Starting phenix.real_space_refine on Fri Dec 27 17:31:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7voj_32050/12_2024/7voj_32050.cif Found real_map, /net/cci-nas-00/data/ceres_data/7voj_32050/12_2024/7voj_32050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7voj_32050/12_2024/7voj_32050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7voj_32050/12_2024/7voj_32050.map" model { file = "/net/cci-nas-00/data/ceres_data/7voj_32050/12_2024/7voj_32050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7voj_32050/12_2024/7voj_32050.cif" } resolution = 3.0 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 Anisotropic ADP refinement not supported. Converting 16 atoms to isotropic. 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 Al 2 5.89 5 S 32 5.16 5 C 4074 2.51 5 N 1052 2.21 5 O 1158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6318 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3150 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 12, 'TRANS': 387} Chain breaks: 1 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Unusual residues: {' AL': 1, 'ACY': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: B Time building chain proxies: 5.19, per 1000 atoms: 0.82 Number of scatterers: 6318 At special positions: 0 Unit cell: (84.162, 84.162, 113.568, 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 32 16.00 Al 2 13.00 O 1158 8.00 N 1052 7.00 C 4074 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 883.6 milliseconds 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: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 1 through 18 removed outlier: 3.753A pdb=" N ASP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 42 removed outlier: 3.723A pdb=" N GLY A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 66 removed outlier: 3.879A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 102 removed outlier: 3.844A 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 133 Processing helix chain 'A' and resid 134 through 150 Processing helix chain 'A' and resid 156 through 183 Processing helix chain 'A' and resid 187 through 214 Processing helix chain 'A' and resid 223 through 241 removed outlier: 4.754A pdb=" N ARG A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 241 " --> pdb=" O LYS A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 removed outlier: 3.716A pdb=" N GLU A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 294 Processing helix chain 'A' and resid 299 through 305 removed outlier: 3.750A pdb=" N LYS A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 330 removed outlier: 3.727A pdb=" N LEU A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 removed outlier: 3.914A pdb=" N ILE A 339 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 344 " --> pdb=" O HIS A 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 399 Processing helix chain 'B' and resid 2 through 18 removed outlier: 3.753A pdb=" N ASP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 42 removed outlier: 3.723A pdb=" N GLY B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.879A pdb=" N VAL B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 102 removed outlier: 3.844A 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 133 Processing helix chain 'B' and resid 134 through 150 Processing helix chain 'B' and resid 156 through 183 Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 223 through 241 removed outlier: 4.754A pdb=" N ARG B 235 " --> pdb=" O LYS B 231 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N TYR B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 241 " --> pdb=" O LYS B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.716A pdb=" N GLU B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 294 Processing helix chain 'B' and resid 299 through 305 removed outlier: 3.750A pdb=" N LYS B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 330 removed outlier: 3.727A pdb=" N LEU B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 removed outlier: 3.914A pdb=" N ILE B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER B 344 " --> pdb=" O HIS B 340 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 356 " --> pdb=" O SER B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 399 521 hydrogen bonds defined for protein. 