrogen bonds : angle 4.31069 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 176 time to evaluate : 0.256 Fit side-chains revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7856 (tm-30) REVERT: A 784 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8136 (tm-30) REVERT: A 940 LEU cc_start: 0.9161 (tp) cc_final: 0.8664 (pp) REVERT: A 959 THR cc_start: 0.8648 (p) cc_final: 0.8421 (t) REVERT: B 14 TYR cc_start: 0.8176 (t80) cc_final: 0.7919 (t80) REVERT: B 61 MET cc_start: 0.8013 (ptm) cc_final: 0.7477 (tmm) REVERT: B 67 ARG cc_start: 0.8690 (ttm170) cc_final: 0.8422 (mmt90) REVERT: B 116 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7604 (mtp-110) REVERT: B 146 MET cc_start: 0.7797 (tpp) cc_final: 0.7281 (mmt) REVERT: B 223 ASP cc_start: 0.8444 (t70) cc_final: 0.8039 (t0) REVERT: B 307 ARG cc_start: 0.7442 (ptt90) cc_final: 0.7066 (ptp-170) REVERT: B 310 ILE cc_start: 0.7933 (OUTLIER) cc_final: 0.7442 (pp) REVERT: B 399 CYS cc_start: 0.6877 (t) cc_final: 0.6598 (t) REVERT: D 55 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7462 (mm-30) REVERT: D 121 HIS cc_start: 0.8059 (t-170) cc_final: 0.7726 (t-170) REVERT: D 154 ILE cc_start: 0.8141 (mp) cc_final: 0.7787 (tt) REVERT: D 183 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7640 (tttt) REVERT: D 186 ASN cc_start: 0.8015 (t0) cc_final: 0.7275 (p0) outliers start: 37 outliers final: 32 residues processed: 197 average time/residue: 0.0736 time to fit residues: 21.3197 Evaluate side-chains 210 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 76 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.162690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.134378 restraints weight = 12305.208| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 3.08 r_work: 0.3750 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8441 Z= 0.131 Angle : 0.557 10.557 11398 Z= 0.291 Chirality : 0.041 0.238 1260 Planarity : 0.004 0.045 1464 Dihedral : 6.445 79.446 1143 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.82 % Allowed : 20.31 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1007 helix: 1.18 (0.21), residues: 629 sheet: -2.59 (0.74), residues: 49 loop : -0.76 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 822 TYR 0.017 0.001 TYR D 13 PHE 0.027 0.002 PHE A 827 TRP 0.010 0.001 TRP A 719 HIS 0.005 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8441) covalent geometry : angle 0.55662 (11398) hydrogen bonds : bond 0.03481 ( 437) hydrogen bonds : angle 4.26753 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8209 (tm-30) cc_final: 0.7114 (tm-30) REVERT: A 720 TYR cc_start: 0.8947 (t80) cc_final: 0.8576 (t80) REVERT: A 784 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 806 PHE cc_start: 0.8717 (m-80) cc_final: 0.8468 (m-80) REVERT: A 940 LEU cc_start: 0.9161 (tp) cc_final: 0.8702 (pp) REVERT: A 959 THR cc_start: 0.8568 (p) cc_final: 0.8322 (t) REVERT: B 14 TYR cc_start: 0.8147 (t80) cc_final: 0.7882 (t80) REVERT: B 61 MET cc_start: 0.7941 (ptm) cc_final: 0.7502 (tmm) REVERT: B 67 ARG cc_start: 0.8644 (ttm170) cc_final: 0.8376 (mmt90) REVERT: B 116 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7583 (mtp-110) REVERT: B 124 GLN cc_start: 0.8943 (mp10) cc_final: 0.8666 (mp10) REVERT: B 146 MET cc_start: 0.7766 (tpp) cc_final: 0.7289 (mmt) REVERT: B 223 ASP cc_start: 0.8422 (t70) cc_final: 0.8001 (t0) REVERT: B 307 ARG cc_start: 0.7427 (ptt90) cc_final: 0.7134 (ptp-170) REVERT: B 310 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7470 (pp) REVERT: B 399 CYS cc_start: 0.6841 (t) cc_final: 0.6590 (t) REVERT: D 55 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7432 (mm-30) REVERT: D 121 HIS cc_start: 0.8012 (t-170) cc_final: 0.7735 (t-170) REVERT: D 154 ILE cc_start: 0.8163 (mp) cc_final: 0.7791 (tt) REVERT: D 183 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7601 (tttt) REVERT: D 186 ASN