Starting phenix.real_space_refine on Fri Jun 13 15:30:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yeg_10792/06_2025/6yeg_10792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yeg_10792/06_2025/6yeg_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_10792/06_2025/6yeg_10792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yeg_10792/06_2025/6yeg_10792.map" model { file = "/net/cci-nas-00/data/ceres_data/6yeg_10792/06_2025/6yeg_10792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yeg_10792/06_2025/6yeg_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.94, per 1000 atoms: 0.57 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: 3.43 Conformation dependent library (CDL) restraints added in 2.0 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: 0.87 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: 2.96 Time building geometry restraints manager: 4.16 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: 0.01 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: 0.490 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 32.980 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.320 ------------------------------------------------------------------------------- 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= 0.275 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 Details of bonding type rmsd hydrogen bonds : bond 0.03789 ( 60) hydrogen bonds : angle 8.32649 ( 180) covalent geometry : bond 0.00584 (16056) covalent geometry : angle 1.07572 (21708) *********************** 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 : 1.867 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: 0.2974 time to fit residues: 83.9794 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 : 1.703 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.067571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.062350 restraints weight = 145495.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.063466 restraints weight = 93931.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.064274 restraints weight = 65684.754| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 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= 0.174 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 Details of bonding type rmsd hydrogen bonds : bond 0.03921 ( 60) hydrogen bonds : angle 6.37719 ( 180) covalent geometry : bond 0.00397 (16056) covalent geometry : angle 0.73047 (21708) *********************** 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 : 1.968 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: 0.7333 (p0) cc_final: 0.6635 (t0) REVERT: E 101 ASN cc_start: 0.7296 (p0) cc_final: 0.6773 (t0) REVERT: G 7 MET cc_start: 0.7338 (mmm) cc_final: 0.7126 (mmm) REVERT: G 101 ASN cc_start: 0.7378 (p0) cc_final: 0.6205 (t0) REVERT: H 101 ASN cc_start: 0.7250 (p0) cc_final: 0.6459 (t0) REVERT: I 101 ASN cc_start: 0.7281 (p0) cc_final: 0.6395 (t0) REVERT: J 7 MET cc_start: 0.7764 (mmm) cc_final: 0.7398 (mmp) REVERT: J 31 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5746 (p90) REVERT: L 31 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.5867 (p90) REVERT: L 101 ASN cc_start: 0.7260 (p0) cc_final: 0.6386 (t0) outliers start: 73 outliers final: 30 residues processed: 168 average time/residue: 0.2932 time to fit residues: 73.7172 Evaluate side-chains 117 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 85 time to evaluate : 1.872 ------------------------------------------------------------------------------- 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 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 31 TYR Chi-restraints excluded: chain J residue 66 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 31 TYR 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 142 optimal weight: 30.0000 chunk 117 optimal weight: 50.0000 chunk 115 optimal weight: 2.9990 chunk 138 optimal weight: 30.0000 chunk 78 optimal weight: 50.0000 chunk 62 optimal weight: 40.0000 chunk 4 optimal weight: 8.9990 chunk 146 optimal weight: 50.0000 chunk 174 optimal weight: 10.0000 chunk 163 optimal weight: 50.0000 chunk 53 optimal weight: 30.0000 overall best weight: 16.3996 ------------------------------------------------------------------------------- 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 ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN K 50 ASN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.067296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.062004 restraints weight = 142376.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.063080 restraints weight = 89956.