1563 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: 1.70 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1610 1.33 - 1.45: 1186 1.45 - 1.57: 3588 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 6440 Sorted by residual: bond pdb=" C CYS A 184 " pdb=" O CYS A 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C CYS B 184 " pdb=" O CYS B 184 " ideal model delta sigma weight residual 1.249 1.229 0.020 8.50e-03 1.38e+04 5.39e+00 bond pdb=" C GLY A 102 " pdb=" N ALA A 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" C GLY B 102 " pdb=" N ALA B 103 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.52e-02 4.33e+03 4.40e+00 bond pdb=" CA TYR B 50 " pdb=" C TYR B 50 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.37e-02 5.33e+03 3.59e+00 ... (remaining 6435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 8322 2.18 - 4.36: 328 4.36 - 6.54: 24 6.54 - 8.72: 18 8.72 - 10.90: 6 Bond angle restraints: 8698 Sorted by residual: angle pdb=" N PHE B 51 " pdb=" CA PHE B 51 " pdb=" C PHE B 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE A 51 " pdb=" CA PHE A 51 " pdb=" C PHE A 51 " ideal model delta sigma weight residual 111.28 122.18 -10.90 1.09e+00 8.42e-01 1.00e+02 angle pdb=" N PHE B 182 " pdb=" CA PHE B 182 " pdb=" C PHE B 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N PHE A 182 " pdb=" CA PHE A 182 " pdb=" C PHE A 182 " ideal model delta sigma weight residual 113.17 122.72 -9.55 1.26e+00 6.30e-01 5.75e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 110.62 117.44 -6.82 1.02e+00 9.61e-01 4.48e+01 ... (remaining 8693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.31: 3354 14.31 - 28.62: 372 28.62 - 42.93: 88 42.93 - 57.24: 30 57.24 - 71.55: 6 Dihedral angle restraints: 3850 sinusoidal: 1526 harmonic: 2324 Sorted by residual: dihedral pdb=" CA ARG B 154 " pdb=" C ARG B 154 " pdb=" N ASP B 155 " pdb=" CA ASP B 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ARG A 154 " pdb=" C ARG A 154 " pdb=" N ASP A 155 " pdb=" CA ASP A 155 " ideal model delta harmonic sigma weight residual 180.00 -153.71 -26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 299 " pdb=" C PRO A 299 " pdb=" N VAL A 300 " pdb=" CA VAL A 300 " ideal model delta harmonic sigma weight residual -180.00 -158.47 -21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 3847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 866 0.081 - 0.162: 110 0.162 - 0.243: 14 0.243 - 0.324: 2 0.324 - 0.404: 4 Chirality restraints: 996 Sorted by residual: chirality pdb=" CA PHE B 182 " pdb=" N PHE B 182 " pdb=" C PHE B 182 " pdb=" CB PHE B 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 182 " pdb=" N PHE A 182 " pdb=" C PHE A 182 " pdb=" CB PHE A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CA PHE A 51 " pdb=" N PHE A 51 " pdb=" C PHE A 51 " pdb=" CB PHE A 51 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 993 not shown) Planarity restraints: 1094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 180 " 0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER B 180 " -0.068 2.00e-02 2.50e+03 pdb=" O SER B 180 " 0.026 2.00e-02 2.50e+03 pdb=" N ILE B 181 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " -0.019 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C SER A 180 " 0.068 2.00e-02 2.50e+03 pdb=" O SER A 180 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A 181 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B 184 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO