Starting phenix.real_space_refine on Tue Dec 31 05:22:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7oo6_13006/12_2024/7oo6_13006.cif Found real_map, /net/cci-nas-00/data/ceres_data/7oo6_13006/12_2024/7oo6_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_13006/12_2024/7oo6_13006.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7oo6_13006/12_2024/7oo6_13006.map" model { file = "/net/cci-nas-00/data/ceres_data/7oo6_13006/12_2024/7oo6_13006.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7oo6_13006/12_2024/7oo6_13006.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F Time building chain proxies: 5.35, per 1000 atoms: 0.37 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: 4.22 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 2.32 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: 5.74 Time building geometry restraints manager: 4.69 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: 0.00 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.170 Set scattering table: 0.150 Process input model: 32.980 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 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:3.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.410 ------------------------------------------------------------------------------- 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= 0.263 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.003 0.001 TRP C 251 PHE 0.006 0.001 PHE C 277 TYR 0.003 0.001 TYR F 250 ARG 0.002 0.000 ARG E 184 *********************** 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 : 1.512 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: 0.3216 time to fit residues: 113.9503 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 : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14721 Z= 0.176 Angle : 0.427 6.149 19873 Z= 0.229 Chirality : 0.041 0.139 2422 Planarity : 0.003 0.021 2457 Dihedral : 12.929 107.477 2730 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.76 % Allowed : 8.46 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.19), residues: 1813 helix: 3.31 (0.15), residues: 1015 sheet: -0.02 (0.30), residues: 273 loop : -0.64 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 240 PHE 0.010 0.001 PHE C 277 TYR 0.003 0.001 TYR B 250 ARG 0.004 0.000 ARG G 128 *********************** 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 252 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 2.331 Fit side-chains REVERT: A 154 THR cc_start: 0.8432 (p) cc_final: 0.8073 (m) REVERT: C 47 MET cc_start: 0.4915 (mmt) cc_final: 0.4596 (tmm) REVERT: D 47 MET cc_start: 0.5187 (tmm) cc_final: 0.4414 (mmm) REVERT: E 97 ILE cc_start: 0.7955 (mt) cc_final: 0.7740 (mt) REVERT: F 154 THR cc_start: 0.8670 (p) cc_final: 0.8282 (m) REVERT: G 47 MET cc_start: 0.5115 (tmm) cc_final: 0.4209 (mmt) outliers start: 26 outliers final: 9 residues processed: 240 average time/residue: 0.3343 time to fit residues: 112.2933 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 1.733 ------------------------------------------------------------------------------- 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 E residue 43 ILE Chi-restraints excluded: chain E residue 213 ASP Chi-restraints excluded: chain G residue 141 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 137 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 45 optimal weight: 0.0970 chunk 165 optimal weight: 0.9990 chunk 178 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14721 Z= 0.154 Angle : 0.402 6.567 19873 Z= 0.214 Chirality : 0.041 0.140 2422 Planarity : 0.002 0.021 2457 Dihedral : 12.748 102.662 2730 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.56 % Allowed : 11.10 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.19), residues: 1813 helix: 3.34 (0.15), residues: 1022 sheet: -0.19 (0.28), residues: 259 loop : -0.71 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 251 PHE 0.010 0.001 PHE D 277 TYR 0.002 0.000 TYR F 250 ARG 0.005 0.000 ARG G 128 *********************** 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 232 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 1.559 Fit side-chains REVERT: A 154 THR cc_start: 0.8563 (p) cc_final: 0.8323 (m) REVERT: A 187 GLU cc_start: 0.8013 (tt0) cc_final: 0.7779 (tt0) REVERT: C 47 MET cc_start: 0.4977 (mmt) cc_final: 0.4653 (tmm) REVERT: D 154 