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.063880 restraints weight = 62143.598| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16056 Z= 0.240 Angle : 0.824 17.483 21708 Z= 0.421 Chirality : 0.046 0.128 2268 Planarity : 0.004 0.032 2952 Dihedral : 7.242 43.575 2226 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.11 % Favored : 82.89 % Rotamer: Outliers : 3.47 % Allowed : 9.73 % Favored : 86.80 % 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: -5.03 (0.15), residues: 2040 helix: -1.49 (0.44), residues: 120 sheet: -2.33 (0.16), residues: 780 loop : -4.50 (0.13), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 92 PHE 0.023 0.002 PHE H 44 TYR 0.027 0.003 TYR B 118 ARG 0.004 0.001 ARG G 93 Details of bonding type rmsd hydrogen bonds : bond 0.04002 ( 60) hydrogen bonds : angle 6.08834 ( 180) covalent geometry : bond 0.00548 (16056) covalent geometry : angle 0.82384 (21708) *********************** 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 131 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 74 time to evaluate : 1.725 Fit side-chains REVERT: D 44 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.7065 (m-10) REVERT: E 101 ASN cc_start: 0.7327 (p0) cc_final: 0.6835 (t0) REVERT: H 101 ASN cc_start: 0.7501 (p0) cc_final: 0.6608 (t0) REVERT: J 31 TYR cc_start: 0.6276 (OUTLIER) cc_final: 0.5840 (p90) REVERT: L 31 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5940 (p90) REVERT: L 101 ASN cc_start: 0.7287 (p0) cc_final: 0.6412 (t0) outliers start: 57 outliers final: 35 residues processed: 124 average time/residue: 0.2779 time to fit residues: 51.3738 Evaluate side-chains 100 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 62 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 A residue 143 ILE Chi-restraints excluded: chain B residue 37 VAL 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 C residue 66 THR 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 66 THR 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 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 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 I residue 11 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 144 optimal weight: 3.9990 chunk 170 optimal weight: 40.0000 chunk 172 optimal weight: 2.9990 chunk 160 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 175 optimal weight: 6.9990 chunk 202 optimal weight: 40.0000 chunk 8 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** D 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.068655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063252 restraints weight = 142646.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.064370 restraints weight = 91228.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.065267 restraints weight = 63564.953| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.3530 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= 0.121 Angle : 0.664 15.543 21708 Z= 0.334 Chirality : 0.043 0.122 2268 Planarity : 0.003 0.031 2952 Dihedral : 6.097 23.961 2222 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 2.07 % Allowed : 13.02 % Favored : 84.91 % 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: -4.83 (0.15), residues: 2040 helix: -0.60 (0.46), residues: 120 sheet: -2.22 (0.16), residues: 780 loop : -4.45 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 92 PHE 0.011 0.001 PHE F 44 TYR 0.018 0.002 TYR L 118 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03545 ( 60) hydrogen bonds : angle 5.79794 ( 180) covalent geometry : bond 0.00279 (16056) covalent geometry : angle 0.66379 (21708) *********************** 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 120 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 1.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 ASP cc_start: 0.5499 (m-30) cc_final: 0.5027 (m-30) REVERT: B 101 ASN cc_start: 0.7186 (p0) cc_final: 0.6483 (t0) REVERT: D 34 ASP cc_start: 0.7021 (m-30) cc_final: 0.6604 (m-30) REVERT: E 101 ASN cc_start: 0.7315 (p0) cc_final: 0.6828 (t0) REVERT: H 101 ASN cc_start: 0.7224 (p0) cc_final: 0.6547 (t0) REVERT: I 101 ASN cc_start: 0.7329 (p0) cc_final: 0.6383 (t0) REVERT: J 31 TYR cc_start: 0.6322 (OUTLIER) cc_final: 0.5814 (p90) REVERT: L 31 TYR cc_start: 0.6595 (OUTLIER) cc_final: 0.5971 (p90) REVERT: L 101 ASN cc_start: 0.7386 (p0) cc_final: 0.6562 (t0) outliers start: 34 outliers final: 18 residues processed: 116 average time/residue: 0.3478 time to fit residues: 58.7324 Evaluate side-chains 96 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 VAL 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 44 PHE Chi-restraints excluded: chain D residue 143 ILE 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 F residue 53 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 4 optimal weight: 30.0000 chunk 190 optimal weight: 50.0000 chunk 105 optimal weight: 50.0000 chunk 152 optimal weight: 30.0000 chunk 198 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 137 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 68 optimal weight: 50.0000 chunk 131 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 overall best weight: 15.