Starting phenix.real_space_refine on Tue Mar 3 14:55:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urg_26712/03_2026/7urg_26712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urg_26712/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2026/7urg_26712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2026/7urg_26712.map" model { file = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2026/7urg_26712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2026/7urg_26712_neut.cif" } 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): 0.01s 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: 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: 1.87, per 1000 atoms: 0.30 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: 0.47 Conformation dependent library (CDL) restraints added in 263.3 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: 0.87 Time building geometry restraints manager: 0.54 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=" CG GLU B 187 " pdb=" CD GLU B 187 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 5.09e-01 bond pdb=" CG GLU A 187 " pdb=" CD GLU A 187 " ideal model delta sigma weight residual 1.516 1.498 0.018 2.50e-02 1.60e+03 4.96e-01 bond pdb=" C LEU B 80 " pdb=" N VAL B 81 " ideal model delta sigma weight residual 1.332 1.325 0.006 9.20e-03 1.18e+04 4.81e-01 bond pdb=" CA VAL B 246 " pdb=" CB VAL B 246 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.25e-01 bond pdb=" CA VAL A 246 " pdb=" CB VAL A 246 " ideal model delta sigma weight residual 1.540 1.549 -0.009 1.36e-02 5.41e+03 4.25e-01 ... (remaining 6393 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 8416 1.19 - 2.37: 214 2.37 - 3.56: 55 3.56 - 4.74: 11 4.74 - 5.93: 6 Bond angle restraints: 8702 Sorted by residual: angle pdb=" CA GLU B 97 " pdb=" CB GLU B 97 " pdb=" CG GLU B 97 " ideal model delta sigma weight residual 114.10 118.03 -3.93 2.00e+00 2.50e-01 3.87e+00 angle pdb=" CA GLU A 97 " pdb=" CB GLU A 97 " pdb=" CG GLU A 97 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.78e+00 angle pdb=" C LEU A 186 " pdb=" CA LEU A 186 " pdb=" CB LEU A 186 " ideal model delta sigma weight residual 110.35 106.67 3.68 1.91e+00 2.74e-01 3.72e+00 angle pdb=" C LEU B 186 " pdb=" CA LEU B 186 " pdb=" CB LEU B 186 " ideal model delta sigma weight residual 110.35 106.69 3.66 1.91e+00 2.74e-01 3.67e+00 angle pdb=" C2' TTP A 801 " pdb=" C3' TTP A 801 " pdb=" C4' TTP A 801 " ideal model delta sigma weight residual 111.00 105.26 5.74 3.00e+00 1.11e-01 3.66e+00 ... (remaining 8697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 3522 23.43 - 46.86: 202 46.86 - 70.29: 44 70.29 - 93.72: 6 93.72 - 117.15: 4 Dihedral angle restraints: 3778 sinusoidal: 1496 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=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual -58.32 -175.47 117.15 1 2.00e+01 2.50e-03 3.50e+01 ... (remaining 3775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 593 0.025 - 0.051: 220 0.051 - 0.076: 70 0.076 - 0.102: 44 0.102 - 0.127: 27 Chirality restraints: 954 Sorted by residual: 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 chirality pdb=" CA ILE B 166 " pdb=" N ILE B 166 " pdb=" C ILE B 166 " pdb=" CB ILE B 166 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.69e-01 chirality pdb=" CA ILE B 314 " pdb=" N ILE B 314 " pdb=" C ILE B 314 " pdb=" CB ILE B 314 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-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: 1.070 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: 0.020 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 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 : 0.002 0.018 6400 Z= 0.108 Angle : 0.500 5.927 8706 Z= 0.255 Chirality : 0.038 0.127 954 Planarity : 0.003 0.030 1122 Dihedral : 15.443 117.149 2324 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 covalent geometry : bond 0.00222 ( 6398) covalent geometry : angle 0.49899 ( 8702) SS BOND : bond 0.01740 ( 2) SS BOND : angle 1.41401 ( 4) hydrogen bonds : bond 0.14782 ( 252) hydrogen bonds : angle 4.96603 ( 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 : 0.234 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: 0.0990 time to fit residues: 9.5160 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 : 0.220 ------------------------------------------------------------------------------- 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: 5.9990 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: 4.