Starting phenix.real_space_refine on Wed Mar 4 16:33:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oo6_13006/03_2026/7oo6_13006.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo6_13006/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7oo6_13006/03_2026/7oo6_13006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo6_13006/03_2026/7oo6_13006.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7oo6_13006/03_2026/7oo6_13006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo6_13006/03_2026/7oo6_13006.map" } 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-5986/lib/python3.9/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: 1.71, per 1000 atoms: 0.12 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: 1.02 Conformation dependent library (CDL) restraints added in 511.6 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: 0.28 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: 2.45 Time building geometry restraints manager: 1.34 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: 8869 21.12 - 42.24: 252 42.24 - 63.37: 91 63.37 - 84.49: 0 84.49 - 105.61: 14 Dihedral angle restraints: 9226 sinusoidal: 3990 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 9223 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: 0.04 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: 1.000 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.410 Find NCS groups from input model: 0.120 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:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 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 : 12.218 105.611 5852 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 covalent geometry : bond 0.00397 (14721) covalent geometry : angle 0.56612 (19873) hydrogen bonds : bond 0.12431 ( 1079) hydrogen bonds : angle 5.84781 ( 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 : 0.345 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: 0.1272 time to fit residues: 45.2614 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 : 0.435 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.156022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.112585 restraints weight = 15638.142| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.55 r_work: 0.3035 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14721 Z= 0.124 Angle : 0.435 6.922 19873 Z= 0.232 Chirality : 0.041 0.138 2422 Planarity : 0.003 0.022 2457 Dihedral : 12.935 107.564 2730 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.79 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: 2.58 (0.19), residues: 1813 helix: 3.31 (0.15), residues: 1015 sheet: -0.02 (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 0.009 0.001 PHE C 277 TRP 0.002 0.000 TRP C 240 Details of bonding type rmsd covalent geometry : bond 0.00274 (14721) covalent geometry : angle 0.43486 (19873) hydrogen bonds : bond 0.03904 ( 1079) hydrogen bonds : angle 4.60016 ( 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 259 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 228 time to evaluate : 0.602 Fit side-chains REVERT: A 154 THR cc_start: 0.8575 (p) cc_final: 0.8208 (m) REVERT: C 47 MET cc_start: 0.5212 (mmt) cc_final: 0.4557 (tmm) REVERT: D 47 MET cc_start: 0.5348 (tmm) cc_final: 0.4518 (mmm) REVERT: E 47 MET cc_start: 0.5410 (tmm) cc_final: 0.4556 (mmt) REVERT: F 154 THR cc_start: 0.8796 (p) cc_final: 0.8420 (m) REVERT: G 47 MET cc_start: 0.5186 (tmm) cc_final: 0.4242 (mmt) outliers start: 31 outliers final: 13 residues processed: 247 average time/residue: 0.1487 time to fit residues: 51.7568 Evaluate side-chains 224 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 161 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3659 r_free = 0.3659 target = 0.152371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.109660 restraints weight = 15820.089| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.48 r_work: 0.3087 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14721 Z= 0.146 Angle : 0.446 6.946 19873 Z= 0.235 Chirality : 0.042 0.145 2422 Planarity : 0.003 0.022 2457 Dihedral : 12.953 104.631 2730 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.10 % Allowed : 10.97 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.19), residues: 1813 helix: 3.18 (0.15), residues: 1022 sheet: -0.18 (0.28), residues: 259 loop : -0.80 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 128 TYR 0.004 0.001 TYR A 250 PHE 0.012 0.001 PHE F 277 TRP 0.004 0.001 TRP C 240 Details of bonding type rmsd covalent geometry : bond 0.00347 (14721) covalent geometry : angle 0.44561 (19873) hydrogen bonds : bond 0.03769 ( 1079) hydrogen bonds : angle 4.34061 ( 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 236 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.554 Fit side-chains REVERT: A 154 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8369 (m) REVERT: C 47 MET cc_start: 0.5265 (mmt) cc_final: 0.4695 (tmm) REVERT: C 159 ASP cc_start: 0.8549 (t70) cc_final: 0.8314 (t70) REVERT: E 47 MET cc_start: 0.5405 (tmm) cc_final: 0.5172 (tmm) REVERT: F 154 THR cc_start: 0.8799 (OUTLIER) cc_final: 0.8444 (m) REVERT: G 47 