Starting phenix.real_space_refine on Tue Dec 31 07:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yeg_10792/12_2024/6yeg_10792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yeg_10792/12_2024/6yeg_10792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6yeg_10792/12_2024/6yeg_10792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yeg_10792/12_2024/6yeg_10792.map" model { file = "/net/cci-nas-00/data/ceres_data/6yeg_10792/12_2024/6yeg_10792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yeg_10792/12_2024/6yeg_10792.cif" } resolution = 4.0 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= 0.075 sd= 0.382 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 9852 2.51 5 N 2592 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 15756 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "B" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "C" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "D" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "E" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "G" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "H" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "I" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "J" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "K" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "L" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Time building chain proxies: 10.86, per 1000 atoms: 0.69 Number of scatterers: 15756 At special positions: 0 Unit cell: (115.005, 114.07, 117.81, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 3300 8.00 N 2592 7.00 C 9852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 2.3 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 5.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'E' and resid 75 through 83 Processing helix chain 'F' and resid 75 through 83 Processing helix chain 'G' and resid 75 through 83 Processing helix chain 'H' and resid 75 through 83 Processing helix chain 'I' and resid 75 through 83 Processing helix chain 'J' and resid 75 through 83 Processing helix chain 'K' and resid 75 through 83 Processing helix chain 'L' and resid 75 through 83 60 hydrogen bonds defined for protein. 180 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: 3.54 Time building geometry restraints manager: 5.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5031 1.33 - 1.45: 2425 1.45 - 1.57: 8576 1.57 - 1.69: 0 1.69 - 1.80: 24 Bond restraints: 16056 Sorted by residual: bond pdb=" C GLN A 162 " pdb=" N PRO A 163 " ideal model delta sigma weight residual 1.337 1.369 -0.033 1.06e-02 8.90e+03 9.59e+00 bond pdb=" C GLN B 162 " pdb=" N PRO B 163 " ideal model delta sigma weight residual 1.337 1.369 -0.032 1.06e-02 8.90e+03 9.36e+00 bond pdb=" C GLN F 162 " pdb=" N PRO F 163 " ideal model delta sigma weight residual 1.337 1.372 -0.035 1.24e-02 6.50e+03 7.97e+00 bond pdb=" C GLN E 162 " pdb=" N PRO E 163 " ideal model delta sigma weight residual 1.337 1.371 -0.033 1.24e-02 6.50e+03 7.30e+00 bond pdb=" C GLN C 162 " pdb=" N PRO C 163 " ideal model delta sigma weight residual 1.337 1.369 -0.032 1.24e-02 6.50e+03 6.51e+00 ... (remaining 16051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 21129 2.70 - 5.41: 496 5.41 - 8.11: 65 8.11 - 10.82: 10 10.82 - 13.52: 8 Bond angle restraints: 21708 Sorted by residual: angle pdb=" C LEU J 27 " pdb=" N PHE J 28 " pdb=" CA PHE J 28 " ideal model delta sigma weight residual 122.31 108.79 13.52 2.34e+00 1.83e-01 3.34e+01 angle pdb=" N VAL E 151 " pdb=" CA VAL E 151 " pdb=" C VAL E 151 " ideal model delta sigma weight residual 113.42 106.78 6.64 1.17e+00 7.31e-01 3.22e+01 angle pdb=" C LEU K 27 " pdb=" N PHE K 28 " pdb=" CA PHE K 28 " ideal model delta sigma weight residual 122.31 109.35 12.96 2.34e+00 1.83e-01 3.07e+01 angle pdb=" N VAL K 151 " pdb=" CA VAL K 151 " pdb=" C VAL K 151 " ideal model delta sigma weight residual 112.96 107.48 5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" N VAL L 151 " pdb=" CA VAL L 151 " pdb=" C VAL L 151 " ideal model delta sigma weight residual 112.96 107.54 5.42 1.00e+00 1.00e+00 2.94e+01 ... (remaining 21703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.14: 8898 16.14 - 32.27: 475 32.27 - 48.41: 101 48.41 - 64.54: 11 64.54 - 80.68: 31 Dihedral angle restraints: 9516 