Starting phenix.real_space_refine on Tue Mar 11 16:54:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7urg_26712/03_2025/7urg_26712_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7urg_26712/03_2025/7urg_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_2025/7urg_26712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2025/7urg_26712.map" model { file = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2025/7urg_26712_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7urg_26712/03_2025/7urg_26712_neut.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.019 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.73, per 1000 atoms: 0.92 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: 1.81 Conformation dependent library (CDL) restraints added in 977.7 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: 0.73 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: 1.68 Time building geometry restraints manager: 2.10 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: 0.03 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: 0.890 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.210 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.280 ------------------------------------------------------------------------------- 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 6398 Z= 0.144 Angle : 0.499 5.927 8702 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (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 TRP 0.004 0.001 TRP A 369 HIS 0.003 0.001 HIS A 390 PHE 0.006 0.001 PHE B 124 TYR 0.006 0.001 TYR A 264 ARG 0.001 0.000 ARG A 342 *********************** 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 : 0.776 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: 0.2467 time to fit residues: 23.6173 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 : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 9.9990 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 390 HIS B 176 ASN B 390 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.213918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.179849 restraints weight = 7241.406| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 2.14 r_work: 0.3782 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 6398 Z= 0.554 Angle : 0.782 11.568 8702 Z= 0.396 Chirality : 0.049 0.153 954 Planarity : 0.005 0.029 1122 Dihedral : 10.626 142.077 906 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.87 % Allowed : 13.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.30), residues: 798 helix: 1.78 (0.28), residues: 312 sheet: -1.46 (0.46), residues: 130 loop : -1.81 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 167 HIS 0.014 0.003 HIS A 390 PHE 0.020 0.003 PHE A 394 TYR 0.016 0.002 TYR A 421 ARG 0.005 0.001 ARG A 193 *********************** 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 75 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 56 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: A 269 ARG cc_start: 0.7215 (mtt-85) cc_final: 0.7008 (mmt90) REVERT: B 148 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6012 (mp0) REVERT: B 269 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.7052 (mmt90) outliers start: 19 outliers final: 8 residues processed: 75 average time/residue: 0.3233 time to fit residues: 31.3890 Evaluate side-chains 55 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 246 VAL Chi-restraints excluded: chain B residue 331 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 10 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN A 200 HIS B 176 ASN B 200 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.219118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.181665 restraints weight = 7343.132| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.43 r_work: 0.3829 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6398 Z= 0.166 Angle : 0.548 8.051 8702 Z= 0.273 Chirality : 0.040 0.124 954 Planarity : 0.003 0.030 1122 Dihedral : 9.924 137.776 906 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.57 % Allowed : 14.80 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.30), residues: 798 helix: 2.13 (0.29), residues: 324 sheet: -1.09 (0.50), residues: 110 loop : -1.57 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.003 0.001 HIS A 226 PHE 0.009 0.001 PHE A 124 TYR 0.007 0.001 TYR A 105 ARG 0.004 0.000 ARG A 179 *********************** 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 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.926 Fit side-chains REVERT: A 148 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.5829 (mp0) REVERT: A 187 GLU cc_start: 0.8389 (pm20) cc_final: 0.7639 (pm20) REVERT: A 322 TYR cc_start: 0.7265 (m-80) cc_final: 0.6974 (m-80) REVERT: B 148 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5826 (mp0) REVERT: B 187 GLU cc_start: 0.8382 (pm20) cc_final: 0.7627 (pm20) REVERT: B 322 TYR cc_start: 0.7242 (m-80) cc_final: 0.6951 (m-80) outliers start: 17 outliers final: 11 residues processed: 65 average time/residue: 0.2418 time to fit residues: 21.2597 Evaluate side-chains 59 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 83 SER Chi-restraints excluded: chain A residue 148 GLU 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 B residue 64 VAL Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 148 GLU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.215548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.179646 restraints weight = 7273.483| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 2.36 r_work: 0.3831 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6398 Z= 0.183 Angle : 0.510 5.987 8702 Z= 0.258 Chirality : 0.039 0.120 954 Planarity : 0.003 0.029 1122 Dihedral : 10.044 147.164 906 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.93 % Allowed : 13.60 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.31), residues: 798 helix: 2.20 (0.29), residues: 324 sheet: -1.50 (0.45), residues: 130 loop : -1.44 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.002 0.001 HIS A 226 PHE 0.009 0.001 PHE A 124 TYR 0.006 0.001 TYR A 189 ARG 0.003 0.000 ARG A 179 *********************** 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 76 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 50 time to evaluate : 0.709 Fit side-chains REVERT: A 120 ASP cc_start: 0.5023 (OUTLIER) cc_final: 0.4812 (m-30) REVERT: A 148 GLU cc_start: 0.6622 (OUTLIER) cc_final: 0.5970 (mp0) REVERT: A 187 GLU cc_start: 0.8458 (pm20) cc_final: 0.8142 (pm20) REVERT: B 120 ASP cc_start: 0.5016 (OUTLIER) cc_final: 0.4805 (m-30) REVERT: B 148 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: B 187 GLU cc_start: 0.8458 (pm20) cc_final: 0.8144 (pm20) outliers start: 26 