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.066967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.061771 restraints weight = 145018.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.062874 restraints weight = 90699.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.063735 restraints weight = 62420.185| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16056 Z= 0.227 Angle : 0.772 16.563 21708 Z= 0.392 Chirality : 0.045 0.150 2268 Planarity : 0.004 0.037 2952 Dihedral : 6.711 28.569 2220 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer: Outliers : 3.77 % Allowed : 13.38 % Favored : 82.85 % 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: -4.86 (0.15), residues: 2040 helix: -0.80 (0.43), residues: 120 sheet: -2.30 (0.16), residues: 792 loop : -4.40 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 92 PHE 0.020 0.002 PHE H 44 TYR 0.021 0.003 TYR I 118 ARG 0.005 0.001 ARG F 93 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 60) hydrogen bonds : angle 5.73047 ( 180) covalent geometry : bond 0.00524 (16056) covalent geometry : angle 0.77224 (21708) *********************** 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 130 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 68 time to evaluate : 1.792 Fit side-chains revert: symmetry clash REVERT: G 7 MET cc_start: 0.7259 (mmm) cc_final: 0.7058 (mmm) REVERT: H 101 ASN cc_start: 0.7355 (p0) cc_final: 0.6538 (t0) REVERT: I 61 ASP cc_start: 0.5663 (m-30) cc_final: 0.5365 (m-30) REVERT: J 31 TYR cc_start: 0.6342 (OUTLIER) cc_final: 0.5842 (p90) REVERT: K 101 ASN cc_start: 0.6791 (OUTLIER) cc_final: 0.6535 (p0) REVERT: L 31 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5978 (p90) REVERT: L 101 ASN cc_start: 0.7336 (p0) cc_final: 0.6375 (t0) outliers start: 62 outliers final: 39 residues processed: 121 average time/residue: 0.2740 time to fit residues: 50.6104 Evaluate side-chains 103 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 61 time to evaluate : 1.782 ------------------------------------------------------------------------------- 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 53 ILE 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 C residue 37 VAL 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 37 VAL 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 43 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 J residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR 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 K residue 101 ASN Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 173 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 149 optimal weight: 40.0000 chunk 54 optimal weight: 7.9990 chunk 11 optimal weight: 30.0000 chunk 194 optimal weight: 6.9990 chunk 201 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.066914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.061731 restraints weight = 147322.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.062883 restraints weight = 93411.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.063569 restraints weight = 64176.813| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16056 Z= 0.141 Angle : 0.670 14.572 21708 Z= 0.336 Chirality : 0.043 0.118 2268 Planarity : 0.003 0.029 2952 Dihedral : 6.120 25.799 2220 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Rotamer: Outliers : 2.98 % Allowed : 15.09 % Favored : 81.93 % 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: -4.72 (0.16), residues: 2040 helix: -0.14 (0.47), residues: 120 sheet: -2.25 (0.17), residues: 792 loop : -4.34 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 92 PHE 0.012 0.001 PHE F 44 TYR 0.021 0.002 TYR L 118 ARG 0.003 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 60) hydrogen bonds : angle 5.53558 ( 180) covalent geometry : bond 0.00328 (16056) covalent geometry : angle 0.66960 (21708) *********************** 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 122 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 73 time to evaluate : 2.483 Fit side-chains revert: symmetry clash REVERT: A 34 ASP cc_start: 0.6848 (m-30) cc_final: 0.6640 (m-30) REVERT: E 101 ASN cc_start: 0.7200 (p0) cc_final: 0.6743 (t0) REVERT: H 101 ASN cc_start: 0.7290 (p0) cc_final: 0.6606 (t0) REVERT: I 101 ASN cc_start: 0.7359 (p0) cc_final: 0.6369 (t0) REVERT: J 31 TYR cc_start: 0.6328 (OUTLIER) cc_final: 0.5884 (p90) REVERT: L 31 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.5974 (p90) REVERT: L 101 ASN cc_start: 0.7354 (p0) cc_final: 0.6478 (t0) outliers start: 49 outliers final: 36 residues processed: 118 average time/residue: 0.3248 time to fit residues: 58.2982 Evaluate