sinusoidal: 3756 harmonic: 5760 Sorted by residual: dihedral pdb=" CA TYR E 158 " pdb=" C TYR E 158 " pdb=" N ASP E 159 " pdb=" CA ASP E 159 " ideal model delta harmonic sigma weight residual -180.00 -149.59 -30.41 0 5.00e+00 4.00e-02 3.70e+01 dihedral pdb=" CA ALA E 170 " pdb=" C ALA E 170 " pdb=" N PRO E 171 " pdb=" CA PRO E 171 " ideal model delta harmonic sigma weight residual 180.00 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA ALA D 170 " pdb=" C ALA D 170 " pdb=" N PRO D 171 " pdb=" CA PRO D 171 " ideal model delta harmonic sigma weight residual -180.00 -152.84 -27.16 0 5.00e+00 4.00e-02 2.95e+01 ... (remaining 9513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1186 0.036 - 0.073: 706 0.073 - 0.109: 272 0.109 - 0.146: 78 0.146 - 0.182: 26 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CB VAL J 134 " pdb=" CA VAL J 134 " pdb=" CG1 VAL J 134 " pdb=" CG2 VAL J 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.31e-01 chirality pdb=" CB VAL D 134 " pdb=" CA VAL D 134 " pdb=" CG1 VAL D 134 " pdb=" CG2 VAL D 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CB VAL G 134 " pdb=" CA VAL G 134 " pdb=" CG1 VAL G 134 " pdb=" CG2 VAL G 134 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 2265 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 160 " -0.015 2.00e-02 2.50e+03 1.37e-02 3.27e+00 pdb=" CG PHE F 160 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE F 160 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE F 160 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE F 160 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE F 160 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 160 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 160 " -0.014 2.00e-02 2.50e+03 1.33e-02 3.10e+00 pdb=" CG PHE E 160 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE E 160 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE E 160 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE E 160 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 160 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE E 160 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 160 " -0.015 2.00e-02 2.50e+03 1.30e-02 2.94e+00 pdb=" CG PHE D 160 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE D 160 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 160 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 160 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 160 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 160 " -0.003 2.00e-02 2.50e+03 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4450 2.81 - 3.34: 14683 3.34 - 3.86: 26222 3.86 - 4.38: 29964 4.38 - 4.90: 49742 Nonbonded interactions: 125061 Sorted by model distance: nonbonded pdb=" OG SER I 62 " pdb=" OE1 GLN I 133 " model vdw 2.293 3.040 nonbonded pdb=" OG SER H 62 " pdb=" OE1 GLN H 133 " model vdw 2.296 3.040 nonbonded pdb=" OE1 GLN H 107 " pdb=" OH TYR I 118 " model vdw 2.308 3.040 nonbonded pdb=" OG SER L 62 " pdb=" OE1 GLN L 133 " model vdw 2.309 3.040 nonbonded pdb=" OG SER G 62 " pdb=" OE1 GLN G 133 " model vdw 2.312 3.040 ... (remaining 125056 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 group one per residue 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.710 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.330 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:4.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 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 : 0.006 0.057 16056 Z= 0.386 Angle : 1.076 13.524 21708 Z= 0.607 Chirality : 0.054 0.182 2268 Planarity : 0.006 0.041 2952 Dihedral : 12.040 80.677 5916 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.39 % Favored : 84.36 % Rotamer: Outliers : 0.85 % Allowed : 5.47 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -5.46 (0.15), residues: 2040 helix: -3.75 (0.31), residues: 192 sheet: -2.48 (0.15), residues: 804 loop : -4.69 (0.14), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP L 92 PHE 0.032 0.003 PHE F 160 TYR 0.024 0.003 TYR I 158 ARG 0.008 0.001 ARG K 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 VAL cc_start: 0.7681 (m) cc_final: 0.7304 (m) REVERT: B 101 ASN cc_start: 0.5449 (p0) cc_final: 0.5030 (t0) REVERT: D 37 VAL cc_start: 0.7698 (m) cc_final: 0.7320 (m) REVERT: E 37 VAL