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4558 r_free = 0.4558 target = 0.228576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.194234 restraints weight = 7389.321| |-----------------------------------------------------------------------------| r_work (start): 0.4145 rms_B_bonded: 2.38 r_work: 0.3878 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1097 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= 0.123 Angle : 0.546 8.844 8706 Z= 0.272 Chirality : 0.041 0.134 954 Planarity : 0.003 0.029 1122 Dihedral : 9.625 128.332 906 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.51 % Allowed : 13.60 % 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: 2.45 (0.29), residues: 328 sheet: -0.82 (0.51), residues: 114 loop : -1.18 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 244 TYR 0.007 0.001 TYR B 264 PHE 0.007 0.001 PHE A 356 TRP 0.005 0.001 TRP A 167 HIS 0.006 0.001 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 6398) covalent geometry : angle 0.54534 ( 8702) SS BOND : bond 0.00100 ( 2) SS BOND : angle 1.39363 ( 4) hydrogen bonds : bond 0.04180 ( 252) hydrogen bonds : angle 3.99758 ( 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 76 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.240 Fit side-chains REVERT: A 178 ASN cc_start: 0.5440 (m-40) cc_final: 0.5158 (p0) REVERT: A 187 GLU cc_start: 0.8498 (pm20) cc_final: 0.7696 (pm20) REVERT: B 178 ASN cc_start: 0.5427 (m-40) cc_final: 0.5138 (p0) REVERT: B 187 GLU cc_start: 0.8499 (pm20) cc_final: 0.7757 (pm20) outliers start: 10 outliers final: 6 residues processed: 76 average time/residue: 0.0942 time to fit residues: 9.3236 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 83 SER 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: 1.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4502 r_free = 0.4502 target = 0.221877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.187479 restraints weight = 7218.283| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 2.15 r_work: 0.3865 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 6400 Z= 0.155 Angle : 0.555 6.569 8706 Z= 0.281 Chirality : 0.042 0.126 954 Planarity : 0.003 0.027 1122 Dihedral : 9.714 131.194 906 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.72 % Allowed : 13.90 % Favored : 83.38 % 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: 2.39 (0.29), residues: 318 sheet: -0.93 (0.50), residues: 114 loop : -1.30 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 342 TYR 0.009 0.001 TYR B 421 PHE 0.008 0.001 PHE A 394 TRP 0.005 0.001 TRP A 167 HIS 0.008 0.002 HIS A 390 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6398) covalent geometry : angle 0.55458 ( 8702) SS BOND : bond 0.00033 ( 2) SS BOND : angle 0.84168 ( 4) hydrogen bonds : bond 0.04572 ( 252) hydrogen bonds : angle 4.07114 ( 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 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.223 Fit side-chains REVERT: A 148 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5862 (mp0) REVERT: A 187 GLU cc_start: 0.8449 (pm20) cc_final: 0.7599 (pm20) REVERT: B 148 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.5854 (mp0) REVERT: B 187 GLU cc_start: 0.8453 (pm20) cc_final: 0.7602 (pm20) outliers start: 18 outliers final: 10 residues processed: 70 average time/residue: 0.0890 time to fit residues: 8.1711 Evaluate side-chains 60 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.209 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.0040 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 3 optimal weight: 0.0870 overall best weight: 0.3708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.194436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152259 restraints weight = 6873.413| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.74 r_work: 0.3539 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6400 Z= 0.087 Angle : 0.477 5.703 8706 Z= 0.241 Chirality : 0.039 0.118 954 Planarity : 0.003 0.027 1122 Dihedral : 9.691 138.855 906 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 15.41 % Favored : 82.93 % 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: 0.56 (0.31), residues: 798 helix: 2.39 (0.29), residues: 330 sheet: -1.01 (0.50), residues: 114 loop : -1.14 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.006 0.001 TYR A 264 PHE 0.012 0.001 PHE A 51 TRP 0.004 0.001 TRP B 369 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 6398) covalent geometry : angle 0.47651 ( 8702) SS BOND : bond 0.00012 ( 2) SS BOND : angle 0.52645 ( 4) hydrogen bonds : bond 0.03203 ( 252) hydrogen bonds : angle 3.80033 ( 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 66 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 0.203 Fit side-chains REVERT: A 148 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5535 (mp0) REVERT: A 178 ASN cc_start: 0.5419 (m-40) cc_final: 