Starting phenix.real_space_refine on Thu Jul 2 03:32:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urg_26712/07_2026/7urg_26712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urg_26712/07_2026/7urg_26712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7urg_26712/07_2026/7urg_26712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urg_26712/07_2026/7urg_26712_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7urg_26712/07_2026/7urg_26712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urg_26712/07_2026/7urg_26712.map" } resolution = 3.46 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= -0.019 sd= 0.302 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 6 5.49 5 S 28 5.16 5 C 3934 2.51 5 N 1082 2.21 5 O 1210 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6260 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 401, 3101 Classifications: {'peptide': 401} Link IDs: {'PTRANS': 17, 'TRANS': 383} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B Time building chain proxies: 1.78, per 1000 atoms: 0.28 Number of scatterers: 6260 At special positions: 0 Unit cell: (138.03, 69.55, 66.34, 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 28 16.00 P 6 15.00 O 1210 8.00 N 1082 7.00 C 3934 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 196 " distance=2.05 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: 0.52 Conformation dependent library (CDL) restraints added in 356.5 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1448 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 12 sheets defined 46.1% alpha, 11.2% 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 44 through 58 removed outlier: 3.674A pdb=" N TYR A 58 " --> pdb=" O HIS A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 103 removed outlier: 3.704A pdb=" N PHE A 88 " --> pdb=" O GLY A 84 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 142 through 149 Processing helix chain 'A' and resid 150 through 163 Processing helix chain 'A' and resid 210 through 227 removed outlier: 4.233A pdb=" N GLY A 227 " --> pdb=" O CYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 229 No H-bonds generated for 'chain 'A' and resid 228 through 229' Processing helix chain 'A' and resid 230 through 235 removed outlier: 3.570A pdb=" N GLU A 233 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER A 234 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 243 Processing helix chain 'A' and resid 252 through 261 removed outlier: 3.688A pdb=" N LEU A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 277 Processing helix chain 'A' and resid 283 through 306 Processing helix chain 'A' and resid 320 through 324 removed outlier: 3.568A pdb=" N ARG A 323 " --> pdb=" O CYS A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 368 through 385 removed outlier: 3.573A pdb=" N TYR A 372 " --> pdb=" O GLY A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 414 Processing helix chain 'B' and resid 44 through 58 removed outlier: 3.675A pdb=" N TYR B 58 " --> pdb=" O HIS B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 103 removed outlier: 3.706A pdb=" N PHE B 88 " --> pdb=" O GLY B 84 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS B 90 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 142 through 149 Processing helix chain 'B' and resid 150 through 163 Processing helix chain 'B' and resid 210 through 227 removed outlier: 4.233A pdb=" N GLY B 227 " --> pdb=" O CYS B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 229 No H-bonds generated for 'chain 'B' and resid 228 through 229' Processing helix chain 'B' and resid 230 through 235 removed outlier: 3.570A pdb=" N GLU B 233 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 234 " --> pdb=" O VAL B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 243 Processing helix chain 'B' and resid 252 through 261 removed outlier: 3.688A pdb=" N LEU B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 283 through 306 Processing helix chain 'B' and resid 320 through 324 removed outlier: 3.568A pdb=" N ARG B 323 " --> pdb=" O CYS B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 368 Processing helix chain 'B' and resid 368 through 385 removed outlier: 3.573A pdb=" N TYR B 372 " --> pdb=" O GLY B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 414 Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 7.657A pdb=" N THR A 31 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N HIS A 65 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE A 33 " --> pdb=" O HIS A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 115 removed outlier: 6.270A pdb=" N CYS A 112 " --> pdb=" O CYS A 138 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN A 140 " --> pdb=" O CYS A 112 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU A 114 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG A 137 