cc_start: 0.7984 (t0) cc_final: 0.7271 (p0) REVERT: D 221 GLU cc_start: 0.8251 (pp20) cc_final: 0.7995 (pt0) outliers start: 35 outliers final: 29 residues processed: 203 average time/residue: 0.0768 time to fit residues: 22.7975 Evaluate side-chains 209 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 177 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 4 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.163722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.135476 restraints weight = 12358.134| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.08 r_work: 0.3728 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8441 Z= 0.126 Angle : 0.554 9.693 11398 Z= 0.291 Chirality : 0.041 0.227 1260 Planarity : 0.004 0.049 1464 Dihedral : 6.419 80.460 1143 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.82 % Allowed : 20.52 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.27), residues: 1007 helix: 1.23 (0.21), residues: 628 sheet: -2.30 (0.73), residues: 47 loop : -0.82 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 822 TYR 0.025 0.001 TYR A 809 PHE 0.033 0.002 PHE A 827 TRP 0.009 0.001 TRP A 719 HIS 0.004 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 8441) covalent geometry : angle 0.55446 (11398) hydrogen bonds : bond 0.03450 ( 437) hydrogen bonds : angle 4.25541 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 720 TYR cc_start: 0.8971 (t80) cc_final: 0.8597 (t80) REVERT: A 784 GLN cc_start: 0.8478 (tm-30) cc_final: 0.8167 (tm-30) REVERT: A 940 LEU cc_start: 0.9158 (tp) cc_final: 0.8724 (pp) REVERT: A 959 THR cc_start: 0.8524 (p) cc_final: 0.8278 (t) REVERT: B 14 TYR cc_start: 0.8114 (t80) cc_final: 0.7841 (t80) REVERT: B 61 MET cc_start: 0.7903 (ptm) cc_final: 0.7509 (tmm) REVERT: B 67 ARG cc_start: 0.8625 (ttm170) cc_final: 0.8357 (mmt90) REVERT: B 116 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7574 (mtp-110) REVERT: B 124 GLN cc_start: 0.8948 (mp10) cc_final: 0.8677 (mp10) REVERT: B 146 MET cc_start: 0.7669 (tpp) cc_final: 0.7249 (mmt) REVERT: B 223 ASP cc_start: 0.8431 (t70) cc_final: 0.8021 (t0) REVERT: B 307 ARG cc_start: 0.7417 (ptt90) cc_final: 0.7176 (ptp-170) REVERT: B 310 ILE cc_start: 0.7884 (OUTLIER) cc_final: 0.7460 (pp) REVERT: B 399 CYS cc_start: 0.6935 (t) cc_final: 0.6627 (t) REVERT: D 55 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7449 (mm-30) REVERT: D 121 HIS cc_start: 0.7990 (t-170) cc_final: 0.7735 (t-170) REVERT: D 154 ILE cc_start: 0.8203 (mp) cc_final: 0.7822 (tt) REVERT: D 183 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7579 (tttt) REVERT: D 186 ASN cc_start: 0.7916 (t0) cc_final: 0.7241 (p0) REVERT: D 221 GLU cc_start: 0.8225 (pp20) cc_final: 0.7957 (pt0) outliers start: 35 outliers final: 29 residues processed: 200 average time/residue: 0.0768 time to fit residues: 22.4865 Evaluate side-chains 212 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 180 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 15 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 366 ASN C 47 ASN ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.162857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.133550 restraints weight = 12332.875| |-----------------------------------------------------------------------------| r_work (start): 0.3896 rms_B_bonded: 3.16 r_work: 0.3743 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 8441 Z= 0.146 Angle : 0.575 8.640 11398 Z= 0.301 Chirality : 0.041 0.202 1260 Planarity : 0.004 0.048 1464 Dihedral : 6.452 80.818 1143 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.60 % Allowed : 20.63 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.27), residues: 1007 helix: 1.17 (0.21), residues: 629 sheet: -2.35 (0.81), residues: 37 loop : -0.87 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 822 TYR 0.023 0.001 TYR A 809 PHE 0.033 0.002 PHE A 827 TRP 0.010 0.001 TRP A 