0.4726 (p0) REVERT: A 187 GLU cc_start: 0.8551 (pm20) cc_final: 0.7844 (pm20) REVERT: A 356 PHE cc_start: 0.6302 (m-10) cc_final: 0.6089 (m-10) REVERT: B 148 GLU cc_start: 0.6205 (OUTLIER) cc_final: 0.5538 (mp0) REVERT: B 178 ASN cc_start: 0.5429 (m-40) cc_final: 0.4734 (p0) REVERT: B 187 GLU cc_start: 0.8552 (pm20) cc_final: 0.7844 (pm20) outliers start: 11 outliers final: 9 residues processed: 64 average time/residue: 0.0788 time to fit residues: 6.7048 Evaluate side-chains 62 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 185 CYS Chi-restraints excluded: chain A residue 222 LEU 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 185 CYS Chi-restraints excluded: chain B residue 222 LEU 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: 0.5980 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.209684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.180794 restraints weight = 6845.961| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.58 r_work: 0.3744 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2186 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 : 0.484 5.752 8706 Z= 0.244 Chirality : 0.039 0.118 954 Planarity : 0.003 0.027 1122 Dihedral : 9.541 138.022 906 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % 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: 0.47 (0.31), residues: 798 helix: 2.31 (0.29), residues: 330 sheet: -1.07 (0.49), residues: 114 loop : -1.19 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 342 TYR 0.006 0.001 TYR A 421 PHE 0.009 0.001 PHE B 124 TRP 0.004 0.001 TRP B 167 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 6398) covalent geometry : angle 0.48394 ( 8702) SS BOND : bond 0.00067 ( 2) SS BOND : angle 0.43022 ( 4) hydrogen bonds : bond 0.03694 ( 252) hydrogen bonds : angle 3.84619 ( 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 : 0.160 Fit side-chains REVERT: A 148 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6040 (mp0) REVERT: A 178 ASN cc_start: 0.5670 (m-40) cc_final: 0.5210 (p0) REVERT: B 148 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5997 (mp0) REVERT: B 178 ASN cc_start: 0.5575 (m-40) cc_final: 0.5167 (p0) outliers start: 16 outliers final: 14 residues processed: 64 average time/residue: 0.0815 time to fit residues: 6.9361 Evaluate side-chains 63 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU 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 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU 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: 0.9980 chunk 16 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.225870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.191453 restraints weight = 7273.226| |-----------------------------------------------------------------------------| r_work (start): 0.4136 rms_B_bonded: 2.27 r_work: 0.3852 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6400 Z= 0.178 Angle : 0.555 6.275 8706 Z= 0.284 Chirality : 0.041 0.148 954 Planarity : 0.004 0.027 1122 Dihedral : 9.840 142.289 906 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.93 % Allowed : 14.65 % 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: 0.23 (0.30), residues: 798 helix: 2.27 (0.29), residues: 318 sheet: -1.30 (0.46), residues: 126 loop : -1.30 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.010 0.001 TYR A 421 PHE 0.009 0.001 PHE A 124 TRP 0.005 0.001 TRP B 167 HIS 0.009 0.002 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 6398) covalent geometry : angle 0.55464 ( 8702) SS BOND : bond 0.00117 ( 2) SS BOND : angle 0.49026 ( 4) hydrogen bonds : bond 0.04801 ( 252) hydrogen bonds : angle 4.13252 ( 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 74 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.232 Fit side-chains REVERT: A 148 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.6048 (mp0) REVERT: A 187 GLU cc_start: 0.8476 (pm20) cc_final: 0.7682 (pm20) REVERT: A 308 MET cc_start: 0.8063 (mmm) cc_final: 0.7849 (mmm) REVERT: B 148 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: B 187 GLU cc_start: 0.8466 (pm20) cc_final: 0.7676 (pm20) REVERT: B 308 MET cc_start: 0.8051 (mmm) cc_final: 0.7835 (mmm) outliers start: 26 outliers final: 18 residues processed: 72 average time/residue: 0.0932 time to fit residues: 8.5893 Evaluate side-chains 69 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 49 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 130 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU 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 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU 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: 2.