outliers final: 20 residues processed: 72 average time/residue: 0.2545 time to fit residues: 23.3466 Evaluate side-chains 77 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 120 ASP 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 222 LEU Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 120 ASP 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 222 LEU Chi-restraints excluded: chain B residue 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 344 VAL 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 50 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 78 optimal weight: 0.1980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4460 r_free = 0.4460 target = 0.215011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.179761 restraints weight = 7235.293| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 2.36 r_work: 0.3801 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6398 Z= 0.219 Angle : 0.520 6.184 8702 Z= 0.264 Chirality : 0.040 0.122 954 Planarity : 0.003 0.028 1122 Dihedral : 9.992 146.518 906 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.53 % Allowed : 13.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 798 helix: 2.21 (0.29), residues: 318 sheet: -1.70 (0.45), residues: 130 loop : -1.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 146 HIS 0.002 0.001 HIS A 54 PHE 0.009 0.001 PHE A 124 TYR 0.007 0.001 TYR A 264 ARG 0.002 0.000 ARG B 179 *********************** 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 81 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 51 time to evaluate : 0.691 Fit side-chains REVERT: A 148 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.6018 (mp0) REVERT: A 180 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8860 (tt) REVERT: A 187 GLU cc_start: 0.8436 (pm20) cc_final: 0.8140 (pm20) REVERT: B 148 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: B 180 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8858 (tt) REVERT: B 187 GLU cc_start: 0.8440 (pm20) cc_final: 0.8142 (pm20) outliers start: 30 outliers final: 18 residues processed: 77 average time/residue: 0.2233 time to fit residues: 22.6287 Evaluate side-chains 72 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 50 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 180 ILE 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 271 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 425 VAL 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 180 ILE 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 271 LEU Chi-restraints excluded: chain B residue 276 SER 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 35 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4480 r_free = 0.4480 target = 0.216914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.182726 restraints weight = 7105.439| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 2.25 r_work: 0.3834 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6398 Z= 0.173 Angle : 0.489 7.109 8702 Z= 0.246 Chirality : 0.039 0.119 954 Planarity : 0.003 0.028 1122 Dihedral : 9.844 146.164 906 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.32 % Allowed : 16.01 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.31), residues: 798 helix: 2.21 (0.30), residues: 324 sheet: -1.68 (0.45), residues: 130 loop : -1.39 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 369 HIS 0.002 0.001 HIS A 54 PHE 0.009 0.001 PHE A 124 TYR 0.005 0.001 TYR B 372 ARG 0.002 0.000 ARG B 179 *********************** 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 76 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 54 time to evaluate : 0.657 Fit side-chains REVERT: A 148 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5942 (mp0) REVERT: A 180 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8827 (tt) REVERT: A 187 GLU cc_start: 0.8416 (pm20) cc_final: 0.8170 (pm20) REVERT: A 308 MET cc_start: 0.7963 (mmm) cc_final: 0.7664 (mmm) REVERT: B 148 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5924 (mp0) REVERT: B 187 GLU cc_start: 0.8413 (pm20) cc_final: 0.8173 (pm20) outliers start: 22 outliers final: 15 residues processed: 72 average time/residue: 0.1926 time to fit residues: 18.7184 Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ILE 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 271 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL 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 251 LEU Chi-restraints excluded: chain B residue 271 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 41 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.212948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176788 restraints weight = 7192.223| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.37 r_work: 0.3786 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 6398 Z= 0.312 Angle : 0.560 6.344 8702 Z= 0.287 Chirality : 0.042 0.125 954 Planarity : 0.004 0.028 1122 Dihedral : 10.297 151.583 906 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 3.93 % Allowed : 16.16 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.31), residues: 798 helix: 2.23 (0.29), residues: 312 sheet: -1.96 (0.44), residues: 130 loop : -1.57 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 146 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.002 PHE B 124 TYR 0.009 0.001 TYR B 105 ARG 0.002 0.000 ARG B 70 *********************** 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: 26 poor density : 49 time to evaluate : 0.702 Fit side-chains REVERT: A 148 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: A 180 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8845 (tt) REVERT: A 187 GLU cc_start: 0.8476 (pm20) cc_final: 0.8242 (pm20) REVERT: A 342 ARG cc_start: 0.6476 (mmm160) cc_final: 0.6170 (mmm160) REVERT: B 148 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5732 (mp0) REVERT: B 180 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8854 (tt) REVERT: B 187 GLU cc_start: 0.8462 (pm20) cc_final: 0.8221 (pm20) REVERT: B 308 MET cc_start: 0.8100 (mmm) cc_final: 0.7695 (mmm) outliers start: 26 outliers final: 19 residues processed: 75 average time/residue: 0.1831 time to fit residues: 18.6015 Evaluate side-chains 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ILE 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 271 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 148 GLU Chi-restraints excluded: chain B residue 180 ILE 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 271 LEU Chi-restraints excluded: chain B residue 276 SER 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 44 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 72 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4476 r_free = 0.4476 