cc_start: 0.7736 (m) cc_final: 0.7452 (m) REVERT: E 101 ASN cc_start: 0.5454 (p0) cc_final: 0.5177 (t0) REVERT: F 101 ASN cc_start: 0.5448 (p0) cc_final: 0.5189 (t0) REVERT: G 101 ASN cc_start: 0.5857 (p0) cc_final: 0.4866 (t0) REVERT: H 101 ASN cc_start: 0.5501 (p0) cc_final: 0.5057 (t0) REVERT: I 37 VAL cc_start: 0.7586 (m) cc_final: 0.7341 (m) REVERT: I 101 ASN cc_start: 0.5776 (p0) cc_final: 0.5144 (t0) REVERT: J 101 ASN cc_start: 0.6225 (p0) cc_final: 0.5368 (t0) REVERT: K 37 VAL cc_start: 0.7752 (m) cc_final: 0.7348 (m) REVERT: L 37 VAL cc_start: 0.7566 (m) cc_final: 0.7259 (m) REVERT: L 101 ASN cc_start: 0.5897 (p0) cc_final: 0.5229 (t0) outliers start: 14 outliers final: 6 residues processed: 195 average time/residue: 0.3217 time to fit residues: 90.8465 Evaluate side-chains 98 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 30.0000 chunk 154 optimal weight: 50.0000 chunk 85 optimal weight: 30.0000 chunk 52 optimal weight: 50.0000 chunk 104 optimal weight: 40.0000 chunk 82 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 97 optimal weight: 20.0000 chunk 119 optimal weight: 50.0000 chunk 185 optimal weight: 0.2980 overall best weight: 10.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 133 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 140 ASN I 140 ASN J 133 GLN J 140 ASN K 133 GLN K 140 ASN L 140 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16056 Z= 0.263 Angle : 0.730 14.384 21708 Z= 0.373 Chirality : 0.044 0.124 2268 Planarity : 0.004 0.037 2952 Dihedral : 7.037 50.785 2232 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 4.44 % Allowed : 7.60 % Favored : 87.96 % 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: -5.17 (0.15), residues: 2040 helix: -2.26 (0.40), residues: 120 sheet: -2.31 (0.16), residues: 804 loop : -4.65 (0.13), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP L 92 PHE 0.017 0.002 PHE A 160 TYR 0.024 0.002 TYR A 118 ARG 0.003 0.001 ARG K 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 99 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.5387 (p0) cc_final: 0.5083 (t0) REVERT: G 7 MET cc_start: 0.6213 (mmm) cc_final: 0.5976 (mmm) REVERT: G 101 ASN cc_start: 0.5853 (p0) cc_final: 0.4966 (t0) REVERT: H 7 MET cc_start: 0.6822 (mmm) cc_final: 0.6534 (mmm) REVERT: H 101 ASN cc_start: 0.5410 (p0) cc_final: 0.5047 (t0) REVERT: H 167 THR cc_start: 0.5718 (OUTLIER) cc_final: 0.5508 (m) REVERT: I 101 ASN cc_start: 0.5851 (p0) cc_final: 0.5346 (t0) REVERT: J 7 MET cc_start: 0.6604 (mmm) cc_final: 0.6322 (mmp) REVERT: J 167 THR cc_start: 0.5934 (OUTLIER) cc_final: 0.5356 (m) REVERT: L 41 ARG cc_start: 0.6364 (ttp-170) cc_final: 0.6112 (ttp-170) REVERT: L 101 ASN cc_start: 0.5693 (p0) cc_final: 0.5191 (t0) outliers start: 73 outliers final: 30 residues processed: 168 average time/residue: 0.2917 time to fit residues: 72.5978 Evaluate side-chains 116 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 44 PHE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain J residue 167 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 50.0000 chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 40.0000 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 200 optimal weight: 50.0000 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 overall best weight: 6.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 165 GLN D 88 GLN F 88 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6043 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16056 Z= 0.196 Angle : 0.670 14.231 21708 Z= 0.339 Chirality : 0.042 0.122 2268 Planarity : 0.004 0.032 2952 Dihedral : 6.193 34.076 2226 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.94 % Favored : 87.06 % Rotamer: Outliers : 2.07 % Allowed : 10.28 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.85 (0.15), residues: 2040 helix: -1.24 (0.43), residues: 120 sheet: -2.13 (0.16), residues: 804 loop : -4.49 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 92 PHE 0.010 0.001 PHE F 160 TYR 0.018 0.002 TYR I 118 ARG 0.002 0.000 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 2.