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.204964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.170808 restraints weight = 6659.730| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.30 r_work: 0.3509 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2479 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 : 0.495 7.279 8706 Z= 0.249 Chirality : 0.039 0.128 954 Planarity : 0.003 0.026 1122 Dihedral : 9.674 143.929 906 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.87 % Allowed : 15.26 % Favored : 81.87 % 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: 0.36 (0.31), residues: 798 helix: 2.30 (0.29), residues: 324 sheet: -1.35 (0.46), residues: 126 loop : -1.16 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.006 0.001 TYR B 372 PHE 0.011 0.001 PHE A 356 TRP 0.005 0.001 TRP A 369 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6398) covalent geometry : angle 0.49515 ( 8702) SS BOND : bond 0.00008 ( 2) SS BOND : angle 0.38975 ( 4) hydrogen bonds : bond 0.03577 ( 252) hydrogen bonds : angle 3.92228 ( 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 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.202 Fit side-chains REVERT: A 148 GLU cc_start: 0.5953 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: A 260 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7325 (mm110) REVERT: B 148 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5216 (mp0) outliers start: 19 outliers final: 17 residues processed: 73 average time/residue: 0.0676 time to fit residues: 6.7677 Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.199 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU 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 64 VAL Chi-restraints excluded: chain B residue 130 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU 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: 0.8980 chunk 2 optimal weight: 0.9980 chunk 63 optimal weight: 0.0970 chunk 53 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.202819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.164979 restraints weight = 6849.372| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 2.55 r_work: 0.3445 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6400 Z= 0.133 Angle : 0.509 6.869 8706 Z= 0.256 Chirality : 0.040 0.128 954 Planarity : 0.003 0.026 1122 Dihedral : 9.729 144.943 906 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.93 % Allowed : 14.50 % 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: 0.20 (0.31), residues: 798 helix: 2.30 (0.29), residues: 320 sheet: -1.68 (0.45), residues: 130 loop : -1.23 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.007 0.001 TYR B 330 PHE 0.009 0.001 PHE A 124 TRP 0.003 0.001 TRP B 167 HIS 0.007 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6398) covalent geometry : angle 0.50893 ( 8702) SS BOND : bond 0.00056 ( 2) SS BOND : angle 0.50296 ( 4) hydrogen bonds : bond 0.04075 ( 252) hydrogen bonds : angle 3.99297 ( 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 81 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.231 Fit side-chains REVERT: A 148 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5334 (mp0) REVERT: A 260 GLN cc_start: 0.7362 (mm-40) cc_final: 0.7129 (mm110) REVERT: A 308 MET cc_start: 0.7804 (mmm) cc_final: 0.7441 (mmm) REVERT: A 424 GLN cc_start: 0.8176 (mp10) cc_final: 0.7749 (mp10) REVERT: B 148 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5348 (mp0) REVERT: B 308 MET cc_start: 0.7752 (mmm) cc_final: 0.7400 (mmm) outliers start: 26 outliers final: 24 residues processed: 79 average time/residue: 0.0672 time to fit residues: 7.3655 Evaluate side-chains 79 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 184 VAL Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 222 LEU 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 331 THR 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 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 331 THR 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: 0.5980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.187838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.146137 restraints weight = 7056.966| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.79 r_work: 0.3462 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2684 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= 0.115 Angle : 0.493 6.881 8706 Z= 0.249 Chirality : 0.040 0.127 954 Planarity : 0.003 0.028 1122 Dihedral : 9.639 144.623 906 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.93 % Allowed : 14.65 % 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: 0.23 (0.31), residues: 798 helix: 2.30 (0.29), residues: 324 sheet: -1.70 (0.45), residues: 130 loop : -1.21 