Starting phenix.real_space_refine on Tue Feb 13 06:08:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hf3_34711/02_2024/8hf3_34711_updated.pdb" } resolution = 3.4 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= 0.003 sd= 0.091 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 1 5.49 5 S 25 5.16 5 C 2267 2.51 5 N 566 2.21 5 O 603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "B GLU 35": "OE1" <-> "OE2" Residue "B GLU 56": "OE1" <-> "OE2" Residue "B GLU 58": "OE1" <-> "OE2" Residue "B GLU 99": "OE1" <-> "OE2" Residue "B GLU 102": "OE1" <-> "OE2" Residue "B GLU 129": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 3464 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2353 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 19, 'TRANS': 275} Chain: "B" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1007 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "A" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 104 Unusual residues: {' ZN': 2, 'PLM': 4, 'PX2': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PLM:plan-1': 4} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1057 SG CYS A 141 54.646 29.363 44.140 1.00 68.60 S ATOM 1082 SG CYS A 144 50.915 26.987 43.066 1.00 71.50 S ATOM 1215 SG CYS A 161 51.365 30.725 43.702 1.00 40.44 S ATOM 1173 SG CYS A 155 47.449 31.773 52.718 1.00 47.66 S ATOM 1193 SG CYS A 158 44.095 28.641 52.624 1.00 54.92 S ATOM 1333 SG CYS A 175 44.200 32.170 51.538 1.00 29.16 S Time building chain proxies: 2.42, per 1000 atoms: 0.70 Number of scatterers: 3464 At special positions: 0 Unit cell: (87.2456, 67.9509, 98.9902, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 25 16.00 P 1 15.00 O 603 8.00 N 566 7.00 C 2267 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 - 3.50 Amino acid : False - 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 675.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 141 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 144 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 161 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 154 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 168 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 175 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 158 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 155 " Number of angles added : 6 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 14 helices and 3 sheets defined 46.1% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 25 through 27 No H-bonds generated for 'chain 'A' and resid 25 through 27' Processing helix chain 'A' and resid 36 through 55 removed outlier: 3.614A pdb=" N LEU A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 68 through 88 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 182 through 210 Processing helix chain 'A' and resid 215 through 221 Processing helix chain 'A' and resid 224 through 248 removed outlier: 4.699A pdb=" N GLY A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 261 removed outlier: 3.628A pdb=" N LYS A 261 " --> pdb=" O ASN A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'B' and resid 40 through 57 Processing helix chain 'B' and resid 63 through 74 removed outlier: 3.973A pdb=" N THR B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 85 through 104 removed outlier: 4.384A pdb=" N LYS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= B, first strand: chain 'A' and resid 153 through 155 removed outlier: 3.904A pdb=" N CYS A 155 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN A 160 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.757A pdb=" N ILE B 127 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS B 11 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 125 " --> pdb=" O LYS B 11 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE B 13 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE B 123 " --> pdb=" O PHE B 13 " (cutoff:3.500A) 138 hydrogen bonds defined for protein. 411 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: 0.82 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 683 1.33 - 1.45: 860 1.45 - 1.58: 1960 1.58 - 1.70: 4 1.70 - 1.83: 31 Bond restraints: 3538 Sorted by residual: bond pdb=" C4 PX2 A 407 " pdb=" O5 PX2 A 407 " ideal model delta sigma weight residual 1.398 1.328 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PLM A 404 " pdb=" C2 PLM A 404 " ideal model delta sigma weight residual 1.542 1.601 -0.059 2.00e-02 2.50e+03 8.63e+00 bond pdb=" C2 PX2 A 407 " pdb=" O7 PX2 A 407 " ideal model delta sigma weight residual 1.399 1.456 -0.057 2.00e-02 2.50e+03 8.11e+00 bond pdb=" C16 PX2 A 407 " pdb=" O7 PX2 A 407 " ideal model delta sigma weight residual 1.398 1.343 0.055 2.00e-02 2.50e+03 7.62e+00 bond pdb=" C1 PX2 A 407 " pdb=" O4 PX2 A 407 " ideal model delta sigma weight residual 1.399 