side-chains 107 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 69 time to evaluate : 2.117 ------------------------------------------------------------------------------- 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 11 VAL 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 66 THR 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 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 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 53 ILE Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 43 LEU 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 31 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 173 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 156 optimal weight: 9.9990 chunk 11 optimal weight: 40.0000 chunk 51 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 68 optimal weight: 60.0000 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 120 optimal weight: 40.0000 chunk 121 optimal weight: 8.9990 chunk 165 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.068186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.062735 restraints weight = 143011.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.063857 restraints weight = 91194.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.064739 restraints weight = 63055.889| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16056 Z= 0.139 Angle : 0.663 14.430 21708 Z= 0.330 Chirality : 0.042 0.117 2268 Planarity : 0.003 0.031 2952 Dihedral : 5.979 24.731 2220 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 3.10 % Allowed : 14.90 % Favored : 82.00 % 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: -4.68 (0.16), residues: 2040 helix: -0.00 (0.47), residues: 120 sheet: -2.23 (0.17), residues: 792 loop : -4.31 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 92 PHE 0.011 0.001 PHE F 160 TYR 0.020 0.002 TYR F 13 ARG 0.003 0.001 ARG F 41 Details of bonding type rmsd hydrogen bonds : bond 0.03202 ( 60) hydrogen bonds : angle 5.37944 ( 180) covalent geometry : bond 0.00327 (16056) covalent geometry : angle 0.66267 (21708) *********************** 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 120 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 69 time to evaluate : 1.740 Fit side-chains revert: symmetry clash REVERT: B 34 ASP cc_start: 0.6963 (m-30) cc_final: 0.6705 (m-30) REVERT: C 7 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7787 (mmm) REVERT: E 34 ASP cc_start: 0.6697 (m-30) cc_final: 0.6333 (m-30) REVERT: E 101 ASN cc_start: 0.7204 (p0) cc_final: 0.6768 (t0) REVERT: H 101 ASN cc_start: 0.7269 (p0) cc_final: 0.6628 (t0) REVERT: I 101 ASN cc_start: 0.7424 (p0) cc_final: 0.6414 (t0) REVERT: J 31 TYR cc_start: 0.6196 (OUTLIER) cc_final: 0.5880 (p90) REVERT: L 31 TYR cc_start: 0.6391 (OUTLIER) cc_final: 0.5966 (p90) REVERT: L 101 ASN cc_start: 0.7313 (p0) cc_final: 0.6454 (t0) outliers start: 51 outliers final: 41 residues processed: 113 average time/residue: 0.3069 time to fit residues: 50.8757 Evaluate side-chains 107 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 63 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 C residue 66 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 THR 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 53 ILE 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 43 LEU 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 31 TYR Chi-restraints excluded: chain J residue 173 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 L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 43 LEU 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 107 optimal weight: 6.9990 chunk 153 optimal weight: 50.0000 chunk 87 optimal weight: 20.0000 chunk 40 optimal weight: 40.0000 chunk 43 optimal weight: 40.0000 chunk 169 optimal weight: 50.0000 chunk 67 optimal weight: 30.0000 chunk 56 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 71 optimal weight: 50.0000 overall best weight: 13.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.067369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.062039 restraints weight = 143006.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.063156 restraints weight = 90527.