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8342 (m) REVERT: E 97 ILE cc_start: 0.7927 (mt) cc_final: 0.7720 (mt) REVERT: F 154 THR cc_start: 0.8580 (p) cc_final: 0.8300 (m) REVERT: G 47 MET cc_start: 0.5002 (tmm) cc_final: 0.4791 (tmm) outliers start: 23 outliers final: 14 residues processed: 224 average time/residue: 0.3218 time to fit residues: 101.3990 Evaluate side-chains 214 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 199 time to evaluate : 1.734 ------------------------------------------------------------------------------- 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 179 SER Chi-restraints excluded: chain A residue 213 ASP 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 154 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 279 ARG 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14721 Z= 0.198 Angle : 0.430 6.866 19873 Z= 0.226 Chirality : 0.042 0.143 2422 Planarity : 0.003 0.023 2457 Dihedral : 12.552 99.895 2730 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.23 % Allowed : 11.98 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.19), residues: 1813 helix: 3.25 (0.15), residues: 1022 sheet: -0.25 (0.27), residues: 294 loop : -0.71 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 240 PHE 0.011 0.001 PHE F 277 TYR 0.004 0.001 TYR B 250 ARG 0.005 0.000 ARG G 128 *********************** 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 234 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 1.590 Fit side-chains REVERT: A 154 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8278 (m) REVERT: A 187 GLU cc_start: 0.8078 (tt0) cc_final: 0.7842 (tt0) REVERT: A 255 GLU cc_start: 0.7986 (tt0) cc_final: 0.7761 (tt0) REVERT: C 47 MET cc_start: 0.4838 (mmt) cc_final: 0.4587 (tmm) REVERT: C 221 MET cc_start: 0.8120 (mtm) cc_final: 0.7877 (mtm) REVERT: D 47 MET cc_start: 0.5522 (tmm) cc_final: 0.4641 (mmm) REVERT: F 154 THR cc_start: 0.8622 (OUTLIER) cc_final: 0.8377 (m) REVERT: G 47 MET cc_start: 0.5044 (tmm) cc_final: 0.4828 (tmm) REVERT: G 153 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8080 (m) outliers start: 33 outliers final: 22 residues processed: 225 average time/residue: 0.2969 time to fit residues: 94.3148 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.515 ------------------------------------------------------------------------------- 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 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 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 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 153 THR 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 146 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 130 optimal weight: 0.0060 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 121 optimal weight: 0.0270 chunk 0 optimal weight: 20.0000 chunk 89 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 14721 Z= 0.156 Angle : 0.395 6.785 19873 Z= 0.209 Chirality : 0.041 0.140 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.827 94.261 2730 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.76 % Allowed : 13.00 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.19), residues: 1813 helix: 3.42 (0.15), residues: 1015 sheet: 0.56 (0.27), residues: 273 loop : -0.98 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 251 PHE 0.010 0.001 PHE F 277 TYR 0.002 0.000 TYR F 250 ARG 0.006 0.000 ARG G 128 *********************** 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 233 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 207 time to evaluate : 1.642 Fit side-chains REVERT: A 154 THR cc_start: 0.8481 (p) cc_final: 0.8225 (m) REVERT: A 255 GLU cc_start: 0.7918 (tt0) cc_final: 0.7688 (tt0) REVERT: C 47 MET cc_start: 0.4934 (mmt) cc_final: 0.4637 (tmm) REVERT: D 154 THR cc_start: 0.8399 (p) cc_final: 0.8147 (m) REVERT: G 47 MET cc_start: 0.5099 (tmm) cc_final: 0.4861 (tmm) outliers start: 26 outliers final: 17 residues processed: 224 average time/residue: 0.2929 time to fit residues: 93.5458 Evaluate side-chains 217 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 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 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 59 optimal weight: 0.9980 chunk 158 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14721 Z= 0.175 Angle : 0.409 7.289 19873 Z= 0.215 Chirality : 0.041 0.141 2422 Planarity : 0.002 0.021 2457 Dihedral : 