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 179 TYR 0.008 0.001 TYR B 330 PHE 0.012 0.001 PHE A 356 TRP 0.004 0.001 TRP A 369 HIS 0.005 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 6398) covalent geometry : angle 0.49301 ( 8702) SS BOND : bond 0.00021 ( 2) SS BOND : angle 0.41504 ( 4) hydrogen bonds : bond 0.03623 ( 252) hydrogen bonds : angle 3.91607 ( 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 80 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.229 Fit side-chains REVERT: A 148 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5255 (mp0) REVERT: A 260 GLN cc_start: 0.7425 (mm-40) cc_final: 0.7185 (mm110) REVERT: A 424 GLN cc_start: 0.8221 (mp10) cc_final: 0.7780 (mp10) REVERT: B 148 GLU cc_start: 0.5938 (OUTLIER) cc_final: 0.5256 (mp0) REVERT: B 260 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7164 (mm110) REVERT: B 308 MET cc_start: 0.7844 (mmm) cc_final: 0.7479 (mmm) outliers start: 26 outliers final: 21 residues processed: 78 average time/residue: 0.0633 time to fit residues: 7.0930 Evaluate side-chains 76 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 184 VAL 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 184 VAL Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU 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: 8.9990 chunk 21 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.202920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.164643 restraints weight = 6710.549| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.62 r_work: 0.3453 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2761 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= 0.128 Angle : 0.507 6.702 8706 Z= 0.255 Chirality : 0.040 0.126 954 Planarity : 0.003 0.028 1122 Dihedral : 9.665 144.004 906 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.47 % Allowed : 15.26 % 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: 0.17 (0.31), residues: 798 helix: 2.25 (0.29), residues: 322 sheet: -1.75 (0.45), residues: 130 loop : -1.21 (0.32), residues: 346 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 0.009 0.001 PHE B 124 TRP 0.003 0.001 TRP B 167 HIS 0.006 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6398) covalent geometry : angle 0.50653 ( 8702) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.48031 ( 4) hydrogen bonds : bond 0.03914 ( 252) hydrogen bonds : angle 3.96494 ( 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 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.234 Fit side-chains REVERT: A 148 GLU cc_start: 0.6064 (OUTLIER) cc_final: 0.5359 (mp0) REVERT: A 260 GLN cc_start: 0.7423 (mm-40) cc_final: 0.7174 (mm110) REVERT: A 424 GLN cc_start: 0.8163 (mp10) cc_final: 0.7741 (mp10) REVERT: B 148 GLU cc_start: 0.6066 (OUTLIER) cc_final: 0.5358 (mp0) REVERT: B 260 GLN cc_start: 0.7384 (mm-40) cc_final: 0.7131 (mm110) REVERT: B 304 LYS cc_start: 0.6965 (pttp) cc_final: 0.6760 (pttm) REVERT: B 424 GLN cc_start: 0.8136 (mp10) cc_final: 0.7737 (mp10) outliers start: 23 outliers final: 20 residues processed: 74 average time/residue: 0.0757 time to fit residues: 7.8325 Evaluate side-chains 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 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 184 VAL 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 184 VAL 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 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: 2.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 61 optimal weight: 0.0470 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 0.3980 chunk 62 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.157291 restraints weight = 6826.855| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.34 r_work: 0.3547 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 6400 Z= 0.088 Angle : 0.469 6.779 8706 Z= 0.235 Chirality : 0.039 0.122 954 Planarity : 0.003 0.028 1122 Dihedral : 9.344 139.709 906 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.17 % Allowed : 15.71 % Favored : 81.12 % 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: 2.37 (0.29), residues: 326 sheet: -1.43 (0.47), residues: 126 loop : -1.06 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 179 TYR 0.008 0.001 TYR B 330 PHE 0.009 0.001 PHE B 124 TRP 0.006 0.001 TRP B 369 HIS 0.003 0.001 HIS B 390 Details of bonding type rmsd covalent geometry : bond 0.00192 ( 6398) covalent geometry : angle 0.46921 ( 8702) SS BOND : bond 0.00016 ( 2) SS BOND : angle 0.37890 ( 4) hydrogen bonds : bond 0.03045 ( 252) hydrogen bonds : angle 3.81055 ( 720) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1371.34 seconds wall clock time: 24 minutes 11.20 seconds (1451.20 seconds total)