MET cc_start: 0.5187 (tmm) cc_final: 0.4936 (tmm) REVERT: G 273 MET cc_start: 0.8883 (ttm) cc_final: 0.8591 (ttm) outliers start: 31 outliers final: 19 residues processed: 225 average time/residue: 0.1443 time to fit residues: 46.0031 Evaluate side-chains 213 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 148 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 137 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 chunk 130 optimal weight: 0.0000 chunk 70 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 overall best weight: 0.6584 ------------------------------------------------------------------------------- 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 = 0.3681 r_free = 0.3681 target = 0.154095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.111755 restraints weight = 15678.095| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.45 r_work: 0.3141 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1543 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= 0.100 Angle : 0.399 6.316 19873 Z= 0.212 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.022 2457 Dihedral : 12.547 100.941 2730 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.69 % Allowed : 12.39 % Favored : 85.92 % 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: 2.56 (0.19), residues: 1813 helix: 3.33 (0.15), residues: 1022 sheet: -0.23 (0.28), residues: 294 loop : -0.68 (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 covalent geometry : bond 0.00215 (14721) covalent geometry : angle 0.39929 (19873) hydrogen bonds : bond 0.03329 ( 1079) hydrogen bonds : angle 4.11649 ( 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 230 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.564 Fit side-chains REVERT: C 47 MET cc_start: 0.5226 (mmt) cc_final: 0.4661 (tmm) REVERT: C 128 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7092 (mtp85) REVERT: C 154 THR cc_start: 0.8676 (p) cc_final: 0.8445 (m) REVERT: C 221 MET cc_start: 0.8708 (mtm) cc_final: 0.8467 (mtm) REVERT: D 47 MET cc_start: 0.5805 (tmm) cc_final: 0.4814 (mmm) REVERT: E 47 MET cc_start: 0.5149 (tmm) cc_final: 0.4879 (tmm) REVERT: G 47 MET cc_start: 0.5192 (tmm) cc_final: 0.4945 (tmm) outliers start: 25 outliers final: 15 residues processed: 226 average time/residue: 0.1395 time to fit residues: 45.1192 Evaluate side-chains 216 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 227 GLU 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 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: 0.9990 chunk 24 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.161376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120730 restraints weight = 15640.910| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.33 r_work: 0.3092 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14721 Z= 0.119 Angle : 0.419 7.139 19873 Z= 0.221 Chirality : 0.041 0.142 2422 Planarity : 0.002 0.022 2457 Dihedral : 12.022 98.028 2730 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.83 % Allowed : 12.53 % Favored : 85.65 % 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: 2.54 (0.19), residues: 1813 helix: 3.29 (0.15), residues: 1015 sheet: -0.07 (0.27), residues: 308 loop : -0.71 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 128 TYR 0.003 0.001 TYR A 250 PHE 0.010 0.001 PHE F 277 TRP 0.002 0.000 TRP C 240 Details of bonding type rmsd covalent geometry : bond 0.00282 (14721) covalent geometry : angle 0.41915 (19873) hydrogen bonds : bond 0.03401 ( 1079) hydrogen bonds : angle 4.10790 ( 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 229 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 0.558 Fit side-chains REVERT: C 47 MET cc_start: 0.5164 (mmt) cc_final: 0.4625 (tmm) REVERT: C 154 THR cc_start: 0.8709 (p) cc_final: 0.8458 (m) REVERT: E 47 MET cc_start: 0.5250 (tmm) cc_final: 0.4910 (tmm) REVERT: G 47 MET cc_start: 0.5228 (tmm) cc_final: 0.4930 (tmm) outliers start: 27 outliers final: 18 residues processed: 222 average time/residue: 0.1392 time to fit residues: 43.9049 Evaluate side-chains 214 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 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 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 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: 7.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 16 optimal weight: 0.0470 chunk 169 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- 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 = 0.3672 r_free = 0.3672 target = 0.154258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.109911 restraints weight = 15612.994| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.65 r_work: 0.3015 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14721 Z= 0.121 Angle : 0.416 7.325 19873 Z= 0.220 Chirality : 0.041 0.143 2422 Planarity : 0.002 0.022 2457 Dihedral : 11.509 93.901 2730 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.90 % Allowed : 13.34 % Favored : 84.77 % 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: 2.58 (0.19), residues: 1813 helix: 3.29 (0.15), residues: 1015 sheet: 0.61 (0.27), residues: 273 loop : -1.02 (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 G 250 PHE 0.010 0.001 PHE F 277 TRP 0.001 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00293 (14721) covalent geometry : angle 0.41640 (19873) hydrogen bonds : bond 0.03364 ( 1079) hydrogen bonds : angle 4.08005 ( 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 232 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.550 Fit side-chains REVERT: C 47 MET cc_start: 0.5052 (mmt) cc_final: 0.4462 (tmm) REVERT: C 154 THR cc_start: 0.8709 (p) cc_final: 0.8437 (m) REVERT: C 210 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8051 (mm110) REVERT: D 47 MET cc_start: 0.5599 (tmm) cc_final: 0.4645 (mmm) REVERT: E 47 MET cc_start: 0.5013 (tmm) cc_final: 0.4657 (tmm) REVERT: G 47 MET cc_start: 0.4906 (tmm) cc_final: 0.4622 (tmm) outliers start: 28 outliers final: 20 residues processed: 223 average time/residue: 0.1316 time to fit residues: 42.1382 Evaluate side-chains 219 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 63 optimal weight: 0.0870 chunk 25 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.3680 r_free = 0.3680 target = 0.154907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.110903 restraints weight = 15573.027| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.64 r_work: 0.3018 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.1855 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= 0.105 Angle : 0.405 7.537 19873 Z= 0.214 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.022 2457 Dihedral : 10.788 83.243 2730 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.62 % Allowed : 13.88 % Favored : 84.50 % 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: 2.65 (0.19), residues: 1813 helix: 3.34 (0.15), residues: 1015 sheet: 0.67 (0.26), residues: 273 loop : -1.01 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 128 TYR 0.003 0.000 TYR F 250 PHE 0.010 0.001 PHE F 277 TRP 0.001 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00242 (14721) covalent geometry : angle 0.40469 (19873) hydrogen bonds : bond 0.03236 ( 1079) hydrogen bonds : angle 3.99303 ( 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 230 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 206 time to evaluate : 0.519 Fit side-chains REVERT: B 39 ILE cc_start: 0.6957 (mm) cc_final: 0.6751 (mm) REVERT: C 47 MET cc_start: 0.5026 (mmt) cc_final: 0.4445 (tmm) REVERT: C 221 MET cc_start: 0.8872 (mtm) cc_final: 0.8585 (mtm) REVERT: C 278 LYS cc_start: 0.8026 (mttt) cc_final: 0.7800 (mttp) REVERT: D 47 MET cc_start: 0.5600 (tmm) cc_final: 0.4658 (mmm) REVERT: E 47 MET cc_start: 0.4981 (tmm) cc_final: 0.4661 (tmm) REVERT: F 47 MET cc_start: 0.5323 (tmm) cc_final: 0.4635 (mmt) REVERT: G 47 MET cc_start: 0.4846 (tmm) cc_final: 0.4583 (tmm) outliers start: 24 outliers final: 19 residues processed: 222 average time/residue: 0.1311 time to fit residues: 42.2466 Evaluate side-chains 222 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 162 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.154813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.110667 restraints weight = 15568.019| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.63 r_work: 0.3015 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14721 Z= 0.108 Angle : 0.404 7.105 19873 Z= 0.214 Chirality : 0.041 0.142 2422 Planarity : 0.002 0.023 2457 Dihedral : 10.361 69.039 2730 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.62 % Allowed : 14.22 % Favored : 84.16 % 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: 2.71 (0.19), residues: 1813 helix: 3.42 (0.15), residues: 1008 sheet: 0.73 (0.26), residues: 273 loop : -1.00 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 128 TYR 0.003 0.000 TYR F 250 PHE 0.010 0.001 PHE D 188 TRP 0.001 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00252 (14721) covalent geometry : angle 0.40418 (19873) hydrogen bonds : bond 0.03242 ( 1079) hydrogen bonds : angle 3.97378 ( 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 231 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 207 time to evaluate : 0.510 Fit side-chains REVERT: C 47 MET cc_start: 0.5020 (mmt) cc_final: 0.4442 (tmm) REVERT: C 221 MET cc_start: 0.8891 (mtm) cc_final: 0.8599 (mtm) REVERT: C 278 LYS cc_start: 0.7965 (mttt) cc_final: 0.7730 (mttp) REVERT: D 47 MET cc_start: 0.5569 (tmm) cc_final: 0.4697 (mmm) REVERT: E 47 MET cc_start: 0.4980 (tmm) cc_final: 0.4670 (tmm) REVERT: G 47 MET cc_start: 0.4762 (tmm) cc_final: 0.4525 (tmm) outliers start: 24 outliers final: 22 residues processed: 222 average time/residue: 0.1335 time to fit residues: 42.9143 Evaluate side-chains 228 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 B residue 202 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 51 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 178 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 chunk 173 optimal weight: 0.7980 chunk 163 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 135 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 = 0.3685 r_free = 0.3685 target = 0.155406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.111442 restraints weight = 