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N ASN A 169 " --> pdb=" O ARG A 137 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL A 139 " --> pdb=" O ASN A 169 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 202 removed outlier: 6.231A pdb=" N GLN A 199 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 251 " --> pdb=" O GLN A 199 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL A 201 " --> pdb=" O LEU A 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 312 through 314 removed outlier: 8.349A pdb=" N PHE A 312 " --> pdb=" O HIS A 390 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR A 392 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE A 314 " --> pdb=" O TYR A 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 348 Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 34 removed outlier: 7.657A pdb=" N THR B 31 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N HIS B 65 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N PHE B 33 " --> pdb=" O HIS B 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 115 removed outlier: 6.271A pdb=" N CYS B 112 " --> pdb=" O CYS B 138 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN B 140 " --> pdb=" O CYS B 112 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 114 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ARG B 137 " --> pdb=" O TRP B 167 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N ASN B 169 " --> pdb=" O ARG B 137 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N VAL B 139 " --> pdb=" O ASN B 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AB1, first strand: chain 'B' and resid 198 through 202 removed outlier: 6.231A pdb=" N GLN B 199 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU B 251 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL B 201 " --> pdb=" O LEU B 251 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 312 through 314 removed outlier: 8.349A pdb=" N PHE B 312 " --> pdb=" O HIS B 390 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR B 392 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE B 314 " --> pdb=" O TYR B 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 343 through 348 252 hydrogen bonds defined for protein. 720 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: 0.70 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2086 1.35 - 1.46: 1491 1.46 - 1.58: 2773 1.58 - 1.70: 10 1.70 - 1.82: 38 Bond restraints: 6398 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" O3A TTP A 801 " pdb=" PB TTP A 801 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" C4 TTP A 801 " pdb=" N3 TTP A 801 " ideal model delta sigma weight residual 1.385 1.333 0.052 2.00e-02 2.50e+03 6.73e+00 ... (remaining 6393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8574 2.04 - 4.08: 82 4.08 - 6.12: 30 6.12 - 8.16: 10 8.16 - 10.21: 6 Bond angle restraints: 8702 Sorted by residual: angle pdb=" O1A TTP A 801 " pdb=" PA TTP A 801 " pdb=" O2A TTP A 801 " ideal model delta sigma weight residual 121.23 111.02 10.21 3.00e+00 1.11e-01 1.16e+01 angle pdb=" O1A TTP B 801 " pdb=" PA TTP B 801 " pdb=" O2A TTP B 801 " ideal model delta sigma weight residual 121.23 111.05 10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " pdb=" O3G TTP B 801 " ideal model delta sigma weight residual 100.73 110.19 -9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" O3B TTP A 801 " pdb=" PG TTP A 801 " pdb=" O3G TTP A 801 " ideal model delta sigma weight residual 100.73 110.18 -9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" O1B TTP A 801 " pdb=" PB TTP A 801 " pdb=" O2B TTP A 801 " ideal model delta sigma weight residual 119.36 110.39 8.97 3.00e+00 1.11e-01 8.93e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3373 17.73 - 35.46: 333 35.46 - 53.19: 88 53.19 - 70.91: 26 70.91 - 88.64: 6 Dihedral angle restraints: 3826 sinusoidal: 1544 harmonic: 2282 Sorted by residual: dihedral pdb=" CB CYS A 30 " pdb=" SG CYS A 30 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual -86.00 -174.64 88.64 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS B 30 " pdb=" SG CYS B 30 " pdb=" SG CYS B 196 " pdb=" CB CYS B 196 " ideal model delta sinusoidal sigma weight residual -86.00 -174.59 88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N GLY B 79 " pdb=" CA GLY B 79 " ideal model delta harmonic sigma weight residual 180.00 -155.89 -24.11 0 5.00e+00 4.00e-02 2.32e+01 ... (remaining 3823 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 685 0.034 - 0.068: 182 0.068 - 0.103: 54 0.103 - 0.137: 31 0.137 - 0.171: 2 Chirality restraints: 954 Sorted by residual: chirality pdb=" C1' TTP B 801 " pdb=" C2' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" C1' TTP A 801 " pdb=" C2' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " both_signs ideal model delta sigma weight residual False 2.35 2.52 -0.17 2.00e-01 2.50e+01 7.19e-01 chirality pdb=" CA VAL A 