B 185 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.042 5.00e-02 4.00e+02 ... (remaining 1091 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 96 2.63 - 3.20: 5470 3.20 - 3.76: 9637 3.76 - 4.33: 12737 4.33 - 4.90: 21603 Nonbonded interactions: 49543 Sorted by model distance: nonbonded pdb=" OD1 ASP A 160 " pdb="AL AL A 603 " model vdw 2.061 2.020 nonbonded pdb=" OD1 ASP B 160 " pdb="AL AL B 603 " model vdw 2.061 2.020 nonbonded pdb=" OD2 ASP B 160 " pdb="AL AL B 603 " model vdw 2.113 2.020 nonbonded pdb=" OD2 ASP A 160 " pdb="AL AL A 603 " model vdw 2.113 2.020 nonbonded pdb=" O ACY B 601 " pdb="AL AL B 603 " model vdw 2.116 2.020 ... (remaining 49538 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.170 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:13.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.008 0.057 6440 Z= 0.529 Angle : 1.008 10.902 8698 Z= 0.626 Chirality : 0.062 0.404 996 Planarity : 0.007 0.071 1094 Dihedral : 13.588 71.548 2346 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 1.73 % Allowed : 12.39 % Favored : 85.88 % 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: -2.46 (0.26), residues: 792 helix: -1.27 (0.17), residues: 664 sheet: None (None), residues: 0 loop : -2.54 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 129 HIS 0.003 0.001 HIS A 340 PHE 0.016 0.002 PHE B 134 TYR 0.015 0.002 TYR A 236 ARG 0.003 0.001 ARG A 154 *********************** 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 151 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.663 Fit side-chains REVERT: A 5 ARG cc_start: 0.6469 (mtt-85) cc_final: 0.5751 (mmp-170) REVERT: A 96 GLN cc_start: 0.7767 (mm110) cc_final: 0.7501 (mm-40) REVERT: A 201 ASP cc_start: 0.7736 (t0) cc_final: 0.7447 (t70) REVERT: A 209 ASP cc_start: 0.7532 (m-30) cc_final: 0.7159 (m-30) REVERT: A 226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p) REVERT: A 370 SER cc_start: 0.9002 (m) cc_final: 0.8750 (p) REVERT: B 5 ARG cc_start: 0.6463 (mtt-85) cc_final: 0.5741 (mmp-170) REVERT: B 96 GLN cc_start: 0.7758 (mm110) cc_final: 0.7491 (mm-40) REVERT: B 201 ASP cc_start: 0.7733 (t0) cc_final: 0.7444 (t70) REVERT: B 209 ASP cc_start: 0.7539 (m-30) cc_final: 0.7165 (m-30) REVERT: B 226 VAL cc_start: 0.6478 (OUTLIER) cc_final: 0.6153 (p) outliers start: 12 outliers final: 10 residues processed: 149 average time/residue: 1.0667 time to fit residues: 167.5493 Evaluate side-chains 103 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 HIS A 96 GLN A 266 HIS A 289 ASN A 293 ASN A 330 GLN A 403 ASN B 24 HIS B 96 GLN B 266 HIS B 289 ASN B 293 ASN B 330 GLN B 403 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6440 Z= 0.174 Angle : 0.533 5.749 8698 Z= 0.295 Chirality : 0.037 0.137 996 Planarity : 0.004 0.042 1094 Dihedral : 5.671 55.926 874 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.88 % Allowed : 19.74 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.30), residues: 792 helix: 1.27 (0.20), residues: 668 sheet: None (None), residues: 0 loop : -2.65 (0.53), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 129 HIS 0.004 0.001 HIS B 193 PHE 0.020 0.001 PHE A 206 TYR 0.011 0.001 TYR B 50 ARG 0.002 0.000 ARG B 235 *********************** 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 125 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.716 Fit side-chains REVERT: A 5 ARG cc_start: 0.6661 (mtt-85) cc_final: 0.6272 (mmp-170) REVERT: A 201 ASP cc_start: 0.7726 (t0) cc_final: 0.7470 (t70) REVERT: A 209 ASP cc_start: 0.7053 (m-30) cc_final: 0.6624 (m-30) REVERT: B 5 ARG cc_start: 0.6618 (mtt-85) cc_final: 0.5923 (mmp-170) REVERT: B 201 ASP cc_start: 0.7726 (t0) cc_final: 0.7468 (t70) REVERT: B 209 ASP cc_start: 0.7064 (m-30) cc_final: 0.6635 (m-30) outliers start: 20 outliers final: 8 residues processed: 121 average time/residue: 1.0109 time to fit residues: 129.7614 