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.063835 restraints weight = 62581.493| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16056 Z= 0.193 Angle : 0.725 15.782 21708 Z= 0.363 Chirality : 0.044 0.122 2268 Planarity : 0.004 0.028 2952 Dihedral : 6.307 26.420 2220 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.78 % Favored : 84.22 % Rotamer: Outliers : 3.95 % Allowed : 14.54 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.16), residues: 2040 helix: -0.28 (0.45), residues: 120 sheet: -2.28 (0.17), residues: 792 loop : -4.30 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 92 PHE 0.013 0.002 PHE H 44 TYR 0.023 0.003 TYR F 118 ARG 0.004 0.001 ARG C 93 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 60) hydrogen bonds : angle 5.42601 ( 180) covalent geometry : bond 0.00450 (16056) covalent geometry : angle 0.72541 (21708) *********************** 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 122 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 57 time to evaluate : 1.909 Fit side-chains revert: symmetry clash REVERT: B 34 ASP cc_start: 0.6905 (m-30) cc_final: 0.6671 (m-30) REVERT: C 7 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7821 (mmm) REVERT: E 34 ASP cc_start: 0.6721 (m-30) cc_final: 0.6417 (m-30) REVERT: H 101 ASN cc_start: 0.7342 (p0) cc_final: 0.6635 (t0) REVERT: J 31 TYR cc_start: 0.6299 (OUTLIER) cc_final: 0.5956 (p90) REVERT: L 31 TYR cc_start: 0.6324 (OUTLIER) cc_final: 0.5930 (p90) REVERT: L 101 ASN cc_start: 0.7292 (p0) cc_final: 0.6385 (t0) outliers start: 65 outliers final: 51 residues processed: 118 average time/residue: 0.3012 time to fit residues: 53.7779 Evaluate side-chains 105 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 51 time to evaluate : 1.656 ------------------------------------------------------------------------------- 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 53 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 ILE 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 37 VAL 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 D residue 37 VAL Chi-restraints excluded: chain D residue 66 THR 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 53 ILE 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 43 LEU 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 31 TYR Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 173 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 65 optimal weight: 40.0000 chunk 5 optimal weight: 40.0000 chunk 20 optimal weight: 50.0000 chunk 197 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 12 optimal weight: 7.9990 chunk 78 optimal weight: 30.0000 chunk 64 optimal weight: 50.0000 chunk 1 optimal weight: 30.0000 chunk 122 optimal weight: 8.9990 overall best weight: 10.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.067916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.062487 restraints weight = 143119.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.063605 restraints weight = 91149.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.064509 restraints weight = 62791.218| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16056 Z= 0.163 Angle : 0.696 15.145 21708 Z= 0.346 Chirality : 0.043 0.118 2268 Planarity : 0.003 0.030 2952 Dihedral : 6.135 25.296 2220 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.54 % Favored : 84.46 % Rotamer: Outliers : 3.35 % Allowed : 15.15 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.66 (0.16), residues: 2040 helix: -0.07 (0.46), residues: 120 sheet: -2.24 (0.17), residues: 792 loop : -4.28 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 92 PHE 0.012 0.001 PHE G 28 TYR 0.021 0.002 TYR D 118 ARG 0.003 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03288 ( 60) hydrogen bonds : angle 5.34836 ( 180) covalent geometry : bond 0.00383 (16056) covalent geometry : angle 0.69567 (21708) *********************** 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 112 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 57 time to evaluate : 1.787 Fit side-chains revert: symmetry clash REVERT: B 34 ASP cc_start: 0.6967 (m-30) cc_final: 0.6729 (m-30) REVERT: B 44 PHE cc_start: 0.7238 (m-80) cc_final: 0.6731 (m-80) REVERT: C 7 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7781 (mmm) REVERT: E 34 ASP cc_start: 0.6678 (m-30) cc_final: 0.6451 (m-30) REVERT: E 101 ASN cc_start: 0.7222 (p0) cc_final: 0.6687 (t0) REVERT: H 101 ASN cc_start: 0.7299 (p0) cc_final: 0.6660 (t0) REVERT: J 31 TYR cc_start: 0.6312 (OUTLIER) cc_final: 0.5940 (p90) REVERT: L 31 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5922 (p90) REVERT: L 101 ASN cc_start: 0.7322 (p0) cc_final: 0.6468 (t0) outliers start: 55 outliers final: 46 residues processed: 109 average time/residue: 0.3038 time to fit residues: 48.9229 Evaluate side-chains 103 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 54 time to evaluate : 1.838 ------------------------------------------------------------------------------- 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 53 ILE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 37 VAL 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 37 VAL 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 D residue 37 VAL Chi-restraints excluded: chain D residue 66 THR 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 53 ILE 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 43 LEU 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 31 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 173 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 89 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 128 optimal weight: 50.0000 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 102 optimal weight: 50.0000 chunk 78 optimal weight: 50.0000 chunk 74 optimal weight: 6.9990 chunk 156 optimal weight: 30.0000 chunk 169 optimal weight: 40.0000 chunk 180 optimal weight: 40.0000 chunk 53 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 overall best weight: 11.