11.312 88.381 2730 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.69 % Allowed : 12.93 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.19), residues: 1813 helix: 3.35 (0.15), residues: 1015 sheet: 0.58 (0.26), residues: 273 loop : -1.02 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP C 240 PHE 0.010 0.001 PHE F 277 TYR 0.003 0.001 TYR G 250 ARG 0.004 0.000 ARG E 128 *********************** 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 229 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 1.470 Fit side-chains REVERT: A 154 THR cc_start: 0.8611 (p) cc_final: 0.8311 (m) REVERT: A 255 GLU cc_start: 0.7938 (tt0) cc_final: 0.7703 (tt0) REVERT: C 47 MET cc_start: 0.4944 (mmt) cc_final: 0.4643 (tmm) REVERT: D 47 MET cc_start: 0.5626 (tmm) cc_final: 0.4682 (mmm) REVERT: D 154 THR cc_start: 0.8519 (p) cc_final: 0.8192 (m) REVERT: G 47 MET cc_start: 0.5087 (tmm) cc_final: 0.4852 (tmm) outliers start: 25 outliers final: 19 residues processed: 221 average time/residue: 0.3190 time to fit residues: 102.3271 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.597 ------------------------------------------------------------------------------- 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 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 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 169 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 chunk 98 optimal weight: 0.9990 chunk 175 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 80 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14721 Z= 0.183 Angle : 0.410 7.582 19873 Z= 0.216 Chirality : 0.041 0.140 2422 Planarity : 0.002 0.021 2457 Dihedral : 10.779 77.085 2730 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.62 % Allowed : 13.47 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.19), residues: 1813 helix: 3.40 (0.15), residues: 1008 sheet: 0.62 (0.26), residues: 273 loop : -0.97 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 240 PHE 0.010 0.001 PHE D 188 TYR 0.003 0.001 TYR F 250 ARG 0.003 0.000 ARG C 128 *********************** 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 : 1.547 Fit side-chains REVERT: A 255 GLU cc_start: 0.7935 (tt0) cc_final: 0.7711 (tt0) REVERT: C 47 MET cc_start: 0.4824 (mmt) cc_final: 0.4580 (tmm) REVERT: D 47 MET cc_start: 0.5598 (tmm) cc_final: 0.4701 (mmm) REVERT: G 47 MET cc_start: 0.5035 (tmm) cc_final: 0.4815 (tmm) outliers start: 24 outliers final: 19 residues processed: 220 average time/residue: 0.2834 time to fit residues: 89.7356 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 : 1.432 ------------------------------------------------------------------------------- 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 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 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 108 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 111 optimal weight: 0.2980 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 137 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1903 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= 0.149 Angle : 0.402 8.057 19873 Z= 0.211 Chirality : 0.041 0.140 2422 Planarity : 0.002 0.021 2457 Dihedral : 10.054 59.770 2730 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.35 % Allowed : 13.81 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.19), residues: 1813 helix: 3.47 (0.15), residues: 1008 sheet: 0.70 (0.26), residues: 273 loop : -0.99 (0.25), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 251 PHE 0.009 0.001 PHE F 277 TYR 0.002 0.000 TYR F 250 ARG 0.004 0.000 ARG C 128 *********************** 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 232 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 1.480 Fit side-chains REVERT: A 47 MET cc_start: 0.5245 (tmm) cc_final: 0.4364 (mmt) REVERT: A 255 GLU cc_start: 0.7913 (tt0) cc_final: 0.7685 (tt0) REVERT: B 88 ARG cc_start: 0.7818 (tpt90) cc_final: 0.7494 (tpt170) REVERT: B 154 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8237 (m) REVERT: C 47 MET cc_start: 0.4929 (mmt) cc_final: 0.4637 (tmm) REVERT: D 47 MET cc_start: 0.5601 (tmm) cc_final: 0.4741 (mmm) REVERT: F 47 MET cc_start: 0.5488 (tmm) cc_final: 0.4724 (mmt) outliers start: 20 outliers final: 17 residues processed: 222 average time/residue: 0.2804 time to fit residues: 90.0487 Evaluate side-chains 222 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 204 time to evaluate : 1.