Evaluate side-chains 94 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 86 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 355 LEU 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: 0.0980 chunk 22 optimal weight: 0.0970 chunk 60 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6440 Z= 0.146 Angle : 0.483 6.021 8698 Z= 0.257 Chirality : 0.035 0.140 996 Planarity : 0.004 0.043 1094 Dihedral : 4.754 55.102 862 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.31 % Allowed : 20.89 % Favored : 75.79 % 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: 2.45 (0.31), residues: 792 helix: 2.40 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.51 (0.50), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 129 HIS 0.001 0.000 HIS B 193 PHE 0.016 0.001 PHE A 206 TYR 0.011 0.001 TYR B 50 ARG 0.007 0.000 ARG A 9 *********************** 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 127 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.694 Fit side-chains REVERT: A 5 ARG cc_start: 0.6906 (mtt-85) cc_final: 0.6205 (mmp-170) REVERT: A 201 ASP cc_start: 0.7623 (t0) cc_final: 0.7338 (t70) REVERT: A 209 ASP cc_start: 0.7116 (m-30) cc_final: 0.6597 (m-30) REVERT: B 5 ARG cc_start: 0.6644 (mtt-85) cc_final: 0.6207 (mmp-170) REVERT: B 201 ASP cc_start: 0.7624 (t0) cc_final: 0.7345 (t0) REVERT: B 209 ASP cc_start: 0.7123 (m-30) cc_final: 0.6602 (m-30) outliers start: 23 outliers final: 5 residues processed: 115 average time/residue: 0.8957 time to fit residues: 109.9226 Evaluate side-chains 92 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 LEU 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: 0.8980 chunk 37 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 0.1980 chunk 77 optimal weight: 0.0970 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 0.3980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6440 Z= 0.139 Angle : 0.456 5.429 8698 Z= 0.246 Chirality : 0.035 0.137 996 Planarity : 0.003 0.042 1094 Dihedral : 3.992 36.020 860 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.31 % Allowed : 23.49 % Favored : 74.21 % 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: 2.98 (0.31), residues: 792 helix: 2.75 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -2.42 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 129 HIS 0.002 0.000 HIS A 193 PHE 0.008 0.001 PHE A 206 TYR 0.008 0.001 TYR B 50 ARG 0.007 0.000 ARG B 9 *********************** 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 117 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.760 Fit side-chains REVERT: A 5 ARG cc_start: 0.6936 (mtt-85) cc_final: 0.6243 (mmp-170) REVERT: A 201 ASP cc_start: 0.7606 (t0) cc_final: 0.7313 (t0) REVERT: A 209 ASP cc_start: 0.7132 (m-30) cc_final: 0.6594 (m-30) REVERT: A 291 TYR cc_start: 0.7900 (t80) cc_final: 0.7653 (t80) REVERT: B 5 ARG cc_start: 0.6950 (mtt-85) cc_final: 0.6267 (mmp-170) REVERT: B 201 ASP cc_start: 0.7605 (t0) cc_final: 0.7310 (t0) REVERT: B 209 ASP cc_start: 0.7138 (m-30) cc_final: 0.6597 (m-30) REVERT: B 291 TYR cc_start: 0.7906 (t80) cc_final: 0.7659 (t80) outliers start: 16 outliers final: 8 residues processed: 110 average time/residue: 0.9738 time to fit residues: 113.9698 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL 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: 4.