201 " pdb=" N VAL A 201 " pdb=" C VAL A 201 " pdb=" CB VAL A 201 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 951 not shown) Planarity restraints: 1122 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 26 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO B 27 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO B 27 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 27 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 26 " 0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 27 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 97 " -0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C GLU A 97 " 0.017 2.00e-02 2.50e+03 pdb=" O GLU A 97 " -0.007 2.00e-02 2.50e+03 pdb=" N ILE A 98 " -0.006 2.00e-02 2.50e+03 ... (remaining 1119 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1090 2.77 - 3.30: 6082 3.30 - 3.83: 9912 3.83 - 4.37: 11229 4.37 - 4.90: 20087 Nonbonded interactions: 48400 Sorted by model distance: nonbonded pdb=" ND2 ASN A 96 " pdb=" O TRP A 134 " model vdw 2.232 3.120 nonbonded pdb=" ND2 ASN B 96 " pdb=" O TRP B 134 " model vdw 2.233 3.120 nonbonded pdb=" O ILE B 45 " pdb=" OG SER B 48 " model vdw 2.264 3.040 nonbonded pdb=" O ILE A 45 " pdb=" OG SER A 48 " model vdw 2.264 3.040 nonbonded pdb=" N GLU B 405 " pdb=" OE1 GLU B 405 " model vdw 2.288 3.120 ... (remaining 48395 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.460 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.940 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 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 : 0.004 0.139 6400 Z= 0.207 Angle : 0.660 10.206 8706 Z= 0.293 Chirality : 0.039 0.171 954 Planarity : 0.003 0.030 1122 Dihedral : 15.460 79.807 2372 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.31), residues: 798 helix: 2.52 (0.30), residues: 322 sheet: -0.69 (0.52), residues: 110 loop : -1.05 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.006 0.001 TYR A 264 PHE 0.006 0.001 PHE B 124 TRP 0.004 0.001 TRP A 369 HIS 0.003 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.21 ( 6398) covalent geometry : angle 0.65994 / 0.29 ( 8702) SS BOND : bond 0.01740 / 0.87 ( 2) SS BOND : angle 1.41401 / 0.62 ( 4) hydrogen bonds : bond 0.14782 / 9.08 ( 252) hydrogen bonds : angle 4.96603 / 3.61 ( 720) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7172 (tmm-80) REVERT: B 100 ARG cc_start: 0.7572 (ttp80) cc_final: 0.7166 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0865 time to fit residues: 8.3962 Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.0870 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.225031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.191264 restraints weight = 7290.342| |-----------------------------------------------------------------------------| r_work (start): 0.4147 rms_B_bonded: 2.13 r_work: 0.3903 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 6400 Z= 0.122 Angle : 0.524 8.902 8706 Z= 0.267 Chirality : 0.040 0.135 954 Planarity : 0.003 0.029 1122 Dihedral : 6.675 57.293 954 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.36 % Allowed : 13.75 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.31), residues: 798 helix: 2.44 (0.29), residues: 328 sheet: -0.81 (0.51), residues: 114 loop : -1.19 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 258 TYR 0.007 0.001 TYR A 264 PHE 0.008 0.001 PHE B 124 TRP 0.005 0.001 TRP A 167 HIS 0.006 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 ( 6398) covalent geometry : angle 0.52341 / 0.27 ( 8702) SS BOND : bond 0.00022 / 0.01 ( 2) SS BOND : angle 1.36151 / 0.58 ( 4) hydrogen bonds : bond 0.04128 / 2.82 ( 252) hydrogen bonds : angle 3.95369 / 2.92 ( 720) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.193 Fit side-chains REVERT: A 178 ASN cc_start: 0.5436 (m-40) cc_final: 0.5160 (p0) REVERT: A 187 GLU cc_start: 0.8488 (pm20) cc_final: 0.7716 (pm20) REVERT: B 178 ASN cc_start: 0.5428 (m-40) cc_final: 0.5142 (p0) REVERT: B 187 GLU cc_start: 0.8486 (pm20) cc_final: 0.7715 (pm20) outliers start: 9 outliers final: 5 residues processed: 77 average time/residue: 0.0822 time to fit residues: 8.3169 Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 176 ASN B 176 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.208484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.174577 restraints weight = 6653.369| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.86 r_work: 0.3727 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6400 Z= 0.107 Angle : 0.482 5.864 8706 Z= 0.251 Chirality : 0.040 0.120 954 Planarity : 0.003 0.028 1122 Dihedral : 6.470 57.732 954 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.11 % Allowed : 14.35 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.31), residues: 798 helix: 2.39 (0.29), residues: 328 sheet: -0.80 (0.50), residues: 114 loop : -1.13 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 