15642.387| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 1.65 r_work: 0.3024 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14721 Z= 0.098 Angle : 0.398 8.254 19873 Z= 0.210 Chirality : 0.041 0.142 2422 Planarity : 0.002 0.029 2457 Dihedral : 9.907 59.977 2730 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.90 % Allowed : 13.88 % Favored : 84.22 % 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: 2.75 (0.19), residues: 1813 helix: 3.46 (0.15), residues: 1008 sheet: 0.78 (0.26), residues: 273 loop : -1.01 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 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 A 251 Details of bonding type rmsd covalent geometry : bond 0.00223 (14721) covalent geometry : angle 0.39848 (19873) hydrogen bonds : bond 0.03139 ( 1079) hydrogen bonds : angle 3.90333 ( 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 240 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 212 time to evaluate : 0.506 Fit side-chains REVERT: A 47 MET cc_start: 0.5293 (tmm) cc_final: 0.4375 (mmt) REVERT: C 47 MET cc_start: 0.5108 (mmt) cc_final: 0.4492 (tmm) REVERT: C 154 THR cc_start: 0.8622 (p) cc_final: 0.8371 (m) REVERT: C 221 MET cc_start: 0.8858 (mtm) cc_final: 0.8566 (mtm) REVERT: C 278 LYS cc_start: 0.7963 (mttt) cc_final: 0.7729 (mttp) REVERT: D 47 MET cc_start: 0.5574 (tmm) cc_final: 0.4702 (mmm) REVERT: E 47 MET cc_start: 0.4945 (tmm) cc_final: 0.4683 (tmm) REVERT: F 47 MET cc_start: 0.5532 (tmm) cc_final: 0.4795 (mmt) REVERT: G 47 MET cc_start: 0.4827 (tmm) cc_final: 0.4609 (tmm) outliers start: 28 outliers final: 24 residues processed: 230 average time/residue: 0.1220 time to fit residues: 41.0772 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 : 0.530 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 134 optimal weight: 4.9990 chunk 164 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 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: 0.9990 chunk 118 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.154896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.110917 restraints weight = 15626.637| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.59 r_work: 0.3019 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14721 Z= 0.115 Angle : 0.415 8.018 19873 Z= 0.218 Chirality : 0.041 0.143 2422 Planarity : 0.002 0.026 2457 Dihedral : 9.858 59.356 2730 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.69 % Allowed : 14.22 % Favored : 84.09 % 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: 2.69 (0.19), residues: 1813 helix: 3.41 (0.15), residues: 1008 sheet: 0.77 (0.26), residues: 273 loop : -1.05 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 128 TYR 0.003 0.001 TYR F 250 PHE 0.010 0.001 PHE D 188 TRP 0.001 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00274 (14721) covalent geometry : angle 0.41530 (19873) hydrogen bonds : bond 0.03250 ( 1079) hydrogen bonds : angle 3.94298 ( 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 233 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.519 Fit side-chains REVERT: A 72 LEU cc_start: 0.3560 (OUTLIER) cc_final: 0.3343 (tt) REVERT: C 47 MET cc_start: 0.5050 (mmt) cc_final: 0.4487 (tmm) REVERT: C 221 MET cc_start: 0.8876 (mtm) cc_final: 0.8600 (mtm) REVERT: C 278 LYS cc_start: 0.8006 (mttt) cc_final: 0.7776 (mttp) REVERT: E 47 MET cc_start: 0.4965 (tmm) cc_final: 0.4673 (tmm) REVERT: G 47 MET cc_start: 0.4851 (tmm) cc_final: 0.4606 (tmm) outliers start: 25 outliers final: 22 residues processed: 225 average time/residue: 0.1329 time to fit residues: 43.3653 Evaluate side-chains 229 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.521 ------------------------------------------------------------------------------- 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 141 VAL 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 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 68 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 78 optimal weight: 20.0000 chunk 155 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 150 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.153801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.109707 restraints weight = 15587.118| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.64 r_work: 0.3002 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14721 Z= 0.125 Angle : 0.430 8.544 19873 Z= 0.225 Chirality : 0.041 0.143 2422 Planarity : 0.002 0.025 2457 Dihedral : 9.720 57.170 2730 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.76 % Allowed : 14.35 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.62 (0.19), residues: 1813 helix: 3.36 (0.15), residues: 1008 sheet: 0.10 (0.26), residues: 308 loop : -0.74 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 128 TYR 0.003 0.001 TYR A 250 PHE 0.011 0.001 PHE D 188 TRP 0.002 0.000 TRP A 240 Details of bonding type rmsd covalent geometry : bond 0.00302 (14721) covalent geometry : angle 0.42950 (19873) hydrogen bonds : bond 0.03331 ( 1079) hydrogen bonds : angle 3.97904 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.55 seconds wall clock time: 63 minutes 54.30 seconds (3834.30 seconds total)