Starting phenix.real_space_refine on Fri Jul 3 15:44:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.cif" model { file = "/net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo6_13006/07_2026/7oo6_13006.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 7 5.49 5 S 42 5.16 5 C 9408 2.51 5 N 2443 2.21 5 O 2646 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14546 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 1989 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 5, 'TRANS': 255} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'LMT': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G Time building chain proxies: 2.02, per 1000 atoms: 0.14 Number of scatterers: 14546 At special positions: 0 Unit cell: (97.842, 97.842, 142.509, 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 42 16.00 P 7 15.00 O 2646 8.00 N 2443 7.00 C 9408 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 623.6 milliseconds 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 56.3% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 22 through 59 Processing helix chain 'A' and resid 62 through 90 Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 111 through 128 Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 197 through 212 Processing helix chain 'A' and resid 245 through 265 Processing helix chain 'B' and resid 22 through 59 Processing helix chain 'B' and resid 62 through 90 Processing helix chain 'B' and resid 93 through 111 Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 197 through 212 Processing helix chain 'B' and resid 245 through 265 Processing helix chain 'C' and resid 22 through 59 Processing helix chain 'C' and resid 62 through 90 Processing helix chain 'C' and resid 93 through 111 Processing helix chain 'C' and resid 111 through 128 Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 197 through 212 Processing helix chain 'C' and resid 245 through 265 Processing helix chain 'D' and resid 22 through 59 Processing helix chain 'D' and resid 62 through 90 Processing helix chain 'D' and resid 93 through 111 Processing helix chain 'D' and resid 111 through 128 Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 197 through 212 Processing helix chain 'D' and resid 245 through 265 Processing helix chain 'E' and resid 22 through 59 Processing helix chain 'E' and resid 62 through 90 Processing helix chain 'E' and resid 93 through 111 Processing helix chain 'E' and resid 111 through 128 Processing helix chain 'E' and resid 167 through 172 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 245 through 265 Processing helix chain 'F' and resid 22 through 59 Processing helix chain 'F' and resid 62 through 90 Processing helix chain 'F' and resid 93 through 111 Processing helix chain 'F' and resid 111 through 128 Processing helix chain 'F' and resid 167 through 172 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 245 through 265 Processing helix chain 'G' and resid 22 through 59 Processing helix chain 'G' and resid 62 through 90 Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 111 through 128 Processing helix chain 'G' and resid 167 through 172 Processing helix chain 'G' and resid 197 through 212 Processing helix chain 'G' and resid 245 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138 removed outlier: 3.820A pdb=" N VAL A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR A 154 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL A 148 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL G 141 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N THR G 154 " --> pdb=" O LEU G 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL G 148 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL F 141 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR F 154 " --> pdb=" O LEU F 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL F 148 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER F 152 " --> pdb=" O VAL F 148 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL E 141 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR E 154 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL E 148 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL D 141 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR D 154 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL D 148 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER D 152 " --> pdb=" O VAL D 148 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL C 141 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR C 154 " --> pdb=" O LEU C 146 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N VAL C 148 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR B 154 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL B 148 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N SER B 152 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 162 " --> pdb=" O ASN A 177 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192 removed outlier: 6.841A pdb=" N ASN A 234 " --> pdb=" O ASN A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 7.104A pdb=" N MET A 273 " --> pdb=" O ASN G 276 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N LYS G 278 " --> pdb=" O MET A 273 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL A 275 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192 removed outlier: 6.842A pdb=" N ASN B 234 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192 removed outlier: 6.841A pdb=" N ASN C 234 " --> pdb=" O ASN C 226 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192 removed outlier: 6.840A pdb=" N ASN D 234 " --> pdb=" O ASN D 226 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192 removed outlier: 6.841A pdb=" N ASN E 234 " --> pdb=" O ASN E 226 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192 removed outlier: 6.841A pdb=" N ASN F 234 " --> pdb=" O ASN F 226 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192 removed outlier: 6.841A pdb=" N ASN G 234 " --> pdb=" O ASN G 226 " (cutoff:3.500A) 1079 hydrogen bonds defined for protein. 3156 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2319 1.32 - 1.44: 3561 1.44 - 1.56: 8743 1.56 - 1.68: 14 1.68 - 1.80: 84 Bond restraints: 14721 Sorted by residual: bond pdb=" C4 PCW G 801 " pdb=" O4P PCW G 801 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" C4 PCW A 801 " pdb=" O4P PCW A 801 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C4 PCW C 801 " pdb=" O4P PCW C 801 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.53e+00 bond pdb=" C4 PCW B 801 " pdb=" O4P PCW B 801 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.50e+00 bond pdb=" C4 PCW D 801 " pdb=" O4P PCW D 801 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.49e+00 ... (remaining 14716 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 19357 1.43 - 2.86: 397 2.86 - 4.29: 77 4.29 - 5.72: 28 5.72 - 7.15: 14 Bond angle restraints: 19873 Sorted by residual: angle pdb=" O3P PCW E 801 " pdb=" P PCW E 801 " pdb=" O4P PCW E 801 " ideal model delta sigma weight residual 96.85 104.00 -7.15 3.00e+00 1.11e-01 5.67e+00 angle pdb=" O3P PCW D 801 " pdb=" P PCW D 801 " pdb=" O4P PCW D 801 " ideal model delta sigma weight residual 96.85 103.99 -7.14 3.00e+00 1.11e-01 5.67e+00 angle pdb=" O3P PCW F 801 " pdb=" P PCW F 801 " pdb=" O4P PCW F 801 " ideal model delta sigma weight residual 96.85 103.98 -7.13 3.00e+00 1.11e-01 5.64e+00 angle pdb=" O3P PCW A 801 " pdb=" P PCW A 801 " pdb=" O4P PCW A 801 " ideal model delta sigma weight residual 96.85 103.97 -7.12 3.00e+00 1.11e-01 5.63e+00 angle pdb=" O3P PCW B 801 " pdb=" P PCW B 801 " pdb=" O4P PCW B 801 " ideal model delta sigma weight residual 96.85 103.96 -7.11 3.00e+00 1.11e-01 5.62e+00 ... (remaining 19868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.12: 8526 21.12 - 42.24: 238 42.24 - 63.37: 28 63.37 - 84.49: 0 84.49 - 105.61: 14 Dihedral angle restraints: 8806 sinusoidal: 3570 harmonic: 5236 Sorted by residual: dihedral pdb=" N PCW B 801 " pdb=" C4 PCW B 801 " pdb=" C5 PCW B 801 " pdb=" O4P PCW B 801 " ideal model delta sinusoidal sigma weight residual -66.66 -172.27 105.61 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" N PCW C 801 " pdb=" C4 PCW C 801 " pdb=" C5 PCW C 801 " pdb=" O4P PCW C 801 " ideal model delta sinusoidal sigma weight residual -66.66 -172.25 105.59 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" N PCW F 801 " pdb=" C4 PCW F 801 " pdb=" C5 PCW F 801 " pdb=" O4P PCW F 801 " ideal model delta sinusoidal sigma weight residual -66.66 -172.24 105.58 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 8803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1975 0.051 - 0.103: 344 0.103 - 0.154: 84 0.154 - 0.205: 12 0.205 - 0.256: 7 Chirality restraints: 2422 Sorted by residual: chirality pdb=" C2 PCW D 801 " pdb=" C1 PCW D 801 " pdb=" C3 PCW D 801 " pdb=" O2 PCW D 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2 PCW B 801 " pdb=" C1 PCW B 801 " pdb=" C3 PCW B 801 " pdb=" O2 PCW B 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C2 PCW A 801 " pdb=" C1 PCW A 801 " pdb=" C3 PCW A 801 " pdb=" O2 PCW A 801 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 2419 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 111 " 0.004 2.00e-02 2.50e+03 8.31e-03 6.90e-01 pdb=" C LEU E 111 " -0.014 2.00e-02 2.50e+03 pdb=" O LEU E 111 " 0.005 2.00e-02 2.50e+03 pdb=" N GLN E 112 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 111 " 0.004 2.00e-02 2.50e+03 8.28e-03 6.86e-01 pdb=" C LEU B 111 " -0.014 2.00e-02 2.50e+03 pdb=" O LEU B 111 " 0.005 2.00e-02 2.50e+03 pdb=" N GLN B 112 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR C 270 " 0.014 5.00e-02 4.00e+02 2.07e-02 6.86e-01 pdb=" N PRO C 271 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO C 271 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO C 271 " 0.012 5.00e-02 4.00e+02 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 4509 2.84 - 3.36: 13974 3.36 - 3.87: 23701 3.87 - 4.39: 26473 4.39 - 4.90: 48161 Nonbonded interactions: 116818 Sorted by model distance: nonbonded pdb=" OE1 GLU C 212 " pdb=" NH2 ARG C 256 " model vdw 2.327 3.120 nonbonded pdb=" OE1 GLU G 212 " pdb=" NH2 ARG G 256 " model vdw 2.327 3.120 nonbonded pdb=" OE1 GLU A 212 " pdb=" NH2 ARG A 256 " model vdw 2.327 3.120 nonbonded pdb=" OE1 GLU E 212 " pdb=" NH2 ARG E 256 " model vdw 2.327 3.120 nonbonded pdb=" OE1 GLU F 212 " pdb=" NH2 ARG F 256 " model vdw 2.327 3.120 ... (remaining 116813 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.180 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: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.530 Find NCS groups from input model: 0.140 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14721 Z= 0.198 Angle : 0.566 7.146 19873 Z= 0.282 Chirality : 0.044 0.256 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.117 105.611 5432 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % 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: 2.48 (0.19), residues: 1813 helix: 3.25 (0.15), residues: 1008 sheet: -0.29 (0.31), residues: 259 loop : -0.52 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 184 TYR 0.003 0.001 TYR F 250 PHE 0.006 0.001 PHE C 277 TRP 0.003 0.001 TRP C 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.20 (14721) covalent geometry : angle 0.56612 / 0.28 (19873) hydrogen bonds : bond 0.12431 / 8.77 ( 1079) hydrogen bonds : angle 5.84781 / 4.08 ( 3156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.464 Fit side-chains REVERT: A 125 VAL cc_start: 0.8512 (t) cc_final: 0.8253 (t) REVERT: C 47 MET cc_start: 0.4892 (mmt) cc_final: 0.4575 (tmm) REVERT: C 227 GLU cc_start: 0.8155 (pt0) cc_final: 0.7909 (pt0) REVERT: E 97 ILE cc_start: 0.7973 (mt) cc_final: 0.7756 (mt) REVERT: F 155 MET cc_start: 0.8604 (ptt) cc_final: 0.8382 (ptt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1217 time to fit residues: 43.6952 Evaluate side-chains 208 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.112582 restraints weight = 15638.075| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.55 r_work: 0.3042 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14721 Z= 0.123 Angle : 0.431 6.333 19873 Z= 0.232 Chirality : 0.041 0.137 2422 Planarity : 0.003 0.022 2457 Dihedral : 10.665 109.374 2310 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.10 % Allowed : 8.19 % Favored : 89.71 % 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: 2.59 (0.19), residues: 1813 helix: 3.32 (0.15), residues: 1015 sheet: -0.01 (0.30), residues: 273 loop : -0.65 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 