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.5384 (p0) cc_final: 0.5054 (t0) REVERT: F 7 MET cc_start: 0.6745 (mmm) cc_final: 0.6461 (mmm) REVERT: G 101 ASN cc_start: 0.5783 (p0) cc_final: 0.4947 (t0) REVERT: H 101 ASN cc_start: 0.5390 (p0) cc_final: 0.5062 (t0) REVERT: I 101 ASN cc_start: 0.5893 (p0) cc_final: 0.5254 (t0) REVERT: K 61 ASP cc_start: 0.4853 (m-30) cc_final: 0.4631 (m-30) REVERT: L 41 ARG cc_start: 0.6338 (ttp-170) cc_final: 0.6098 (ttp-170) REVERT: L 101 ASN cc_start: 0.5768 (p0) cc_final: 0.5253 (t0) outliers start: 34 outliers final: 19 residues processed: 122 average time/residue: 0.3294 time to fit residues: 57.9882 Evaluate side-chains 101 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 44 PHE Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 50.0000 chunk 139 optimal weight: 9.9990 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 50.0000 chunk 88 optimal weight: 50.0000 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 50.0000 chunk 197 optimal weight: 50.0000 chunk 97 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 8.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16056 Z= 0.227 Angle : 0.678 15.101 21708 Z= 0.341 Chirality : 0.042 0.116 2268 Planarity : 0.004 0.031 2952 Dihedral : 6.047 23.603 2220 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 2.43 % Allowed : 11.19 % Favored : 86.37 % 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: -4.68 (0.16), residues: 2040 helix: -0.56 (0.46), residues: 120 sheet: -2.11 (0.16), residues: 792 loop : -4.35 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 92 PHE 0.015 0.001 PHE F 28 TYR 0.019 0.002 TYR B 118 ARG 0.003 0.001 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 91 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 7 MET cc_start: 0.6826 (mmm) cc_final: 0.6595 (mmm) REVERT: H 101 ASN cc_start: 0.5484 (p0) cc_final: 0.5084 (t0) REVERT: I 61 ASP cc_start: 0.5627 (OUTLIER) cc_final: 0.5411 (t0) REVERT: I 101 ASN cc_start: 0.5953 (p0) cc_final: 0.5284 (t0) REVERT: L 41 ARG cc_start: 0.6496 (ttp-170) cc_final: 0.6269 (ttp-170) REVERT: L 101 ASN cc_start: 0.5805 (p0) cc_final: 0.5197 (t0) outliers start: 40 outliers final: 27 residues processed: 124 average time/residue: 0.3622 time to fit residues: 65.7450 Evaluate side-chains 113 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 4.9990 chunk 111 optimal weight: 50.0000 chunk 2 optimal weight: 0.7980 chunk 146 optimal weight: 50.0000 chunk 81 optimal weight: 10.0000 chunk 168 optimal weight: 50.0000 chunk 136 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 100 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 133 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16056 Z= 0.187 Angle : 0.636 13.909 21708 Z= 0.318 Chirality : 0.042 0.119 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.752 26.720 2220 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 2.80 % Allowed : 12.53 % Favored : 84.67 % 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: -4.60 (0.16), residues: 2040 helix: -0.01 (0.47), residues: 120 sheet: -2.11 (0.16), residues: 792 loop : -4.31 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP G 92 PHE 0.009 0.001 PHE F 160 TYR 0.016 0.002 TYR B 118 ARG 0.002 0.000 ARG G 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.5142 (OUTLIER) cc_final: 0.4679 (t80) REVERT: G 101 ASN cc_start: 0.5879 (p0) cc_final: 0.5029 (t0) REVERT: H 43 LEU cc_start: 0.5296 (OUTLIER) cc_final: 0.5064 (tp) REVERT: H 101 ASN cc_start: 0.5468 (p0) cc_final: 0.5156 (t0) REVERT: I 101 ASN cc_start: 0.5852 (p0) cc_final: 0.5229 (t0) REVERT: L 101 ASN cc_start: 0.5630 (p0) cc_final: 0.5172 (t0) outliers start: 46 outliers final: 30 residues processed: 127 average time/residue: 0.3304 time to fit residues: 60.8516 Evaluate side-chains 110 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 78 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 43 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 38 optimal weight: 0.2980 chunk 115 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 197 optimal weight: 10.0000 chunk 163 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 30.0000 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 overall best weight: 6.