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6440 Z= 0.168 Angle : 0.494 6.803 8698 Z= 0.261 Chirality : 0.035 0.136 996 Planarity : 0.003 0.042 1094 Dihedral : 3.852 17.845 860 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.88 % Allowed : 23.34 % Favored : 73.78 % 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: 3.17 (0.31), residues: 792 helix: 2.92 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -2.41 (0.49), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 129 HIS 0.003 0.001 HIS B 193 PHE 0.010 0.001 PHE B 206 TYR 0.008 0.001 TYR A 236 ARG 0.006 0.000 ARG B 9 *********************** 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 121 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.741 Fit side-chains REVERT: A 5 ARG cc_start: 0.7023 (mtt-85) cc_final: 0.6434 (mmp-170) REVERT: A 147 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8587 (tt) REVERT: A 201 ASP cc_start: 0.7641 (t0) cc_final: 0.7426 (t0) REVERT: A 209 ASP cc_start: 0.7262 (m-30) cc_final: 0.6679 (m-30) REVERT: A 291 TYR cc_start: 0.7989 (t80) cc_final: 0.7738 (t80) REVERT: A 334 SER cc_start: 0.8650 (m) cc_final: 0.8329 (p) REVERT: B 5 ARG cc_start: 0.7006 (mtt-85) cc_final: 0.6433 (mmp-170) REVERT: B 147 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8590 (tt) REVERT: B 201 ASP cc_start: 0.7643 (t0) cc_final: 0.7428 (t0) REVERT: B 209 ASP cc_start: 0.7227 (m-30) cc_final: 0.6650 (m-30) REVERT: B 291 TYR cc_start: 0.7997 (t80) cc_final: 0.7746 (t80) REVERT: B 307 GLU cc_start: 0.6582 (pm20) cc_final: 0.6378 (pm20) REVERT: B 334 SER cc_start: 0.8637 (m) cc_final: 0.8285 (p) outliers start: 20 outliers final: 12 residues processed: 117 average time/residue: 0.8683 time to fit residues: 108.6024 Evaluate side-chains 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 45 optimal weight: 0.0170 chunk 19 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.4105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6440 Z= 0.138 Angle : 0.472 6.646 8698 Z= 0.248 Chirality : 0.035 0.124 996 Planarity : 0.003 0.038 1094 Dihedral : 3.727 17.589 858 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.87 % Allowed : 24.50 % Favored : 73.63 % 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: 3.41 (0.30), residues: 792 helix: 3.06 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.29 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 129 HIS 0.002 0.001 HIS A 95 PHE 0.007 0.001 PHE A 206 TYR 0.008 0.001 TYR A 236 ARG 0.006 0.000 ARG A 9 *********************** 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 116 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.780 Fit side-chains REVERT: A 5 ARG cc_start: 0.7000 (mtt-85) cc_final: 0.6437 (mmp-170) REVERT: A 201 ASP cc_start: 0.7561 (t0) cc_final: 0.7352 (t0) REVERT: A 209 ASP cc_start: 0.7185 (m-30) cc_final: 0.6533 (m-30) REVERT: A 291 TYR cc_start: 0.7849 (t80) cc_final: 0.7578 (t80) REVERT: A 334 SER cc_start: 0.8597 (m) cc_final: 0.8289 (p) REVERT: B 5 ARG cc_start: 0.6997 (mtt-85) cc_final: 0.6415 (mmp-170) REVERT: B 201 ASP cc_start: 0.7560 (t0) cc_final: 0.7352 (t0) REVERT: B 209 ASP cc_start: 0.7190 (m-30) cc_final: 0.6537 (m-30) REVERT: B 291 TYR cc_start: 0.7855 (t80) cc_final: 0.7584 (t80) REVERT: B 334 SER cc_start: 0.8569 (m) cc_final: 0.8265 (p) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.9707 time to fit residues: 111.6013 Evaluate side-chains 98 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 205 HIS Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 35 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6440 Z= 0.152 Angle : 0.487 8.764 8698 Z= 0.258 Chirality : 0.035 0.129 996 Planarity : 0.003 0.038 1094 Dihedral : 3.701 16.362 858 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.73 % Allowed : 26.22 % Favored : 72.05 % 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: 3.52 (0.30), residues: 792 helix: 3.13 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -2.22 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 129 HIS 0.002 0.001 HIS B 193 PHE 0.008 0.001 PHE A 206 TYR 0.007 0.001 TYR B 236 ARG 0.007 0.000 ARG B 9 *********************** 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 109 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 97 time to evaluate : 0.644 Fit side-chains REVERT: A 5 ARG cc_start: 0.7029 (mtt-85) cc_final: 0.6351 (mmp-170) REVERT: A 7 ILE cc_start: 0.8369 (tt) cc_final: 0.8164 (mt) REVERT: A 201 ASP cc_start: 0.7614 (t0) cc_final: 0.7410 (t0) REVERT: A 209 ASP cc_start: 0.7167 (m-30) cc_final: 0.6524 (m-30) REVERT: A 334 SER cc_start: 0.8600 (m) cc_final: 0.8321 (p) REVERT: B 5 ARG cc_start: 0.7011 (mtt-85) cc_final: 0.6385 (mmp-170) REVERT: B 163 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7678 (mt-10) REVERT: B 201 ASP cc_start: 0.7568 (t0) cc_final: 0.7359 (t0) REVERT: B 209 ASP cc_start: 0.7169 (m-30) cc_final: 0.6530 (m-30) REVERT: B 334 SER cc_start: 0.8539 (m) cc_final: 0.8134 (p) outliers start: 12 outliers final: 6 residues processed: 105 average time/residue: 0.9391 time to fit residues: 105.2154 Evaluate side-chains 89 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN B 293 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6440 Z= 0.218 Angle : 0.558 9.584 8698 Z= 0.291 Chirality : 0.037 0.132 996 Planarity : 0.003 0.038 1094 Dihedral : 3.884 16.841 858 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.16 % Allowed : 25.79 % Favored : 72.05 % 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: 3.34 (0.30), residues: 792 helix: 2.99 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.20 (0.52), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 129 HIS 0.004 0.001 HIS B 193 PHE 0.015 0.001 PHE B 206 TYR 0.009 0.001 TYR A 236 ARG 0.006 0.000 ARG A 9 *********************** 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 111 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.758 Fit side-chains REVERT: A 5 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6585 (mmp-170) REVERT: A 7 ILE cc_start: 0.8386 (tt) cc_final: 0.8163 (mt) REVERT: A 147 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8628 (tt) REVERT: A 201 ASP cc_start: 0.7634 (t0) cc_final: 0.7423 (t0) REVERT: A 209 ASP cc_start: 0.7230 (m-30) cc_final: 0.6670 (m-30) REVERT: A 291 TYR cc_start: 0.8115 (t80) cc_final: 0.7815 (t80) REVERT: A 332 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8351 (tt) REVERT: A 334 SER cc_start: 0.8568 (m) cc_final: 0.8194 (p) REVERT: A 372 MET cc_start: 0.8728 (mmt) cc_final: 0.8445 (mmm) REVERT: B 5 ARG cc_start: 0.7058 (mtt-85) cc_final: 0.6524 (mmp-170) REVERT: B 7 ILE cc_start: 0.8384 (tt) cc_final: 0.8170 (mt) REVERT: B 201 ASP cc_start: 0.7636 (t0) cc_final: 0.7423 (t0) REVERT: B 209 ASP cc_start: 0.7175 (m-30) cc_final: 0.6608 (m-30) REVERT: B 291 TYR cc_start: 0.8115 (t80) cc_final: 0.7817 (t80) REVERT: B 334 SER cc_start: 0.8416 (m) cc_final: 0.8033 (p) REVERT: B 372 MET cc_start: 0.8693 (mmt) cc_final: 0.8410 (mmm) outliers start: 15 outliers final: 8 residues processed: 107 average time/residue: 0.9047 time to fit residues: 103.2761 Evaluate side-chains 100 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 0.0980 chunk 46 optimal weight: 0.8980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6440 Z= 0.162 Angle : 0.532 10.308 8698 Z= 0.275 Chirality : 0.036 0.154 996 Planarity : 0.003 0.038 1094 Dihedral : 3.823 16.786 858 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.30 % Allowed : 27.38 % Favored : 71.33 % 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: 3.55 (0.30), residues: 792 helix: 3.19 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.47 (0.49), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 129 HIS 0.002 0.001 HIS A 95 PHE 0.009 0.001 PHE B 206 TYR 0.013 0.001 TYR B 50 ARG 0.008 0.000 ARG A 9 *********************** 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 107 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.784 Fit side-chains REVERT: A 5 ARG cc_start: 0.7099 (mtt-85) cc_final: 0.6547 (mmp-170) REVERT: A 7 ILE cc_start: 0.8399 (tt) cc_final: 0.8164 (mt) REVERT: A 201 ASP cc_start: 0.7642 (t0) cc_final: 0.7434 (t0) REVERT: A 209 ASP cc_start: 0.7144 (m-30) cc_final: 0.6517 (m-30) REVERT: A 291 TYR cc_start: 0.8108 (t80) cc_final: 0.7803 (t80) REVERT: A 334 SER cc_start: 