128 TYR 0.003 0.001 TYR B 250 PHE 0.010 0.001 PHE C 277 TRP 0.002 0.000 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14721) covalent geometry : angle 0.43123 / 0.23 (19873) hydrogen bonds : bond 0.03905 / 2.77 ( 1079) hydrogen bonds : angle 4.60471 / 3.27 ( 3156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.536 Fit side-chains REVERT: A 154 THR cc_start: 0.8598 (p) cc_final: 0.8231 (m) REVERT: C 47 MET cc_start: 0.5256 (mmt) cc_final: 0.4601 (tmm) REVERT: D 47 MET cc_start: 0.5326 (tmm) cc_final: 0.4471 (mmm) REVERT: F 154 THR cc_start: 0.8798 (p) cc_final: 0.8413 (m) REVERT: G 47 MET cc_start: 0.5232 (tmm) cc_final: 0.4273 (mmt) outliers start: 31 outliers final: 14 residues processed: 246 average time/residue: 0.1398 time to fit residues: 48.8009 Evaluate side-chains 225 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 211 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 43 ILE Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 113 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 161 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.151638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.108805 restraints weight = 15855.425| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.49 r_work: 0.3096 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14721 Z= 0.163 Angle : 0.465 7.018 19873 Z= 0.245 Chirality : 0.043 0.145 2422 Planarity : 0.003 0.022 2457 Dihedral : 10.436 110.649 2310 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.17 % Allowed : 11.24 % Favored : 86.59 % 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: 2.40 (0.19), residues: 1813 helix: 3.16 (0.15), residues: 1015 sheet: -0.12 (0.27), residues: 308 loop : -0.73 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 128 TYR 0.005 0.001 TYR G 250 PHE 0.013 0.002 PHE F 277 TRP 0.003 0.001 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (14721) covalent geometry : angle 0.46510 / 0.24 (19873) hydrogen bonds : bond 0.03886 / 2.74 ( 1079) hydrogen bonds : angle 4.37943 / 3.13 ( 3156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.537 Fit side-chains REVERT: A 154 THR cc_start: 0.8751 (OUTLIER) cc_final: 0.8368 (m) REVERT: C 47 MET cc_start: 0.5242 (mmt) cc_final: 0.4658 (tmm) REVERT: C 159 ASP cc_start: 0.8608 (t70) cc_final: 0.8388 (t70) REVERT: D 47 MET cc_start: 0.5153 (tmm) cc_final: 0.4944 (tmm) REVERT: E 169 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8195 (ttpp) REVERT: F 154 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8431 (m) REVERT: G 47 MET cc_start: 0.5168 (tmm) cc_final: 0.4908 (tmm) REVERT: G 273 MET cc_start: 0.8927 (ttm) cc_final: 0.8656 (ttm) outliers start: 32 outliers final: 21 residues processed: 224 average time/residue: 0.1362 time to fit residues: 43.5267 Evaluate side-chains 216 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 154 THR Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 106 optimal weight: 3.9990 chunk 148 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 137 optimal weight: 0.0970 chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.111525 restraints weight = 15708.118| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.46 r_work: 0.3110 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14721 Z= 0.099 Angle : 0.398 6.442 19873 Z= 0.212 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.022 2457 Dihedral : 10.116 109.374 2310 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.90 % Allowed : 12.25 % Favored : 85.85 % 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: 2.53 (0.19), residues: 1813 helix: 3.30 (0.15), residues: 1022 sheet: -0.24 (0.28), residues: 294 loop : -0.69 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 128 TYR 0.002 0.000 TYR F 250 PHE 0.010 0.001 PHE F 277 TRP 0.002 0.000 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.10 (14721) covalent geometry : angle 0.39752 / 0.21 (19873) hydrogen bonds : bond 0.03349 / 2.37 ( 1079) hydrogen bonds : angle 4.12154 / 2.94 ( 3156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.412 Fit side-chains REVERT: C 47 MET cc_start: 0.5249 (mmt) cc_final: 0.4676 (tmm) REVERT: C 154 THR cc_start: 0.8661 (p) cc_final: 