Starting phenix.real_space_refine on Fri Dec 27 17:08:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq3_32084/12_2024/7vq3_32084.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq3_32084/12_2024/7vq3_32084.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq3_32084/12_2024/7vq3_32084.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq3_32084/12_2024/7vq3_32084.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq3_32084/12_2024/7vq3_32084.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq3_32084/12_2024/7vq3_32084.cif" } resolution = 3.2 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= 0.005 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4070 2.51 5 N 1052 2.21 5 O 1150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6306 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3153 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 5.30, per 1000 atoms: 0.84 Number of scatterers: 6306 At special positions: 0 Unit cell: (84.162, 84.162, 109.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1150 8.00 N 1052 7.00 C 4070 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: 2.04 Conformation dependent library (CDL) restraints added in 1.7 seconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1504 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 84.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.531A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.709A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 66 Processing helix chain 'A' and resid 69 through 102 removed outlier: 3.854A pdb=" N THR A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 125 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 134 through 151 Processing helix chain 'A' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU A 163 " --> pdb=" O MET A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 398 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.531A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.709A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 66 Processing helix chain 'B' and resid 69 through 102 removed outlier: 3.854A pdb=" N THR B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 125 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 158 through 183 removed outlier: 3.673A pdb=" N GLU B 163 " --> pdb=" O MET B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.395A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 254 removed outlier: 3.543A pdb=" N ASN B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 removed outlier: 3.640A pdb=" N TYR B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 305 removed outlier: 4.030A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.658A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 4.206A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 398 515 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 2.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2010 1.34 - 1.46: 1360 1.46 - 1.58: 3004 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 6434 Sorted by residual: bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB THR B 168 " pdb=" CG2 THR B 168 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.57e+00 bond pdb=" CB MET A 377 " pdb=" CG MET A 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB MET B 377 " pdb=" CG MET B 377 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.15e-01 bond pdb=" CB THR B 73 " pdb=" CG2 THR B 73 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.82e-01 ... (remaining 6429 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 8260 1.13 - 2.27: 370 2.27 - 3.40: 44 3.40 - 4.54: 10 4.54 - 5.67: 8 Bond angle restraints: 8692 Sorted by residual: angle pdb=" C VAL A 105 " pdb=" N GLU A 106 " pdb=" CA GLU A 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" C VAL B 105 " pdb=" N GLU B 106 " pdb=" CA GLU B 106 " ideal model delta sigma weight residual 119.78 122.06 -2.28 1.24e+00 6.50e-01 3.37e+00 angle pdb=" N GLU A 307 " pdb=" CA GLU A 307 " pdb=" C GLU A 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" N GLU B 307 " pdb=" CA GLU B 307 " pdb=" C GLU B 307 " ideal model delta sigma weight residual 111.11 113.15 -2.04 1.20e+00 6.94e-01 2.88e+00 angle pdb=" C PHE B 182 " pdb=" N VAL B 183 " pdb=" CA VAL B 183 " ideal model delta sigma weight residual 121.97 119.01 2.96 1.80e+00 3.09e-01 2.70e+00 ... (remaining 8687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 3366 16.81 - 33.61: 404 33.61 - 50.42: 74 50.42 - 67.23: 2 67.23 - 84.03: 10 Dihedral angle restraints: 3856 sinusoidal: 1532 harmonic: 