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16056 Z= 0.192 Angle : 0.639 14.043 21708 Z= 0.317 Chirality : 0.042 0.117 2268 Planarity : 0.003 0.034 2952 Dihedral : 5.664 25.484 2220 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % Rotamer: Outliers : 3.16 % Allowed : 12.83 % Favored : 84.00 % 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: -4.56 (0.16), residues: 2040 helix: 0.14 (0.47), residues: 120 sheet: -2.15 (0.16), residues: 792 loop : -4.25 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 92 PHE 0.010 0.001 PHE F 44 TYR 0.019 0.002 TYR H 13 ARG 0.002 0.000 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 80 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.5030 (OUTLIER) cc_final: 0.4659 (t80) REVERT: H 101 ASN cc_start: 0.5470 (p0) cc_final: 0.5140 (t0) REVERT: I 101 ASN cc_start: 0.5869 (p0) cc_final: 0.5218 (t0) REVERT: L 101 ASN cc_start: 0.5747 (p0) cc_final: 0.5222 (t0) outliers start: 52 outliers final: 37 residues processed: 128 average time/residue: 0.3159 time to fit residues: 58.8320 Evaluate side-chains 117 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 50.0000 chunk 22 optimal weight: 8.9990 chunk 112 optimal weight: 50.0000 chunk 144 optimal weight: 20.0000 chunk 111 optimal weight: 50.0000 chunk 166 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 196 optimal weight: 30.0000 chunk 123 optimal weight: 30.0000 chunk 119 optimal weight: 50.0000 chunk 90 optimal weight: 5.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN C 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16056 Z= 0.232 Angle : 0.669 14.960 21708 Z= 0.333 Chirality : 0.043 0.119 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.900 26.831 2220 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 2.86 % Allowed : 13.56 % Favored : 83.58 % 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: -4.58 (0.16), residues: 2040 helix: 0.02 (0.46), residues: 120 sheet: -2.21 (0.17), residues: 792 loop : -4.20 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 92 PHE 0.016 0.001 PHE H 44 TYR 0.018 0.002 TYR H 118 ARG 0.003 0.001 ARG F 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 75 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.5059 (OUTLIER) cc_final: 0.4791 (t80) REVERT: H 101 ASN cc_start: 0.5571 (p0) cc_final: 0.5241 (t0) REVERT: I 101 ASN cc_start: 0.5949 (p0) cc_final: 0.5186 (t0) REVERT: L 101 ASN cc_start: 0.5685 (p0) cc_final: 0.5121 (t0) outliers start: 47 outliers final: 40 residues processed: 119 average time/residue: 0.3235 time to fit residues: 55.6846 Evaluate side-chains 109 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 68 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 125 optimal weight: 0.0170 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 18 optimal weight: 40.0000 chunk 154 optimal weight: 40.0000 chunk 178 optimal weight: 8.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.4245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16056 Z= 0.177 Angle : 0.635 14.263 21708 Z= 0.312 Chirality : 0.042 0.118 2268 Planarity : 0.003 0.029 2952 Dihedral : 5.593 24.799 2220 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.11 % Favored : 87.89 % Rotamer: Outliers : 2.43 % Allowed : 14.54 % Favored : 83.03 % 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: -4.52 (0.16), residues: 2040 helix: 0.32 (0.48), residues: 120 sheet: -2.19 (0.17), residues: 792 loop : -4.18 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 92 PHE 0.009 0.001 PHE F 44 TYR 0.019 0.002 TYR L 118 ARG 0.002 0.000 ARG F 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 73 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.4925 (OUTLIER) cc_final: 0.4547 (t80) REVERT: H 101 ASN cc_start: 0.5344 (p0) cc_final: 0.5137 (t0) REVERT: I 101 ASN cc_start: 0.5822 (p0) cc_final: 0.5248 (t0) REVERT: L 101 ASN cc_start: 0.5744 (p0) cc_final: 0.5250 (t0) outliers start: 40 outliers final: 36 residues processed: 109 average time/residue: 0.3371 time to fit residues: 53.0616 Evaluate side-chains 106 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 69 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 40.0000 chunk 171 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 110 optimal weight: 10.0000 chunk 79 optimal weight: 40.0000 chunk 143 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 173 optimal weight: 50.0000 chunk 182 optimal weight: 30.0000 chunk 120 optimal weight: 10.0000 overall best weight: 7.