342 TYR 0.007 0.001 TYR B 264 PHE 0.008 0.001 PHE A 356 TRP 0.004 0.001 TRP B 167 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 6398) covalent geometry : angle 0.48168 / 0.25 ( 8702) SS BOND : bond 0.00012 / 0.01 ( 2) SS BOND : angle 0.84480 / 0.38 ( 4) hydrogen bonds : bond 0.03754 / 2.57 ( 252) hydrogen bonds : angle 3.88635 / 2.90 ( 720) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 56 time to evaluate : 0.264 Fit side-chains REVERT: A 148 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: A 178 ASN cc_start: 0.5358 (m-40) cc_final: 0.5052 (p0) REVERT: A 187 GLU cc_start: 0.8523 (pm20) cc_final: 0.7792 (pm20) REVERT: B 148 GLU cc_start: 0.6658 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: B 178 ASN cc_start: 0.5361 (m-40) cc_final: 0.5041 (p0) REVERT: B 187 GLU cc_start: 0.8523 (pm20) cc_final: 0.7845 (pm20) outliers start: 14 outliers final: 6 residues processed: 69 average time/residue: 0.0777 time to fit residues: 7.1253 Evaluate side-chains 61 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.208293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.172442 restraints weight = 6633.194| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 2.02 r_work: 0.3797 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 6400 Z= 0.104 Angle : 0.471 7.041 8706 Z= 0.243 Chirality : 0.039 0.118 954 Planarity : 0.003 0.027 1122 Dihedral : 5.977 54.136 954 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.11 % Allowed : 13.44 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.31), residues: 798 helix: 2.36 (0.29), residues: 330 sheet: -0.90 (0.50), residues: 114 loop : -1.10 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 258 TYR 0.007 0.001 TYR A 264 PHE 0.009 0.001 PHE B 356 TRP 0.004 0.001 TRP B 167 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 ( 6398) covalent geometry : angle 0.47056 / 0.24 ( 8702) SS BOND : bond 0.00008 / 0.00 ( 2) SS BOND : angle 0.58780 / 0.26 ( 4) hydrogen bonds : bond 0.03568 / 2.45 ( 252) hydrogen bonds : angle 3.85683 / 2.87 ( 720) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.163 Fit side-chains REVERT: A 148 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: A 187 GLU cc_start: 0.8518 (pm20) cc_final: 0.8215 (pm20) REVERT: B 148 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.6007 (mp0) REVERT: B 178 ASN cc_start: 0.5455 (m-40) cc_final: 0.5128 (p0) REVERT: B 187 GLU cc_start: 0.8519 (pm20) cc_final: 0.8124 (pm20) outliers start: 14 outliers final: 12 residues processed: 72 average time/residue: 0.0679 time to fit residues: 6.6398 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.216613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181612 restraints weight = 7311.368| |-----------------------------------------------------------------------------| r_work (start): 0.4099 rms_B_bonded: 2.31 r_work: 0.3822 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6400 Z= 0.144 Angle : 0.499 5.917 8706 Z= 0.260 Chirality : 0.040 0.121 954 Planarity : 0.003 0.029 1122 Dihedral : 6.352 48.067 954 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.42 % Allowed : 15.41 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.31), residues: 798 helix: 2.37 (0.29), residues: 320 sheet: -1.21 (0.47), residues: 130 loop : -1.17 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 342 TYR 0.009 0.001 TYR B 421 PHE 0.009 0.001 PHE B 124 TRP 0.005 0.001 TRP A 167 HIS 0.007 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 6398) covalent geometry : angle 0.49898 / 0.26 ( 8702) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 0.54254 / 0.23 ( 4) hydrogen bonds : bond 0.04305 / 2.94 ( 252) hydrogen bonds : angle 4.01019 / 2.98 ( 720) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 50 time to evaluate : 0.210 Fit side-chains REVERT: A 148 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5903 (mp0) REVERT: A 178 ASN cc_start: 0.5568 (p0) cc_final: 0.4560 (m110) REVERT: A 187 GLU cc_start: 0.8448 (pm20) cc_final: 0.8069 (pm20) REVERT: B 148 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5903 (mp0) REVERT: B 187 GLU cc_start: 0.8434 (pm20) cc_final: 0.8055 (pm20) outliers start: 16 outliers final: 12 residues processed: 66 average time/residue: 0.0802 time to fit residues: 7.0937 Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 51 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.218318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.183199 restraints weight = 7161.913| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 2.33 r_work: 0.3845 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6400 Z= 0.118 Angle : 0.467 5.921 8706 Z= 0.243 Chirality : 0.040 0.119 954 Planarity : 0.003 0.028 1122 Dihedral : 6.026 47.834 954 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.02 % Allowed : 15.41 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.30), residues: 