2324 Sorted by residual: dihedral pdb=" CA HIS B 259 " pdb=" C HIS B 259 " pdb=" N GLY B 260 " pdb=" CA GLY B 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CA HIS A 259 " pdb=" C HIS A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual -180.00 -153.41 -26.59 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" CB GLU B 307 " pdb=" CG GLU B 307 " pdb=" CD GLU B 307 " pdb=" OE1 GLU B 307 " ideal model delta sinusoidal sigma weight residual 0.00 84.03 -84.03 1 3.00e+01 1.11e-03 9.56e+00 ... (remaining 3853 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 516 0.027 - 0.054: 346 0.054 - 0.081: 98 0.081 - 0.108: 20 0.108 - 0.135: 16 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA THR A 308 " pdb=" N THR A 308 " pdb=" C THR A 308 " pdb=" CB THR A 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA THR B 308 " pdb=" N THR B 308 " pdb=" C THR B 308 " pdb=" CB THR B 308 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.57e-01 chirality pdb=" CA ILE A 298 " pdb=" N ILE A 298 " pdb=" C ILE A 298 " pdb=" CB ILE A 298 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 ... (remaining 993 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 364 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO A 365 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 364 " -0.024 5.00e-02 4.00e+02 3.66e-02 2.15e+00 pdb=" N PRO B 365 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO B 365 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 365 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 257 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.019 5.00e-02 4.00e+02 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 42 2.63 - 3.20: 5928 3.20 - 3.76: 9359 3.76 - 4.33: 12910 4.33 - 4.90: 21301 Nonbonded interactions: 49540 Sorted by model distance: nonbonded pdb=" OH TYR A 291 " pdb=" OG SER B 376 " model vdw 2.061 3.040 nonbonded pdb=" OG SER A 376 " pdb=" OH TYR B 291 " model vdw 2.061 3.040 nonbonded pdb=" OE1 GLU B 213 " pdb=" ND2 ASN B 232 " model vdw 2.284 3.120 nonbonded pdb=" OE1 GLU A 213 " pdb=" ND2 ASN A 232 " model vdw 2.284 3.120 nonbonded pdb=" O SER A 294 " pdb=" NE2 GLN A 297 " model vdw 2.316 3.120 ... (remaining 49535 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' } 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.590 Find NCS groups from input model: 0.160 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 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 : 0.005 0.053 6434 Z= 0.332 Angle : 0.550 5.673 8692 Z= 0.316 Chirality : 0.039 0.135 996 Planarity : 0.004 0.037 1090 Dihedral : 14.665 84.030 2352 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.28), residues: 792 helix: 0.06 (0.18), residues: 642 sheet: None (None), residues: 0 loop : -3.31 (0.49), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 129 HIS 0.003 0.001 HIS A 259 PHE 0.012 0.001 PHE A 200 TYR 0.012 0.001 TYR B 291 ARG 0.002 0.000 ARG B 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.829 Fit side-chains REVERT: A 50 TYR cc_start: 0.7738 (t80) cc_final: 0.7338 (t80) REVERT: A 229 ARG cc_start: 0.6960 (mmt90) cc_final: 0.6567 (ttp80) REVERT: A 261 GLN cc_start: 0.7859 (tp-100) cc_final: 0.7021 (tt0) REVERT: A 387 LYS cc_start: 0.7991 (mttt) cc_final: 0.7667 (mptt) REVERT: B 229 ARG cc_start: 0.6964 (mmt90) cc_final: 0.6578 (ttp80) REVERT: B 261 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7002 (tt0) REVERT: B 387 LYS cc_start: 0.8007 (mttt) cc_final: 0.7690 (mptt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2661 time to fit residues: 42.2569 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN A 96 GLN A 251 ASN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 361 ASN B 54 ASN B 96 GLN B 251 ASN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 361 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6434 Z= 0.235 Angle : 0.529 5.874 8692 Z= 0.281 Chirality : 0.039 0.129 996 Planarity : 0.004 0.044 1090 Dihedral : 4.094 19.532 858 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.72 % Allowed : 8.76 % Favored : 89.51 % 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: 1.31 (0.30), residues: 792 helix: 1.62 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -2.57 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 129 HIS 0.002 0.001 HIS B 259 PHE 0.014 0.001 PHE A 206 TYR 0.013 0.001 TYR B 236 ARG 0.004 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.662 Fit side-chains REVERT: A 229 ARG cc_start: 0.7056 (mmt90) cc_final: 0.6733 (ttp80) REVERT: A 230 LYS cc_start: 0.8465 (tptt) cc_final: 