1.452 -0.053 2.00e-02 2.50e+03 7.02e+00 ... (remaining 3533 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.72: 87 105.72 - 112.79: 1814 112.79 - 119.87: 1272 119.87 - 126.94: 1550 126.94 - 134.02: 39 Bond angle restraints: 4762 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" CA ARG B 23 " pdb=" CB ARG B 23 " ideal model delta sigma weight residual 109.50 104.45 5.05 1.69e+00 3.50e-01 8.94e+00 angle pdb=" C CYS A 25 " pdb=" N ASP A 26 " pdb=" CA ASP A 26 " ideal model delta sigma weight residual 125.66 131.04 -5.38 1.85e+00 2.92e-01 8.47e+00 angle pdb=" C5 PX2 A 407 " pdb=" C4 PX2 A 407 " pdb=" O5 PX2 A 407 " ideal model delta sigma weight residual 119.99 111.26 8.73 3.00e+00 1.11e-01 8.46e+00 angle pdb=" C17 PX2 A 407 " pdb=" C16 PX2 A 407 " pdb=" O7 PX2 A 407 " ideal model delta sigma weight residual 120.00 111.37 8.63 3.00e+00 1.11e-01 8.28e+00 angle pdb=" N ARG A 151 " pdb=" CA ARG A 151 " pdb=" CB ARG A 151 " ideal model delta sigma weight residual 114.17 111.25 2.92 1.14e+00 7.69e-01 6.56e+00 ... (remaining 4757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 1797 17.40 - 34.80: 247 34.80 - 52.19: 72 52.19 - 69.59: 17 69.59 - 86.99: 4 Dihedral angle restraints: 2137 sinusoidal: 914 harmonic: 1223 Sorted by residual: dihedral pdb=" CA ASN A 174 " pdb=" CB ASN A 174 " pdb=" CG ASN A 174 " pdb=" OD1 ASN A 174 " ideal model delta sinusoidal sigma weight residual -90.00 -153.16 63.16 2 2.00e+01 2.50e-03 9.55e+00 dihedral pdb=" N ILE A 196 " pdb=" CA ILE A 196 " pdb=" CB ILE A 196 " pdb=" CG1 ILE A 196 " ideal model delta sinusoidal sigma weight residual -180.00 -121.68 -58.32 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA ARG A 164 " pdb=" CB ARG A 164 " pdb=" CG ARG A 164 " pdb=" CD ARG A 164 " ideal model delta sinusoidal sigma weight residual -180.00 -121.87 -58.13 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 2134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 378 0.042 - 0.084: 112 0.084 - 0.127: 33 0.127 - 0.169: 1 0.169 - 0.211: 1 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA ARG B 23 " pdb=" N ARG B 23 " pdb=" C ARG B 23 " pdb=" CB ARG B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ASP A 26 " pdb=" N ASP A 26 " pdb=" C ASP A 26 " pdb=" CB ASP A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 522 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 22 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C THR B 22 " 0.029 2.00e-02 2.50e+03 pdb=" O THR B 22 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG B 23 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 116 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 117 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 106 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.55e+00 pdb=" N PRO B 107 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 107 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 107 " -0.018 5.00e-02 4.00e+02 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 474 2.75 - 3.28: 3379 3.28 - 3.82: 5545 3.82 - 4.36: 6379 4.36 - 4.90: 11135 Nonbonded interactions: 26912 Sorted by model distance: nonbonded pdb=" O THR B 74 " pdb=" OG1 THR B 77 " model vdw 2.207 2.440 nonbonded pdb=" NH2 ARG A 182 " pdb=" O GLY A 289 " model vdw 2.208 2.520 nonbonded pdb=" OE2 GLU A 101 " pdb=" NH2 ARG B 121 " model vdw 2.279 2.520 nonbonded pdb=" OH TYR A 185 " pdb=" OG1 THR A 247 " model vdw 2.294 2.440 nonbonded pdb=" NE2 GLN A 134 " pdb=" O GLN A 271 " model vdw 2.302 2.520 ... (remaining 26907 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.860 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: 3.670 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.010 Find NCS groups from input model: 0.090 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 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 : 0.007 0.070 3538 Z= 0.413 Angle : 0.787 8.725 4762 Z= 0.385 Chirality : 0.043 0.211 525 Planarity : 0.004 0.033 594 Dihedral : 17.616 86.988 1349 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.81 % Allowed : 24.53 % Favored : 74.66 % 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: -2.61 (0.36), residues: 415 helix: -0.71 (0.32), residues: 206 sheet: -2.64 (1.10), residues: 24 loop : -2.81 (0.37), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.001 0.001 HIS A 168 PHE 0.018 0.001 PHE A 104 TYR 0.013 0.001 TYR A 197 ARG 0.007 0.000 ARG B 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.408 Fit side-chains REVERT: A 108 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7848 (mp0) REVERT: B 25 GLN cc_start: 0.8265 (mm110) cc_final: 0.7796 (mm110) REVERT: B 48 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8190 (mtp-110) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.2233 time to fit residues: 16.1749 Evaluate side-chains 57 