798 helix: 2.41 (0.29), residues: 320 sheet: -0.94 (0.50), residues: 110 loop : -1.18 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.006 0.001 TYR B 372 PHE 0.011 0.001 PHE B 356 TRP 0.004 0.001 TRP B 369 HIS 0.006 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6398) covalent geometry : angle 0.46682 / 0.24 ( 8702) SS BOND : bond 0.00016 / 0.01 ( 2) SS BOND : angle 0.54552 / 0.23 ( 4) hydrogen bonds : bond 0.03725 / 2.55 ( 252) hydrogen bonds : angle 3.94693 / 2.95 ( 720) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.184 Fit side-chains REVERT: A 148 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.5893 (mp0) REVERT: A 187 GLU cc_start: 0.8483 (pm20) cc_final: 0.8227 (pm20) REVERT: A 260 GLN cc_start: 0.7703 (mm-40) cc_final: 0.7486 (mm110) REVERT: B 148 GLU cc_start: 0.6579 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: B 187 GLU cc_start: 0.8448 (pm20) cc_final: 0.8236 (pm20) outliers start: 20 outliers final: 16 residues processed: 81 average time/residue: 0.0845 time to fit residues: 8.8272 Evaluate side-chains 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 0.0370 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 5.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.214258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179524 restraints weight = 6844.242| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 2.21 r_work: 0.3775 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 6400 Z= 0.111 Angle : 0.458 5.623 8706 Z= 0.239 Chirality : 0.039 0.116 954 Planarity : 0.003 0.028 1122 Dihedral : 5.954 48.485 954 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.02 % Allowed : 15.56 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.31), residues: 798 helix: 2.36 (0.29), residues: 324 sheet: -1.24 (0.46), residues: 126 loop : -1.15 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.005 0.001 TYR A 372 PHE 0.011 0.001 PHE A 356 TRP 0.004 0.001 TRP B 369 HIS 0.005 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 ( 6398) covalent geometry : angle 0.45767 / 0.24 ( 8702) SS BOND : bond 0.00007 / 0.00 ( 2) SS BOND : angle 0.48619 / 0.21 ( 4) hydrogen bonds : bond 0.03641 / 2.49 ( 252) hydrogen bonds : angle 3.91184 / 2.93 ( 720) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.239 Fit side-chains REVERT: A 148 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5998 (mp0) REVERT: A 260 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7563 (mm110) REVERT: B 148 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6035 (mp0) outliers start: 20 outliers final: 16 residues processed: 72 average time/residue: 0.0555 time to fit residues: 5.5637 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 51 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 70 optimal weight: 6.9990 chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.0060 chunk 44 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.208238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.171629 restraints weight = 6738.055| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 1.99 r_work: 0.3621 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6400 Z= 0.097 Angle : 0.454 5.440 8706 Z= 0.238 Chirality : 0.039 0.137 954 Planarity : 0.003 0.030 1122 Dihedral : 5.776 49.707 954 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.96 % Allowed : 16.47 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.31), residues: 798 helix: 2.36 (0.29), residues: 330 sheet: -1.25 (0.46), residues: 126 loop : -1.06 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.006 0.001 TYR A 189 PHE 0.012 0.001 PHE B 356 TRP 0.004 0.001 TRP B 369 HIS 0.004 0.001 HIS B 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 ( 6398) covalent geometry : angle 0.45447 / 0.24 ( 8702) SS BOND : bond 0.00023 / 0.01 ( 2) SS BOND : angle 0.46615 / 0.20 ( 4) hydrogen bonds : bond 0.03306 / 2.27 ( 252) hydrogen bonds : angle 3.82005 / 2.86 ( 720) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.198 Fit side-chains REVERT: A 148 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5813 (mp0) REVERT: A 187 GLU cc_start: 0.8324 (pm20) cc_final: 0.7496 (pm20) REVERT: A 260 GLN cc_start: 0.7751 (mm-40) cc_final: 0.7505 (mm110) REVERT: A 308 MET cc_start: 0.7896 (mmm) cc_final: 0.7367 (tpp) REVERT: A 424 GLN cc_start: 0.8077 (mp10) cc_final: 0.7715 (mp10) REVERT: B 148 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5808 (mp0) REVERT: B 187 GLU cc_start: 0.8339 (pm20) cc_final: 0.7454 (pm20) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.0681 time to fit residues: 6.1998 Evaluate side-chains 61 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 61 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 0.0980 overall best weight: 0.8364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.209757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178295 restraints