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.067625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.062237 restraints weight = 144308.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.063365 restraints weight = 91512.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.064160 restraints weight = 62989.796| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16056 Z= 0.176 Angle : 0.718 15.629 21708 Z= 0.357 Chirality : 0.044 0.120 2268 Planarity : 0.003 0.029 2952 Dihedral : 6.239 25.959 2220 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.88 % Favored : 84.12 % Rotamer: Outliers : 3.35 % Allowed : 15.15 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.16), residues: 2040 helix: -0.24 (0.44), residues: 120 sheet: -2.21 (0.17), residues: 792 loop : -4.26 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 92 PHE 0.012 0.002 PHE D 160 TYR 0.022 0.003 TYR D 13 ARG 0.003 0.001 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03334 ( 60) hydrogen bonds : angle 5.30892 ( 180) covalent geometry : bond 0.00412 (16056) covalent geometry : angle 0.71812 (21708) ********************** 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 111 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 56 time to evaluate : 1.915 Fit side-chains revert: symmetry clash REVERT: B 44 PHE cc_start: 0.7262 (m-80) cc_final: 0.6988 (m-80) REVERT: C 7 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7789 (mmm) REVERT: E 34 ASP cc_start: 0.6803 (m-30) cc_final: 0.6528 (m-30) REVERT: H 101 ASN cc_start: 0.7322 (p0) cc_final: 0.6583 (t0) REVERT: J 31 TYR cc_start: 0.6383 (OUTLIER) cc_final: 0.6006 (p90) REVERT: L 31 TYR cc_start: 0.6302 (OUTLIER) cc_final: 0.5937 (p90) REVERT: L 101 ASN cc_start: 0.7358 (p0) cc_final: 0.6487 (t0) outliers start: 55 outliers final: 48 residues processed: 108 average time/residue: 0.3069 time to fit residues: 49.1523 Evaluate side-chains 105 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 54 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 37 VAL 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 37 VAL 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 D residue 37 VAL Chi-restraints excluded: chain D residue 66 THR 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 F residue 143 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 53 ILE 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 43 LEU 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 31 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 14 LEU Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 66 THR Chi-restraints excluded: chain L residue 173 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 164 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 chunk 156 optimal weight: 30.0000 chunk 119 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 chunk 35 optimal weight: 40.0000 chunk 160 optimal weight: 30.0000 chunk 90 optimal weight: 50.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 133 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.068432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.062993 restraints weight = 142429.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.064127 restraints weight = 90954.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.064927 restraints weight = 63156.289| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4876 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= 0.131 Angle : 0.665 14.255 21708 Z= 0.329 Chirality : 0.042 0.115 2268 Planarity : 0.003 0.030 2952 Dihedral : 5.889 23.859 2220 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 3.04 % Allowed : 15.45 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.16), residues: 2040 helix: 0.19 (0.47), residues: 120 sheet: -2.13 (0.18), residues: 792 loop : -4.23 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 92 PHE 0.011 0.001 PHE G 28 TYR 0.021 0.002 TYR H 118 ARG 0.003 0.000 ARG G 116 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 60) hydrogen bonds : angle 5.22464 ( 180) covalent geometry : bond 0.00309 (16056) covalent geometry : angle 0.66522 (21708) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3848.71 seconds wall clock time: 68 minutes 44.79 seconds (4124.79 seconds total)