0.8000 (tttt) REVERT: A 261 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7047 (tt0) REVERT: A 297 GLN cc_start: 0.7954 (mm110) cc_final: 0.7714 (mm110) REVERT: A 387 LYS cc_start: 0.7865 (mttt) cc_final: 0.7556 (mptt) REVERT: B 229 ARG cc_start: 0.7071 (mmt90) cc_final: 0.6734 (ttp80) REVERT: B 230 LYS cc_start: 0.8466 (tptt) cc_final: 0.8010 (tttt) REVERT: B 261 GLN cc_start: 0.7854 (tp-100) cc_final: 0.7016 (tt0) REVERT: B 297 GLN cc_start: 0.7962 (mm110) cc_final: 0.7712 (mm110) REVERT: B 387 LYS cc_start: 0.7915 (mttt) cc_final: 0.7583 (mptt) outliers start: 12 outliers final: 8 residues processed: 118 average time/residue: 0.2316 time to fit residues: 34.8838 Evaluate side-chains 95 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 58 optimal weight: 0.0370 chunk 71 optimal weight: 2.9990 overall best weight: 1.3864 ------------------------------------------------------------------------------- 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: 0.7928 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6434 Z= 0.213 Angle : 0.500 5.821 8692 Z= 0.268 Chirality : 0.038 0.131 996 Planarity : 0.004 0.046 1090 Dihedral : 3.965 19.428 858 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.87 % Allowed : 12.50 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.31), residues: 792 helix: 2.10 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.90 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.015 0.001 PHE B 206 TYR 0.010 0.001 TYR B 39 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.744 Fit side-chains REVERT: A 230 LYS cc_start: 0.8518 (tptt) cc_final: 0.8047 (ttmt) REVERT: A 387 LYS cc_start: 0.7848 (mttt) cc_final: 0.7552 (mptt) REVERT: B 230 LYS cc_start: 0.8519 (tptt) cc_final: 0.8056 (ttmt) REVERT: B 387 LYS cc_start: 0.7861 (mttt) cc_final: 0.7578 (mptt) outliers start: 13 outliers final: 8 residues processed: 94 average time/residue: 0.2249 time to fit residues: 27.0853 Evaluate side-chains 87 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7874 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6434 Z= 0.157 Angle : 0.465 5.855 8692 Z= 0.247 Chirality : 0.037 0.128 996 Planarity : 0.004 0.045 1090 Dihedral : 3.804 16.969 858 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.01 % Allowed : 13.79 % Favored : 84.20 % 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 (0.31), residues: 792 helix: 2.47 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.94 (0.53), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE A 206 TYR 0.008 0.001 TYR B 39 ARG 0.001 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.789 Fit side-chains REVERT: A 229 ARG cc_start: 0.7054 (mmt180) cc_final: 0.6708 (ttp80) REVERT: A 230 LYS cc_start: 0.8445 (tptt) cc_final: 0.8072 (ttmt) REVERT: A 261 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7251 (tt0) REVERT: A 374 THR cc_start: 0.8784 (m) cc_final: 0.8575 (m) REVERT: A 387 LYS cc_start: 0.7854 (mttt) cc_final: 0.7547 (mptt) REVERT: B 229 ARG cc_start: 0.7054 (mmt180) cc_final: 0.6713 (ttp80) REVERT: B 230 LYS cc_start: 0.8457 (tptt) cc_final: 0.8095 (ttmt) REVERT: B 261 GLN cc_start: 0.7899 (tp-100) cc_final: 0.7234 (tt0) REVERT: B 387 LYS cc_start: 0.7879 (mttt) cc_final: 0.7586 (mptt) outliers start: 14 outliers final: 9 residues processed: 100 average time/residue: 0.2046 time to fit residues: 26.8005 Evaluate side-chains 94 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 0 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 69 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6434 Z= 0.161 Angle : 0.482 7.823 8692 Z= 0.249 Chirality : 0.037 0.126 996 Planarity : 0.004 0.045 1090 Dihedral : 3.742 16.491 858 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.01 % Allowed : 15.80 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.81 (0.31), residues: 792 helix: 2.70 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.88 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE A 206 TYR 0.008 0.001 TYR B 39 ARG 0.001 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.720 Fit side-chains REVERT: A 230 LYS cc_start: 0.8473 (tptt) cc_final: 0.8111 (ttmt) REVERT: A 261 GLN cc_start: 0.7853 (tp-100) cc_final: 0.7377 (tt0) REVERT: A 322 LYS cc_start: 0.7952 (tttm) cc_final: 0.7744 (tppt) REVERT: A 387 LYS cc_start: 0.7835 (mttt) cc_final: 0.7569 (mptt) REVERT: B 229 ARG cc_start: 0.7243 (mmt180) cc_final: 0.6692 (ttp80) REVERT: B 230 LYS cc_start: 0.8478 (tptt) cc_final: 0.8143 (ttmt) REVERT: B 261 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7367 (tt0) REVERT: B 387 LYS cc_start: 0.7898 (mttt) cc_final: 0.7579 (mptt) outliers start: 14 outliers final: 10 residues processed: 97 average time/residue: 0.2200 time to fit residues: 27.7136 Evaluate side-chains 92 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 6434 Z= 0.164 Angle : 0.479 6.835 8692 Z= 0.249 Chirality : 0.037 0.126 996 Planarity : 0.004 0.044 1090 Dihedral : 3.696 15.809 858 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 15.23 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.04 (0.31), residues: 792 helix: 2.87 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.62 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.013 0.001 PHE B 206 TYR 0.008 0.001 TYR B 39 ARG 0.002 0.000 ARG B 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.687 Fit side-chains REVERT: A 230 LYS cc_start: 0.8428 (tptt) cc_final: 0.8115 (ttmt) REVERT: A 261 GLN cc_start: 0.7852 (tp-100) cc_final: 0.7407 (tt0) REVERT: A 322 LYS cc_start: 0.7953 (tttm) cc_final: 0.7727 (tppt) REVERT: A 387 LYS cc_start: 0.7807 (mttt) cc_final: 0.7544 (mptt) REVERT: B 230 LYS cc_start: 0.8426 (tptt) cc_final: 0.8132 (ttmt) REVERT: B 261 GLN cc_start: 0.7855 (tp-100) cc_final: 0.7395 (tt0) REVERT: B 322 LYS cc_start: 0.7955 (tttm) cc_final: 0.7706 (tptt) REVERT: B 387 LYS cc_start: 0.7848 (mttt) cc_final: 0.7583 (mptt) outliers start: 19 outliers final: 14 residues processed: 104 average time/residue: 0.2097 time to fit residues: 28.5333 Evaluate side-chains 98 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 285 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN ** B 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6434 Z= 0.155 Angle : 0.482 7.260 8692 Z= 0.249 Chirality : 0.036 0.130 996 Planarity : 0.004 0.047 1090 Dihedral : 3.685 15.805 858 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.59 % Allowed : 16.67 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.13 (0.31), residues: 792 helix: 2.93 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.59 (0.56), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 57 HIS 0.003 0.001 HIS B 259 PHE 0.012 0.001 PHE B 206 TYR 0.007 0.001 TYR B 39 ARG 0.002 0.000 ARG B 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.735 Fit side-chains REVERT: A 41 TYR cc_start: 0.6658 (m-80) cc_final: 0.6321 (m-10) REVERT: A 230 LYS cc_start: 0.8338 (tptt) cc_final: 0.8036 (ttmt) REVERT: A 261 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7413 (tt0) REVERT: A 322 LYS cc_start: 0.7955 (tttm) cc_final: 0.7694 (tptt) REVERT: A 387 LYS cc_start: 0.7813 (mttt) cc_final: 0.7545 (mptt) REVERT: B 230 LYS cc_start: 0.8342 (tptt) cc_final: 0.8048 (ttmt) REVERT: B 261 GLN cc_start: 0.7823 (tp-100) cc_final: 0.7403 (tt0) REVERT: B 322 LYS cc_start: 0.7946 (tttm) cc_final: 0.7699 (tptt) REVERT: B 387 LYS cc_start: 0.7825 (mttt) cc_final: 0.7565 (mptt) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.1904 time to fit residues: 26.7141 Evaluate side-chains 106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 14 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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: 0.7854 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6434 Z= 0.154 Angle : 0.492 7.953 8692 Z= 0.253 Chirality : 0.037 0.132 996 Planarity : 0.004 0.047 1090 Dihedral : 3.656 14.978 858 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.30 % Allowed : 17.53 % Favored : 80.17 % 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: 3.10 (0.31), residues: 792 helix: 2.89 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.75 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.003 0.001 HIS B 259 PHE 0.028 0.001 PHE B 206 TYR 0.014 0.001 TYR A 50 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.704 Fit side-chains REVERT: A 41 TYR cc_start: 0.6630 (m-80) cc_final: 0.5778 (m-80) REVERT: A 194 SER cc_start: 0.8450 (OUTLIER) cc_final: 0.8030 (m) REVERT: A 230 LYS cc_start: 0.8346 (tptt) cc_final: 0.8058 (ttmt) REVERT: A 261 GLN cc_start: 0.7778 (tp-100) cc_final: 0.7408 (tt0) REVERT: A 322 LYS cc_start: 0.7914 (tttm) cc_final: 0.7625 (tptt) REVERT: A 324 MET cc_start: 0.7631 (ttm) cc_final: 0.7282 (ttm) REVERT: A 387 LYS cc_start: 0.7853 (mttt) cc_final: 0.7542 (mptt) REVERT: B 41 TYR cc_start: 0.6629 (m-80) cc_final: 0.5778 (m-80) REVERT: B 230 LYS cc_start: 0.8342 (tptt) cc_final: 0.8062 (ttmt) REVERT: B 261 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7388 (tt0) REVERT: B 322 LYS cc_start: 0.7931 (tttm) cc_final: 0.7634 (tptt) REVERT: B 324 MET cc_start: 0.7624 (ttm) cc_final: 0.7273 (ttm) REVERT: B 387 LYS cc_start: 0.7859 (mttt) cc_final: 0.7578 (mptt) outliers start: 16 outliers final: 14 residues processed: 112 average time/residue: 0.1870 time to fit residues: 27.9218 Evaluate side-chains 112 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 168 THR Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.7873 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6434 Z= 0.174 Angle : 0.505 8.000 8692 Z= 0.262 Chirality : 0.037 0.131 996 Planarity : 0.004 0.047 1090 Dihedral : 3.685 15.972 858 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.44 % Allowed : 17.96 % Favored : 79.60 % 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: 3.03 (0.31), residues: 792 helix: 2.84 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.79 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 255 HIS 0.003 0.001 HIS B 259 PHE 0.028 0.001 PHE A 206 TYR 0.025 0.002 TYR B 50 ARG 0.002 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.731 Fit side-chains REVERT: A 230 LYS cc_start: 0.8325 (tptt) cc_final: 0.8049 (ttmt) REVERT: A 261 GLN cc_start: 0.7767 (tp-100) cc_final: 0.7402 (tt0) REVERT: A 322 LYS cc_start: 0.7948 (tttm) cc_final: 0.7694 (tptt) REVERT: A 324 MET cc_start: 0.7701 (ttm) cc_final: 0.7337 (ttm) REVERT: A 387 LYS cc_start: 0.7848 (mttt) cc_final: 0.7555 (mptt) REVERT: B 41 TYR cc_start: 0.6658 (m-80) cc_final: 0.5830 (m-80) REVERT: B 230 LYS cc_start: 0.8330 (tptt) cc_final: 0.8068 (ttmt) REVERT: B 261 GLN cc_start: 0.7751 (tp-100) cc_final: 0.7370 (tt0) REVERT: B 322 LYS cc_start: 0.7953 (tttm) cc_final: 0.7695 (tptt) REVERT: B 324 MET cc_start: 0.7711 (ttm) cc_final: 0.7346 (ttm) REVERT: B 332 ILE cc_start: 0.7064 (mt) cc_final: 0.6395 (tt) REVERT: B 387 LYS cc_start: 0.7838 (mttt) cc_final: 0.7576 (mptt) outliers start: 17 outliers final: 14 residues processed: 116 average time/residue: 0.2038 time to fit residues: 31.2472 Evaluate side-chains 116 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 168 THR Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6434 Z= 0.204 Angle : 0.524 8.150 8692 Z= 0.271 Chirality : 0.038 0.131 996 Planarity : 0.004 0.047 1090 Dihedral : 3.733 16.263 858 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.44 % Allowed : 18.53 % Favored : 79.02 % 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: 3.00 (0.31), residues: 792 helix: 2.84 (0.20), residues: 654 sheet: None (None), residues: 0 loop : -2.65 (0.55), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 129 HIS 0.002 0.001 HIS A 259 PHE 0.028 0.001 PHE A 206 TYR 0.025 0.002 TYR B 236 ARG 0.002 0.000 ARG A 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.719 Fit side-chains REVERT: A 230 LYS cc_start: 0.8282 (tptt) cc_final: 0.8026 (ttmt) REVERT: A 261 GLN cc_start: 0.7786 (tp-100) cc_final: 0.7394 (tt0) REVERT: A 322 LYS cc_start: 0.7971 (tttm) cc_final: 0.7755 (tppt) REVERT: A 324 MET cc_start: 0.7755 (ttm) cc_final: 0.7403 (ttm) REVERT: A 387 LYS cc_start: 0.7854 (mttt) cc_final: 0.7567 (mptt) REVERT: B 230 LYS cc_start: 0.8311 (tptt) cc_final: 0.8058 (ttmt) REVERT: B 261 GLN cc_start: 0.7784 (tp-100) cc_final: 0.7398 (tt0) REVERT: B 322 LYS cc_start: 0.7973 (tttm) cc_final: 0.7755 (tppt) REVERT: B 324 MET cc_start: 0.7751 (ttm) cc_final: 0.7399 (ttm) REVERT: B 387 LYS cc_start: 0.7842 (mttt) cc_final: 0.7563 (mptt) outliers start: 17 outliers final: 13 residues processed: 115 average time/residue: 0.1977 time to fit residues: 29.9670 Evaluate side-chains 113 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain B residue 56 MET Chi-restraints excluded: chain B residue 179 ILE Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3866 r_free = 0.3866 target = 0.163842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122100 restraints weight = 7364.655| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.05 r_work: 0.3262 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6434 Z= 0.168 Angle : 0.515 8.346 8692 Z= 0.265 Chirality : 0.037 0.129 996 Planarity : 0.004 0.047 1090 Dihedral : 3.658 15.793 858 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.59 % Allowed : 18.53 % Favored : 78.88 % 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: 3.11 (0.31), residues: 792 helix: 2.89 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.71 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 129 HIS 0.003 0.001 HIS B 259 PHE 0.027 0.001 PHE A 206 TYR 0.025 0.001 TYR A 236 ARG 0.009 0.000 ARG A 154 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1501.91 seconds wall clock time: 28 minutes 32.51 seconds (1712.51 seconds total)