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 CYS Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 299 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 0.0020 chunk 20 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 174 ASN B 36 ASN B 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3538 Z= 0.155 Angle : 0.530 5.802 4762 Z= 0.262 Chirality : 0.040 0.131 525 Planarity : 0.004 0.030 594 Dihedral : 11.590 59.668 541 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.85 % Allowed : 23.72 % Favored : 71.43 % 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: -1.06 (0.39), residues: 415 helix: 0.46 (0.35), residues: 210 sheet: -2.41 (0.91), residues: 32 loop : -1.81 (0.42), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.001 0.001 HIS A 246 PHE 0.013 0.001 PHE A 104 TYR 0.008 0.001 TYR A 197 ARG 0.006 0.001 ARG A 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 62 time to evaluate : 0.386 Fit side-chains REVERT: A 30 MET cc_start: 0.7985 (ttm) cc_final: 0.7671 (ttm) REVERT: A 108 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7765 (mp0) REVERT: A 125 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.6126 (mmt90) REVERT: A 258 GLU cc_start: 0.8788 (mt-10) cc_final: 0.7992 (mt-10) REVERT: A 299 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7714 (mmm-85) REVERT: B 48 ARG cc_start: 0.8423 (ttm110) cc_final: 0.8089 (mtp-110) outliers start: 18 outliers final: 11 residues processed: 76 average time/residue: 0.1979 time to fit residues: 17.7278 Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 56 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain B residue 81 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.0020 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 25 optimal weight: 0.0170 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.4226 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3538 Z= 0.146 Angle : 0.491 5.297 4762 Z= 0.244 Chirality : 0.040 0.131 525 Planarity : 0.004 0.030 594 Dihedral : 11.062 57.027 540 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.66 % Allowed : 25.88 % Favored : 68.46 % 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: -0.48 (0.40), residues: 415 helix: 0.85 (0.35), residues: 209 sheet: -2.01 (0.95), residues: 32 loop : -1.40 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.001 0.000 HIS A 154 PHE 0.011 0.001 PHE A 201 TYR 0.008 0.001 TYR A 197 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 0.419 Fit side-chains REVERT: A 108 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7789 (mp0) REVERT: A 125 ARG cc_start: 0.6561 (OUTLIER) cc_final: 0.6121 (mmt90) REVERT: A 299 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.7475 (mmm-85) REVERT: B 48 ARG cc_start: 0.8422 (ttm110) cc_final: 0.8069 (mtp-110) REVERT: B 100 GLN cc_start: 0.7966 (tp-100) cc_final: 0.7640 (tp-100) outliers start: 21 outliers final: 15 residues processed: 75 average time/residue: 0.1898 time to fit residues: 16.8865 Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 299 ARG Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 81 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3538 Z= 0.154 Angle : 0.496 8.156 4762 Z= 0.241 Chirality : 0.040 0.129 525 Planarity : 0.003 0.031 594 Dihedral : 10.179 59.563 540 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.39 % Allowed : 24.53 % Favored : 70.08 % 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: -0.11 (0.41), residues: 415 helix: 1.00 (0.36), residues: 212 sheet: -2.02 (0.93), residues: 34 loop : -0.98 (0.46), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.001 0.000 HIS A 167 PHE 0.012 0.001 PHE A 201 TYR 0.009 0.001 TYR A 197 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.402 Fit side-chains REVERT: A 108 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7804 (mp0) REVERT: A 125 ARG cc_start: 0.6527 (OUTLIER) cc_final: 0.6194 (mmt90) REVERT: A 258 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8255 (mt-10) REVERT: B 48 ARG cc_start: 0.8388 (ttm110) cc_final: 0.8069 (mtp-110) REVERT: B 73 LEU cc_start: 0.8695 (tp) cc_final: 0.8388 (mp) outliers start: 20 outliers final: 15 residues processed: 76 average time/residue: 0.1701 time to fit residues: 15.6675 Evaluate side-chains 73 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 57 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 81 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 16 optimal weight: 0.0170 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.8202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 3538 Z= 0.388 Angle : 0.614 7.146 4762 Z= 0.305 Chirality : 0.044 0.151 525 Planarity : 0.004 0.034 594 Dihedral : 10.024 58.594 534 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 7.55 % Allowed : 22.64 % Favored : 69.81 % 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: -0.28 (0.41), residues: 415 helix: 0.78 (0.36), residues: 212 sheet: -1.69 (0.96), residues: 32 loop : -1.05 (0.46), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 14 HIS 0.002 0.001 HIS A 168 PHE 0.023 0.002 PHE A 201 TYR 0.017 0.002 TYR A 197 ARG 0.007 0.001 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 60 time to evaluate : 0.394 Fit side-chains REVERT: A 108 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7909 (mp0) REVERT: A 125 ARG cc_start: 0.6582 (OUTLIER) cc_final: 0.6322 (mmt90) REVERT: A 258 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 25 GLN cc_start: 0.8404 (mm110) cc_final: 0.7903 (mm110) REVERT: B 48 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8111 (mtp-110) REVERT: B 73 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8492 (mp) REVERT: B 96 TYR cc_start: 0.8599 (t80) cc_final: 0.7964 (t80) outliers start: 28 outliers final: 23 residues processed: 79 average time/residue: 0.1632 time to fit residues: 15.7805 Evaluate side-chains 82 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 57 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 190 SER Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 285 GLU Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 84 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 0.0970 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3538 Z= 0.166 Angle : 0.519 6.430 4762 Z= 0.250 Chirality : 0.040 0.130 525 Planarity : 0.003 0.031 594 Dihedral : 9.674 59.382 534 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.93 % Allowed : 24.53 % Favored : 69.54 % 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: 0.11 (0.42), residues: 415 helix: 1.12 (0.36), residues: 211 sheet: -1.90 (0.90), residues: 34 loop : -0.76 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.001 0.000 HIS B 85 PHE 0.017 0.001 PHE A 201 TYR 0.007 0.001 TYR A 142 ARG 0.007 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 0.386 Fit side-chains REVERT: A 108 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7874 (mp0) REVERT: A 125 ARG cc_start: 0.6544 (OUTLIER) cc_final: 0.6327 (mmt90) REVERT: A 258 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8263 (mt-10) REVERT: B 25 GLN cc_start: 0.8366 (mm110) cc_final: 0.7853 (mm110) REVERT: B 48 ARG cc_start: 0.8376 (ttm110) cc_final: 0.8041 (mtp-110) REVERT: B 73 LEU cc_start: 0.8708 (tp) cc_final: 0.8414 (mp) REVERT: B 96 TYR cc_start: 0.8521 (t80) cc_final: 0.7946 (t80) outliers start: 22 outliers final: 19 residues processed: 71 average time/residue: 0.1761 time to fit residues: 15.0422 Evaluate side-chains 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 81 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3538 Z= 0.194 Angle : 0.520 7.498 4762 Z= 0.254 Chirality : 0.041 0.132 525 Planarity : 0.004 0.032 594 Dihedral : 9.524 59.910 534 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 5.93 % Allowed : 25.07 % Favored : 69.00 % 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: 0.23 (0.42), residues: 415 helix: 1.16 (0.36), residues: 213 sheet: -1.83 (0.90), residues: 34 loop : -0.65 (0.48), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.002 0.001 HIS A 246 PHE 0.017 0.001 PHE A 201 TYR 0.008 0.001 TYR A 197 ARG 0.007 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 56 time to evaluate : 0.377 Fit side-chains REVERT: A 108 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7905 (mp0) REVERT: A 125 ARG cc_start: 0.6528 (OUTLIER) cc_final: 0.6317 (mmt90) REVERT: A 258 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8236 (mt-10) REVERT: B 25 GLN cc_start: 0.8386 (mm110) cc_final: 0.7879 (mm110) REVERT: B 48 ARG cc_start: 0.8383 (ttm110) cc_final: 0.8073 (mtp-110) REVERT: B 73 LEU cc_start: 0.8692 (tp) cc_final: 0.8400 (mp) REVERT: B 96 TYR cc_start: 0.8523 (t80) cc_final: 0.7968 (t80) outliers start: 22 outliers final: 19 residues processed: 72 average time/residue: 0.1818 time to fit residues: 15.8590 Evaluate side-chains 75 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 81 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 28 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3538 Z= 0.141 Angle : 0.500 7.373 4762 Z= 0.243 Chirality : 0.039 0.128 525 Planarity : 0.003 0.032 594 Dihedral : 9.217 59.272 534 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 6.20 % Allowed : 24.53 % Favored : 69.27 % 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: 0.49 (0.42), residues: 415 helix: 1.39 (0.37), residues: 211 sheet: -1.59 (0.90), residues: 34 loop : -0.56 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.001 0.000 HIS B 85 PHE 0.016 0.001 PHE A 129 TYR 0.006 0.001 TYR A 197 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 58 time to evaluate : 0.411 Fit side-chains REVERT: A 26 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7487 (t70) REVERT: A 125 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.6268 (mmt90) REVERT: A 258 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 48 ARG cc_start: 0.8354 (ttm110) cc_final: 0.8049 (mtp-110) REVERT: B 73 LEU cc_start: 0.8675 (tp) cc_final: 0.8369 (mp) REVERT: B 96 TYR cc_start: 0.8511 (t80) cc_final: 0.7913 (t80) REVERT: B 104 ILE cc_start: 0.7719 (OUTLIER) cc_final: 0.7396 (pt) outliers start: 23 outliers final: 15 residues processed: 77 average time/residue: 0.1703 time to fit residues: 16.1306 Evaluate side-chains 72 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 54 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 31 MET Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 125 ARG Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.0020 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 36 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 40 optimal weight: 0.0050 chunk 37 optimal weight: 0.5980 overall best weight: 0.2700 ------------------------------------------------------------------------------- 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: 0.7936 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3538 Z= 0.128 Angle : 0.517 8.506 4762 Z= 0.248 Chirality : 0.039 0.125 525 Planarity : 0.003 0.032 594 Dihedral : 8.941 58.757 534 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.04 % Allowed : 27.22 % Favored : 68.73 % 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: 0.67 (0.42), residues: 415 helix: 1.43 (0.37), residues: 214 sheet: -1.18 (0.94), residues: 32 loop : -0.42 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 14 HIS 0.001 0.000 HIS A 154 PHE 0.021 0.001 PHE A 129 TYR 0.007 0.001 TYR A 197 ARG 0.009 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 54 time to evaluate : 0.405 Fit side-chains REVERT: A 26 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7467 (t70) REVERT: A 139 LYS cc_start: 0.8978 (mtpt) cc_final: 0.8729 (mtmm) REVERT: B 48 ARG cc_start: 0.8334 (ttm110) cc_final: 0.8029 (mtp-110) REVERT: B 96 TYR cc_start: 0.8475 (t80) cc_final: 0.7859 (t80) REVERT: B 104 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7395 (pt) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.1796 time to fit residues: 14.3126 Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 51 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7992 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3538 Z= 0.212 Angle : 0.547 8.470 4762 Z= 0.264 Chirality : 0.041 0.129 525 Planarity : 0.004 0.033 594 Dihedral : 9.003 59.433 534 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.04 % Allowed : 26.95 % Favored : 69.00 % 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: 0.65 (0.42), residues: 415 helix: 1.43 (0.37), residues: 212 sheet: -1.16 (0.93), residues: 34 loop : -0.43 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.002 0.001 HIS A 246 PHE 0.018 0.001 PHE A 129 TYR 0.009 0.001 TYR A 197 ARG 0.008 0.000 ARG B 23 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.361 Fit side-chains REVERT: A 26 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7516 (t70) REVERT: B 48 ARG cc_start: 0.8363 (ttm110) cc_final: 0.8068 (mtp-110) REVERT: B 83 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7848 (tt0) REVERT: B 96 TYR cc_start: 0.8513 (t80) cc_final: 0.7889 (t80) REVERT: B 104 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7429 (pt) outliers start: 15 outliers final: 12 residues processed: 62 average time/residue: 0.1824 time to fit residues: 13.7849 Evaluate side-chains 63 residues out of total 371 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 8 VAL Chi-restraints excluded: chain B residue 81 CYS Chi-restraints excluded: chain B residue 83 GLU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 104 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.0970 overall best weight: 0.3334 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.177220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.132914 restraints weight = 3959.211| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.38 r_work: 0.3201 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3538 Z= 0.139 Angle : 0.526 8.362 4762 Z= 0.253 Chirality : 0.039 0.118 525 Planarity : 0.003 0.031 594 Dihedral : 8.851 59.838 534 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.04 % Allowed : 26.95 % Favored : 69.00 % 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: 0.81 (0.42), residues: 415 helix: 1.55 (0.37), residues: 212 sheet: -1.13 (0.93), residues: 34 loop : -0.33 (0.47), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 14 HIS 0.001 0.000 HIS B 85 PHE 0.019 0.001 PHE A 129 TYR 0.007 0.001 TYR A 197 ARG 0.008 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1232.69 seconds wall clock time: 23 minutes 8.44 seconds (1388.44 seconds total)