weight = 6918.018| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.85 r_work: 0.3716 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6400 Z= 0.124 Angle : 0.474 5.179 8706 Z= 0.248 Chirality : 0.040 0.148 954 Planarity : 0.003 0.029 1122 Dihedral : 5.984 46.981 954 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.72 % Allowed : 16.01 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.31), residues: 798 helix: 2.44 (0.29), residues: 320 sheet: -1.38 (0.46), residues: 126 loop : -1.13 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.008 0.001 TYR B 264 PHE 0.011 0.001 PHE A 356 TRP 0.003 0.001 TRP A 146 HIS 0.006 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 6398) covalent geometry : angle 0.47422 / 0.25 ( 8702) SS BOND : bond 0.00031 / 0.02 ( 2) SS BOND : angle 0.42308 / 0.18 ( 4) hydrogen bonds : bond 0.03835 / 2.62 ( 252) hydrogen bonds : angle 3.93771 / 2.93 ( 720) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 49 time to evaluate : 0.229 Fit side-chains REVERT: A 148 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6088 (mp0) REVERT: A 260 GLN cc_start: 0.7808 (mm-40) cc_final: 0.7556 (mm110) REVERT: A 308 MET cc_start: 0.7929 (mmm) cc_final: 0.7367 (tpp) REVERT: A 424 GLN cc_start: 0.8041 (mp10) cc_final: 0.7766 (mp10) REVERT: B 148 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6075 (mp0) REVERT: B 308 MET cc_start: 0.7727 (mmm) cc_final: 0.7358 (tpp) outliers start: 18 outliers final: 15 residues processed: 67 average time/residue: 0.0702 time to fit residues: 6.7112 Evaluate side-chains 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 60 optimal weight: 0.0070 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 3 optimal weight: 0.7980 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.210879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175498 restraints weight = 6851.678| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.23 r_work: 0.3722 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 6400 Z= 0.159 Angle : 0.511 5.077 8706 Z= 0.268 Chirality : 0.041 0.155 954 Planarity : 0.003 0.029 1122 Dihedral : 6.375 43.584 954 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.02 % Allowed : 15.71 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.31), residues: 798 helix: 2.40 (0.29), residues: 314 sheet: -1.52 (0.47), residues: 126 loop : -1.22 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 179 TYR 0.008 0.001 TYR B 330 PHE 0.010 0.002 PHE A 356 TRP 0.004 0.001 TRP B 167 HIS 0.008 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 6398) covalent geometry : angle 0.51110 / 0.27 ( 8702) SS BOND : bond 0.00075 / 0.04 ( 2) SS BOND : angle 0.45789 / 0.20 ( 4) hydrogen bonds : bond 0.04426 / 3.01 ( 252) hydrogen bonds : angle 4.10363 / 3.05 ( 720) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 53 time to evaluate : 0.252 Fit side-chains REVERT: A 148 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5930 (mp0) REVERT: A 221 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6913 (mt-10) REVERT: A 260 GLN cc_start: 0.7705 (mm-40) cc_final: 0.7473 (mm110) REVERT: A 308 MET cc_start: 0.7967 (mmm) cc_final: 0.7457 (tpp) REVERT: A 424 GLN cc_start: 0.8007 (mp10) cc_final: 0.7724 (mp10) REVERT: B 148 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5922 (mp0) REVERT: B 221 GLU cc_start: 0.7205 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 308 MET cc_start: 0.7722 (mmm) cc_final: 0.7440 (tpp) outliers start: 20 outliers final: 17 residues processed: 73 average time/residue: 0.0812 time to fit residues: 8.3404 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 425 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.0770 chunk 74 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.203518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168464 restraints weight = 6637.802| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.05 r_work: 0.3606 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6400 Z= 0.098 Angle : 0.458 5.284 8706 Z= 0.240 Chirality : 0.039 0.130 954 Planarity : 0.003 0.029 1122 Dihedral : 5.805 47.571 954 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.27 % Allowed : 16.47 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.31), residues: 798 helix: 2.45 (0.29), residues: 320 sheet: -1.37 (0.48), residues: 122 loop : -1.12 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 179 TYR 0.008 0.001 TYR A 330 PHE 0.013 0.001 PHE A 356 TRP 0.005 0.001 TRP B 369 HIS 0.004 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 6398) covalent geometry : angle 0.45834 / 0.24 ( 8702) SS BOND : bond 0.00004 / 0.00 ( 2) SS BOND : angle 0.38954 / 0.17 ( 4) hydrogen bonds : bond 0.03296 / 2.25 ( 252) hydrogen bonds : angle 3.86456 / 2.89 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1363.91 seconds wall clock time: 24 minutes 10.99 seconds (1450.99 seconds total)