0.8323 (m) cc_final: 0.7918 (p) REVERT: A 405 MET cc_start: 0.6035 (mmt) cc_final: 0.5536 (mtp) REVERT: B 5 ARG cc_start: 0.7023 (mtt-85) cc_final: 0.6531 (mmp-170) REVERT: B 7 ILE cc_start: 0.8391 (tt) cc_final: 0.8165 (mt) REVERT: B 201 ASP cc_start: 0.7650 (t0) cc_final: 0.7439 (t0) REVERT: B 209 ASP cc_start: 0.7147 (m-30) cc_final: 0.6544 (m-30) REVERT: B 291 TYR cc_start: 0.8109 (t80) cc_final: 0.7806 (t80) REVERT: B 334 SER cc_start: 0.8359 (m) cc_final: 0.8072 (p) outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 0.9925 time to fit residues: 109.6767 Evaluate side-chains 97 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.0870 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.7562 ------------------------------------------------------------------------------- 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: 0.7906 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6440 Z= 0.167 Angle : 0.531 9.890 8698 Z= 0.278 Chirality : 0.035 0.138 996 Planarity : 0.003 0.039 1094 Dihedral : 3.771 16.231 858 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.44 % Allowed : 27.52 % Favored : 71.04 % 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: 3.54 (0.30), residues: 792 helix: 3.20 (0.19), residues: 658 sheet: None (None), residues: 0 loop : -2.53 (0.48), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 129 HIS 0.002 0.001 HIS A 95 PHE 0.015 0.001 PHE A 264 TYR 0.013 0.001 TYR B 50 ARG 0.008 0.000 ARG B 9 ********************** 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 102 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.751 Fit side-chains REVERT: A 5 ARG cc_start: 0.7114 (mtt-85) cc_final: 0.6597 (mmp-170) REVERT: A 7 ILE cc_start: 0.8405 (tt) cc_final: 0.8169 (mt) REVERT: A 201 ASP cc_start: 0.7640 (t0) cc_final: 0.7422 (t0) REVERT: A 209 ASP cc_start: 0.7131 (m-30) cc_final: 0.6502 (m-30) REVERT: A 334 SER cc_start: 0.8402 (m) cc_final: 0.8052 (p) REVERT: A 372 MET cc_start: 0.8658 (mmt) cc_final: 0.8376 (mmm) REVERT: A 405 MET cc_start: 0.6088 (mmt) cc_final: 0.5626 (mtp) REVERT: B 5 ARG cc_start: 0.7035 (mtt-85) cc_final: 0.6533 (mmp-170) REVERT: B 7 ILE cc_start: 0.8399 (tt) cc_final: 0.8172 (mt) REVERT: B 163 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7666 (mt-10) REVERT: B 201 ASP cc_start: 0.7647 (t0) cc_final: 0.7437 (t0) REVERT: B 209 ASP cc_start: 0.7134 (m-30) cc_final: 0.6505 (m-30) REVERT: B 307 GLU cc_start: 0.6484 (pm20) cc_final: 0.6235 (pm20) REVERT: B 334 SER cc_start: 0.8331 (m) cc_final: 0.7968 (p) REVERT: B 405 MET cc_start: 0.6036 (mmt) cc_final: 0.5437 (mtp) outliers start: 10 outliers final: 6 residues processed: 99 average time/residue: 0.9760 time to fit residues: 102.7718 Evaluate side-chains 95 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 HIS Chi-restraints excluded: chain A residue 281 CYS Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 281 CYS Chi-restraints excluded: chain B residue 363 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.155113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105935 restraints weight = 7365.189| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.14 r_work: 0.3087 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6440 Z= 0.205 Angle : 0.558 10.026 8698 Z= 0.291 Chirality : 0.036 0.134 996 Planarity : 0.003 0.039 1094 Dihedral : 3.842 16.508 858 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.86 % Allowed : 28.24 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.47 (0.30), residues: 792 helix: 3.10 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.27 (0.51), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 129 HIS 0.004 0.001 HIS B 193 PHE 0.015 0.001 PHE A 206 TYR 0.014 0.001 TYR B 50 ARG 0.008 0.000 ARG A 9 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2384.70 seconds wall clock time: 45 minutes 6.47 seconds (2706.47 seconds total)