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16056 Z= 0.197 Angle : 0.653 14.319 21708 Z= 0.319 Chirality : 0.042 0.115 2268 Planarity : 0.003 0.032 2952 Dihedral : 5.599 24.331 2220 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 2.86 % Allowed : 14.11 % Favored : 83.03 % 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: -4.50 (0.16), residues: 2040 helix: 0.22 (0.47), residues: 120 sheet: -2.16 (0.17), residues: 792 loop : -4.16 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 92 PHE 0.011 0.001 PHE H 44 TYR 0.026 0.002 TYR K 13 ARG 0.002 0.001 ARG D 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 72 time to evaluate : 1.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.4951 (OUTLIER) cc_final: 0.4583 (t80) REVERT: H 101 ASN cc_start: 0.5376 (p0) cc_final: 0.5156 (t0) REVERT: I 101 ASN cc_start: 0.5927 (p0) cc_final: 0.5254 (t0) REVERT: L 101 ASN cc_start: 0.5767 (p0) cc_final: 0.5223 (t0) outliers start: 47 outliers final: 40 residues processed: 116 average time/residue: 0.3332 time to fit residues: 56.0207 Evaluate side-chains 106 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 65 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 53 ILE Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 173 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 7.9990 chunk 118 optimal weight: 0.0980 chunk 91 optimal weight: 10.0000 chunk 134 optimal weight: 0.0980 chunk 203 optimal weight: 7.9990 chunk 187 optimal weight: 40.0000 chunk 161 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 125 optimal weight: 0.0060 chunk 99 optimal weight: 20.0000 chunk 128 optimal weight: 0.7980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 GLN F 88 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 165 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16056 Z= 0.141 Angle : 0.606 11.717 21708 Z= 0.297 Chirality : 0.041 0.125 2268 Planarity : 0.003 0.035 2952 Dihedral : 5.040 22.765 2220 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.75 % Favored : 90.25 % Rotamer: Outliers : 1.70 % Allowed : 15.27 % Favored : 83.03 % 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: -4.44 (0.15), residues: 2040 helix: 0.94 (0.48), residues: 120 sheet: -2.22 (0.17), residues: 708 loop : -4.05 (0.13), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 92 PHE 0.008 0.001 PHE I 91 TYR 0.013 0.001 TYR L 118 ARG 0.003 0.000 ARG J 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 101 ASN cc_start: 0.5446 (p0) cc_final: 0.4979 (t0) REVERT: I 101 ASN cc_start: 0.5475 (p0) cc_final: 0.5111 (t0) REVERT: J 101 ASN cc_start: 0.5967 (p0) cc_final: 0.5433 (t0) REVERT: L 167 THR cc_start: 0.6296 (OUTLIER) cc_final: 0.5978 (m) outliers start: 28 outliers final: 19 residues processed: 102 average time/residue: 0.3833 time to fit residues: 55.6194 Evaluate side-chains 86 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain G residue 53 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 167 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 0.9980 chunk 49 optimal weight: 30.0000 chunk 149 optimal weight: 0.0000 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 50.0000 chunk 162 optimal weight: 50.0000 chunk 67 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 20.0000 chunk 142 optimal weight: 40.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.068836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.063233 restraints weight = 142680.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.064368 restraints weight = 92552.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.065217 restraints weight = 64705.804| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 16056 Z= 0.242 Angle : 0.693 14.084 21708 Z= 0.340 Chirality : 0.043 0.119 2268 Planarity : 0.004 0.043 2952 Dihedral : 5.560 23.750 2220 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.89 % Favored : 87.11 % Rotamer: Outliers : 1.58 % Allowed : 15.21 % Favored : 83.21 % 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: -4.46 (0.16), residues: 2040 helix: 0.24 (0.46), residues: 120 sheet: -2.12 (0.17), residues: 792 loop : -4.14 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 92 PHE 0.016 0.001 PHE H 44 TYR 0.022 0.002 TYR G 13 ARG 0.003 0.001 ARG E 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2399.93 seconds wall clock time: 45 minutes 49.09 seconds (2749.09 seconds total)