0.8429 (m) REVERT: C 221 MET cc_start: 0.8684 (mtm) cc_final: 0.8446 (mtm) REVERT: E 169 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8219 (ttpp) REVERT: G 47 MET cc_start: 0.5213 (tmm) cc_final: 0.4957 (tmm) outliers start: 28 outliers final: 16 residues processed: 233 average time/residue: 0.1225 time to fit residues: 40.6688 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 144 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 131 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.153437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111199 restraints weight = 15678.361| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.45 r_work: 0.3108 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14721 Z= 0.114 Angle : 0.413 6.961 19873 Z= 0.219 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.021 2457 Dihedral : 9.959 108.533 2310 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 2.10 % Allowed : 12.86 % Favored : 85.04 % 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: 2.60 (0.19), residues: 1813 helix: 3.30 (0.15), residues: 1015 sheet: 0.60 (0.27), residues: 273 loop : -1.00 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 128 TYR 0.003 0.001 TYR F 250 PHE 0.010 0.001 PHE F 277 TRP 0.002 0.000 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (14721) covalent geometry : angle 0.41327 / 0.22 (19873) hydrogen bonds : bond 0.03367 / 2.38 ( 1079) hydrogen bonds : angle 4.09393 / 2.92 ( 3156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 204 time to evaluate : 0.511 Fit side-chains REVERT: C 47 MET cc_start: 0.5257 (mmt) cc_final: 0.4695 (tmm) REVERT: C 154 THR cc_start: 0.8680 (p) cc_final: 0.8454 (m) REVERT: D 47 MET cc_start: 0.5799 (tmm) cc_final: 0.4812 (mmm) REVERT: G 47 MET cc_start: 0.5313 (tmm) cc_final: 0.5007 (tmm) outliers start: 31 outliers final: 21 residues processed: 225 average time/residue: 0.1248 time to fit residues: 40.5023 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 160 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.153153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.108989 restraints weight = 15627.260| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.58 r_work: 0.3013 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14721 Z= 0.147 Angle : 0.446 7.680 19873 Z= 0.234 Chirality : 0.042 0.145 2422 Planarity : 0.003 0.021 2457 Dihedral : 10.051 109.576 2310 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.03 % Allowed : 13.61 % Favored : 84.36 % 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: 2.42 (0.19), residues: 1813 helix: 3.18 (0.15), residues: 1015 sheet: -0.06 (0.26), residues: 308 loop : -0.77 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 128 TYR 0.004 0.001 TYR G 250 PHE 0.011 0.001 PHE G 188 TRP 0.002 0.001 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (14721) covalent geometry : angle 0.44612 / 0.23 (19873) hydrogen bonds : bond 0.03569 / 2.52 ( 1079) hydrogen bonds : angle 4.15785 / 2.96 ( 3156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.489 Fit side-chains REVERT: C 47 MET cc_start: 0.5113 (mmt) cc_final: 0.4504 (tmm) REVERT: C 210 GLN cc_start: 0.8324 (mm-40) cc_final: 0.8070 (mm110) REVERT: C 221 MET cc_start: 0.8889 (mtm) cc_final: 0.8642 (mtm) REVERT: D 47 MET cc_start: 0.5702 (tmm) cc_final: 0.4724 (mmm) REVERT: G 47 MET cc_start: 0.5017 (tmm) cc_final: 0.4709 (tmm) outliers start: 30 outliers final: 23 residues processed: 222 average time/residue: 0.1214 time to fit residues: 38.8997 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 165 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.153845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.109536 restraints weight = 15540.202| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.63 r_work: 0.3018 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14721 Z= 0.122 Angle : 0.419 7.836 19873 Z= 0.221 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.022 2457 Dihedral : 9.975 109.170 2310 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.56 % Allowed : 14.42 % Favored : 84.02 % 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: 2.48 (0.19), residues: 1813 helix: 3.25 (0.15), residues: 1015 sheet: -0.09 (0.26), residues: 308 loop : -0.76 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 128 TYR 0.003 0.001 TYR A 250 PHE 0.010 0.001 PHE F 277 TRP 0.001 0.000 TRP A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (14721) covalent geometry : angle 0.41925 / 0.22 (19873) hydrogen bonds : bond 0.03393 / 2.39 ( 1079) hydrogen bonds : angle 4.08876 / 2.91 ( 3156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.575 Fit side-chains REVERT: A 72 LEU cc_start: 0.3568 (OUTLIER) cc_final: 0.3353 (tt) REVERT: C 47 MET cc_start: 0.5041 (mmt) cc_final: 0.4433 (tmm) REVERT: C 278 LYS cc_start: 0.8072 (mttt) cc_final: 0.7844 (mttp) REVERT: E 47 MET cc_start: 0.5343 (tmm) cc_final: 0.4408 (mmt) REVERT: G 47 MET cc_start: 0.4855 (tmm) cc_final: 0.4574 (tmm) outliers start: 23 outliers final: 20 residues processed: 221 average time/residue: 0.1155 time to fit residues: 37.1509 Evaluate side-chains 223 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 45 optimal weight: 0.0050 chunk 31 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 162 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.154834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.110793 restraints weight = 15514.645| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.63 r_work: 0.3037 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14721 Z= 0.102 Angle : 0.405 8.251 19873 Z= 0.213 Chirality : 0.041 0.142 2422 Planarity : 0.002 0.022 2457 Dihedral : 9.780 106.371 2310 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.90 % Allowed : 14.08 % Favored : 84.02 % 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: 2.63 (0.19), residues: 1813 helix: 3.40 (0.15), residues: 1008 sheet: -0.01 (0.25), residues: 308 loop : -0.70 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 128 TYR 0.002 0.000 TYR F 250 PHE 0.010 0.001 PHE F 277 TRP 0.001 0.000 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.10 (14721) covalent geometry : angle 0.40525 / 0.21 (19873) hydrogen bonds : bond 0.03240 / 2.29 ( 1079) hydrogen bonds : angle 3.99042 / 2.84 ( 3156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.536 Fit side-chains REVERT: C 47 MET cc_start: 0.5062 (mmt) cc_final: 0.4480 (tmm) REVERT: C 154 THR cc_start: 0.8543 (p) cc_final: 0.8306 (m) REVERT: C 278 LYS cc_start: 0.7999 (mttt) cc_final: 0.7770 (mttp) REVERT: D 47 MET cc_start: 0.5738 (tmm) cc_final: 0.4849 (mmm) REVERT: F 47 MET cc_start: 0.5324 (tmm) cc_final: 0.4607 (mmt) REVERT: G 47 MET cc_start: 0.4881 (tmm) cc_final: 0.4626 (tmm) outliers start: 28 outliers final: 22 residues processed: 228 average time/residue: 0.1245 time to fit residues: 41.7020 Evaluate side-chains 229 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 207 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 51 optimal weight: 0.9980 chunk 138 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 173 optimal weight: 0.8980 chunk 163 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 135 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.154174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.109989 restraints weight = 15612.759| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.65 r_work: 0.3027 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14721 Z= 0.112 Angle : 0.421 9.498 19873 Z= 0.220 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.021 2457 Dihedral : 9.706 105.075 2310 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.23 % Allowed : 14.01 % Favored : 83.75 % 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: 2.61 (0.19), residues: 1813 helix: 3.37 (0.15), residues: 1008 sheet: 0.04 (0.26), residues: 308 loop : -0.74 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 128 TYR 0.003 0.001 TYR F 250 PHE 0.010 0.001 PHE F 277 TRP 0.001 0.000 TRP C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (14721) covalent geometry : angle 0.42128 / 0.22 (19873) hydrogen bonds : bond 0.03280 / 2.32 ( 1079) hydrogen bonds : angle 3.98696 / 2.84 ( 3156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.518 Fit side-chains REVERT: A 72 LEU cc_start: 0.3558 (OUTLIER) cc_final: 0.3342 (tt) REVERT: C 47 MET cc_start: 0.5065 (mmt) cc_final: 0.4487 (tmm) REVERT: C 221 MET cc_start: 0.8745 (mtm) cc_final: 0.8465 (mtm) REVERT: C 278 LYS cc_start: 0.7994 (mttt) cc_final: 0.7765 (mttp) REVERT: D 47 MET cc_start: 0.5732 (tmm) cc_final: 0.4774 (mmm) REVERT: G 47 MET cc_start: 0.4792 (tmm) cc_final: 0.4544 (tmm) outliers start: 33 outliers final: 25 residues processed: 230 average time/residue: 0.1243 time to fit residues: 41.7871 Evaluate side-chains 234 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 134 optimal weight: 0.0000 chunk 164 optimal weight: 0.8980 chunk 135 optimal weight: 9.9990 chunk 19 optimal weight: 0.0270 chunk 127 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.155679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.111808 restraints weight = 15540.996| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.64 r_work: 0.3030 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14721 Z= 0.093 Angle : 0.412 9.773 19873 Z= 0.214 Chirality : 0.041 0.138 2422 Planarity : 0.002 0.022 2457 Dihedral : 9.537 101.905 2310 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.69 % Allowed : 14.83 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.72 (0.19), residues: 1813 helix: 3.46 (0.15), residues: 1008 sheet: 0.11 (0.26), residues: 308 loop : -0.71 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 128 TYR 0.002 0.000 TYR B 250 PHE 0.010 0.001 PHE F 277 TRP 0.001 0.000 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.09 (14721) covalent geometry : angle 0.41203 / 0.21 (19873) hydrogen bonds : bond 0.03119 / 2.21 ( 1079) hydrogen bonds : angle 3.90773 / 2.78 ( 3156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3626 Ramachandran restraints generated. 1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.436 Fit side-chains REVERT: B 88 ARG cc_start: 0.7704 (tpt90) cc_final: 0.7442 (tpt170) REVERT: C 47 MET cc_start: 0.5120 (mmt) cc_final: 0.4510 (tmm) REVERT: C 221 MET cc_start: 0.8705 (mtm) cc_final: 0.8427 (mtm) REVERT: C 278 LYS cc_start: 0.7962 (mttt) cc_final: 0.7731 (mttp) REVERT: D 47 MET cc_start: 0.5717 (tmm) cc_final: 0.4818 (mmm) REVERT: F 47 MET cc_start: 0.5291 (tmm) cc_final: 0.4577 (mmt) REVERT: G 47 MET cc_start: 0.4824 (tmm) cc_final: 0.4602 (tmm) outliers start: 25 outliers final: 24 residues processed: 229 average time/residue: 0.1143 time to fit residues: 38.5121 Evaluate side-chains 231 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 154 THR Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 202 LYS Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 154 THR Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain E residue 154 THR Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Chi-restraints excluded: chain G residue 171 ILE Chi-restraints excluded: chain G residue 179 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 68 optimal weight: 0.0010 chunk 11 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 135 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.0770 chunk 155 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 150 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.155508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113881 restraints weight = 15656.144| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.44 r_work: 0.3143 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14721 Z= 0.090 Angle : 0.403 9.800 19873 Z= 0.209 Chirality : 0.040 0.138 2422 Planarity : 0.002 0.022 2457 Dihedral : 9.218 96.972 2310 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.62 % Allowed : 15.10 % Favored : 83.28 % 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: 2.78 (0.19), residues: 1813 helix: 3.50 (0.15), residues: 1008 sheet: 0.19 (0.26), residues: 308 loop : -0.71 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 128 TYR 0.002 0.000 TYR B 27 PHE 0.010 0.001 PHE F 277 TRP 0.002 0.000 TRP A 251 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.09 (14721) covalent geometry : angle 0.40303 / 0.21 (19873) hydrogen bonds : bond 0.03036 / 2.15 ( 1079) hydrogen bonds : angle 3.83567 / 2.73 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3502.66 seconds wall clock time: 60 minutes 35.49 seconds (3635.49 seconds total)