target = 0.216503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181049 restraints weight = 7137.817| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 2.37 r_work: 0.3828 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6398 Z= 0.174 Angle : 0.499 7.430 8702 Z= 0.251 Chirality : 0.039 0.117 954 Planarity : 0.003 0.030 1122 Dihedral : 10.053 151.236 906 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.17 % Allowed : 17.52 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 798 helix: 2.24 (0.29), residues: 318 sheet: -1.90 (0.45), residues: 130 loop : -1.47 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 369 HIS 0.002 0.001 HIS A 54 PHE 0.010 0.001 PHE A 124 TYR 0.006 0.001 TYR A 105 ARG 0.002 0.000 ARG B 342 *********************** 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 73 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.786 Fit side-chains REVERT: A 148 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5865 (mp0) REVERT: A 180 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 148 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.5719 (mp0) REVERT: B 180 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 187 GLU cc_start: 0.8449 (pm20) cc_final: 0.8199 (pm20) REVERT: B 308 MET cc_start: 0.7963 (mmm) cc_final: 0.7687 (mmm) outliers start: 21 outliers final: 14 residues processed: 71 average time/residue: 0.2152 time to fit residues: 20.4896 Evaluate side-chains 64 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 148 GLU Chi-restraints excluded: chain A residue 180 ILE 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 271 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 185 CYS Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 251 LEU 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 15 optimal weight: 0.0270 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6640 ------------------------------------------------------------------------------- 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 = 0.4342 r_free = 0.4342 target = 0.208101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.175403 restraints weight = 6789.278| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.92 r_work: 0.3698 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6398 Z= 0.165 Angle : 0.503 7.349 8702 Z= 0.253 Chirality : 0.040 0.129 954 Planarity : 0.003 0.032 1122 Dihedral : 9.896 149.576 906 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.02 % Allowed : 17.82 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.31), residues: 798 helix: 2.15 (0.30), residues: 324 sheet: -1.63 (0.46), residues: 126 loop : -1.43 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 369 HIS 0.002 0.001 HIS B 226 PHE 0.009 0.001 PHE A 124 TYR 0.009 0.001 TYR A 330 ARG 0.006 0.000 ARG A 342 *********************** 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 71 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.714 Fit side-chains REVERT: A 304 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7389 (mmtp) REVERT: A 308 MET cc_start: 0.8148 (mmm) cc_final: 0.7593 (tpp) REVERT: B 148 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5879 (mp0) REVERT: B 304 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7407 (mmtp) outliers start: 20 outliers final: 16 residues processed: 69 average time/residue: 0.2097 time to fit residues: 19.2582 Evaluate side-chains 67 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 48 SER Chi-restraints excluded: chain B residue 64 VAL 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 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 386 THR 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 79 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 4 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.208657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174714 restraints weight = 6900.743| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.04 r_work: 0.3635 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6398 Z= 0.264 Angle : 0.557 7.123 8702 Z= 0.284 Chirality : 0.042 0.137 954 Planarity : 0.004 0.031 1122 Dihedral : 10.112 150.633 906 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.72 % Allowed : 17.67 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.31), residues: 798 helix: 2.25 (0.30), residues: 312 sheet: -1.87 (0.45), residues: 126 loop : -1.54 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 146 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE A 124 TYR 0.008 0.001 TYR A 330 ARG 0.006 0.001 ARG A 342 ********************** 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 70 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 52 time to evaluate : 0.733 Fit side-chains REVERT: A 148 GLU cc_start: 0.6605 (OUTLIER) cc_final: 0.5917 (mp0) REVERT: A 304 LYS cc_start: 0.7935 (mtmm) cc_final: 0.7538 (mmtp) REVERT: A 308 MET cc_start: 0.8214 (mmm) cc_final: 0.7689 (tpp) REVERT: B 148 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5958 (mp0) REVERT: B 304 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7583 (mmtp) REVERT: B 308 MET cc_start: 0.8208 (mmm) cc_final: 0.7452 (tpp) outliers start: 18 outliers final: 16 residues processed: 70 average time/residue: 0.2132 time to fit residues: 19.8267 Evaluate side-chains 68 residues out of total 662 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 148 GLU 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 271 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 48 SER Chi-restraints excluded: chain B residue 64 VAL 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 223 CYS Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 271 LEU 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 46 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 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 = 0.4358 r_free = 0.4358 target = 0.210802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.179655 restraints weight = 6934.528| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.80 r_work: 0.3701 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6398 Z= 0.181 Angle : 0.520 7.229 8702 Z= 0.264 Chirality : 0.040 0.131 954 Planarity : 0.004 0.031 1122 Dihedral : 10.018 152.112 906 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.72 % Allowed : 17.52 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.31), residues: 798 helix: 2.26 (0.30), residues: 318 sheet: -1.78 (0.46), residues: 126 loop : -1.51 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 369 HIS 0.002 0.001 HIS A 54 PHE 0.009 0.001 PHE A 124 TYR 0.009 0.001 TYR A 330 ARG 0.007 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2968.37 seconds wall clock time: 51 minutes 41.14 seconds (3101.14 seconds total)