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 153 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 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 97 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 F residue 179 SER Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 141 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 2.9990 chunk 168 optimal weight: 0.1980 chunk 153 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 147 optimal weight: 0.0570 chunk 154 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14721 Z= 0.143 Angle : 0.409 9.296 19873 Z= 0.212 Chirality : 0.040 0.139 2422 Planarity : 0.002 0.021 2457 Dihedral : 9.730 55.055 2730 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.42 % Allowed : 14.01 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.19), residues: 1813 helix: 3.50 (0.15), residues: 1008 sheet: 0.76 (0.26), residues: 273 loop : -1.02 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP F 251 PHE 0.009 0.001 PHE G 188 TYR 0.002 0.000 TYR F 250 ARG 0.004 0.000 ARG C 128 *********************** 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 228 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 1.571 Fit side-chains REVERT: A 255 GLU cc_start: 0.7907 (tt0) cc_final: 0.7684 (tt0) REVERT: B 88 ARG cc_start: 0.7820 (tpt90) cc_final: 0.7488 (tpt170) REVERT: C 47 MET cc_start: 0.4914 (mmt) cc_final: 0.4635 (tmm) REVERT: D 47 MET cc_start: 0.5599 (tmm) cc_final: 0.4740 (mmm) REVERT: G 47 MET cc_start: 0.5639 (tmm) cc_final: 0.4708 (mmt) outliers start: 21 outliers final: 17 residues processed: 218 average time/residue: 0.2817 time to fit residues: 89.1201 Evaluate side-chains 220 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 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 141 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 97 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 F residue 179 SER Chi-restraints excluded: chain G residue 141 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14721 Z= 0.282 Angle : 0.477 10.349 19873 Z= 0.246 Chirality : 0.043 0.145 2422 Planarity : 0.003 0.023 2457 Dihedral : 10.017 59.420 2730 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.35 % Allowed : 14.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.19), residues: 1813 helix: 3.23 (0.15), residues: 1008 sheet: 0.73 (0.26), residues: 273 loop : -1.12 (0.24), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 240 PHE 0.012 0.001 PHE G 188 TYR 0.005 0.001 TYR B 250 ARG 0.004 0.000 ARG G 128 ********************** 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 221 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.738 Fit side-chains REVERT: A 255 GLU cc_start: 0.7956 (tt0) cc_final: 0.7737 (tt0) REVERT: C 47 MET cc_start: 0.4854 (mmt) cc_final: 0.4578 (tmm) REVERT: F 47 MET cc_start: 0.5272 (tmm) cc_final: 0.4566 (mmt) REVERT: G 47 MET cc_start: 0.5551 (tmm) cc_final: 0.4580 (mmt) outliers start: 20 outliers final: 17 residues processed: 215 average time/residue: 0.3019 time to fit residues: 92.8867 Evaluate side-chains 217 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 153 THR 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 154 THR 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 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 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 114 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.152753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.110490 restraints weight = 15550.531| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.43 r_work: 0.3102 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2048 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= 0.213 Angle : 0.448 10.183 19873 Z= 0.231 Chirality : 0.041 0.142 2422 Planarity : 0.002 0.021 2457 Dihedral : 9.881 57.175 2730 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.42 % Allowed : 14.62 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.19), residues: 1813 helix: 3.28 (0.15), residues: 1008 sheet: 0.03 (0.25), residues: 308 loop : -0.79 (0.25), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 240 PHE 0.012 0.001 PHE D 188 TYR 0.003 0.001 TYR A 250 ARG 0.004 0.000 ARG C 128 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.88 seconds wall clock time: 55 minutes 20.96 seconds (3320.96 seconds total)