719 HIS 0.004 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8441) covalent geometry : angle 0.57485 (11398) hydrogen bonds : bond 0.03505 ( 437) hydrogen bonds : angle 4.28120 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 711 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7215 (tm-30) REVERT: A 720 TYR cc_start: 0.8975 (t80) cc_final: 0.8611 (t80) REVERT: A 784 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8149 (tm-30) REVERT: A 914 GLU cc_start: 0.8316 (tt0) cc_final: 0.7887 (tm-30) REVERT: A 915 GLU cc_start: 0.7395 (tt0) cc_final: 0.6902 (tt0) REVERT: A 940 LEU cc_start: 0.9161 (tp) cc_final: 0.8722 (pp) REVERT: A 959 THR cc_start: 0.8565 (p) cc_final: 0.8334 (t) REVERT: B 14 TYR cc_start: 0.8159 (t80) cc_final: 0.7895 (t80) REVERT: B 61 MET cc_start: 0.7917 (ptm) cc_final: 0.7505 (tmm) REVERT: B 67 ARG cc_start: 0.8633 (ttm170) cc_final: 0.8431 (mmt90) REVERT: B 116 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7583 (mtp-110) REVERT: B 124 GLN cc_start: 0.8951 (mp10) cc_final: 0.8662 (mp10) REVERT: B 146 MET cc_start: 0.7688 (tpp) cc_final: 0.7231 (mmt) REVERT: B 223 ASP cc_start: 0.8464 (t70) cc_final: 0.8059 (t0) REVERT: B 307 ARG cc_start: 0.7405 (ptt90) cc_final: 0.7134 (ptp-170) REVERT: B 310 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7482 (pp) REVERT: B 399 CYS cc_start: 0.6985 (t) cc_final: 0.6673 (t) REVERT: D 55 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: D 121 HIS cc_start: 0.8014 (t-170) cc_final: 0.7740 (t-170) REVERT: D 154 ILE cc_start: 0.8179 (mp) cc_final: 0.7792 (tt) REVERT: D 183 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7570 (tttt) REVERT: D 186 ASN cc_start: 0.7971 (t0) cc_final: 0.7366 (p0) REVERT: D 221 GLU cc_start: 0.8287 (pp20) cc_final: 0.7976 (pt0) outliers start: 33 outliers final: 29 residues processed: 206 average time/residue: 0.0755 time to fit residues: 22.8528 Evaluate side-chains 205 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 741 ASP Chi-restraints excluded: chain A residue 743 LEU Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain B residue 35 HIS Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 116 ARG Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 156 THR Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 362 CYS Chi-restraints excluded: chain B residue 366 ASN Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain D residue 55 GLU Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 99 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 MET Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 172 THR Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 977 HIS ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 HIS B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.163975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.134353 restraints weight = 12480.518| |-----------------------------------------------------------------------------| r_work (start): 0.3911 rms_B_bonded: 3.19 r_work: 0.3758 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8441 Z= 0.132 Angle : 0.572 8.552 11398 Z= 0.300 Chirality : 0.041 0.218 1260 Planarity : 0.004 0.049 1464 Dihedral : 6.444 81.745 1143 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.04 % Allowed : 21.18 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.27), residues: 1007 helix: 1.18 (0.21), residues: 628 sheet: -2.25 (0.73), residues: 47 loop : -0.78 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 822 TYR 0.020 0.001 TYR A 809 PHE 0.049 0.002 PHE A 827 TRP 0.009 0.001 TRP A 719 HIS 0.004 0.001 HIS D 121 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8441) covalent geometry : angle 0.57185 (11398) hydrogen bonds : bond 0.03463 ( 437) hydrogen bonds : angle 4.27084 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1836.35 seconds wall clock time: 32 minutes 21.71 seconds (1941.71 seconds total)