Starting phenix.real_space_refine on Wed Mar 4 17:24:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6yeg_10792/03_2026/6yeg_10792.cif Found real_map, /net/cci-nas-00/data/ceres_data/6yeg_10792/03_2026/6yeg_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_10792/03_2026/6yeg_10792.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6yeg_10792/03_2026/6yeg_10792.map" model { file = "/net/cci-nas-00/data/ceres_data/6yeg_10792/03_2026/6yeg_10792.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6yeg_10792/03_2026/6yeg_10792.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.48, per 1000 atoms: 0.22 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: 1.23 Conformation dependent library (CDL) restraints added in 533.4 milliseconds 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: 0.24 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: 1.66 Time building geometry restraints manager: 1.65 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: 0.520 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.750 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.320 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG K 93 TYR 0.024 0.003 TYR I 158 PHE 0.032 0.003 PHE F 160 TRP 0.028 0.005 TRP L 92 Details of bonding type rmsd covalent geometry : bond 0.00584 (16056) covalent geometry : angle 1.07572 (21708) hydrogen bonds : bond 0.03789 ( 60) hydrogen bonds : angle 8.32649 ( 180) *********************** 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 : 0.480 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: 0.7682 (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: 0.5176 (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: 0.5777 (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: 0.1263 time to fit residues: 35.8715 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 : 0.554 ------------------------------------------------------------------------------- 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 98 optimal weight: 40.0000 chunk 194 optimal weight: 40.0000 chunk 107 optimal weight: 40.0000 chunk 10 optimal weight: 40.0000 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 50.0000 chunk 103 optimal weight: 40.0000 chunk 200 optimal weight: 50.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 30.0000 overall best weight: 22.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 133 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 140 ASN I 140 ASN J 50 ASN J 133 GLN J 140 ASN K 50 ASN K 133 GLN K 140 ASN L 50 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 = 0.3753 r_free = 0.3753 target = 0.066724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.061426 restraints weight = 144402.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.062518 restraints weight = 90842.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.063340 restraints weight = 62291.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.063841 restraints weight = 44974.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.064352 restraints weight = 35301.208| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 16056 Z= 0.326 Angle : 0.930 17.703 21708 Z= 0.481 Chirality : 0.049 0.154 2268 Planarity : 0.005 0.042 2952 Dihedral : 7.932 44.172 2232 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.70 % Favored : 82.30 % Rotamer: Outliers : 4.62 % Allowed : 8.03 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.31 (0.14), residues: 2040 helix: -3.53 (0.29), residues: 192 sheet: -2.52 (0.16), residues: 756 loop : -4.43 (0.14), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG L 52 TYR 0.036 0.004 TYR B 118 PHE 0.029 0.003 PHE F 44 TRP 0.021 0.004 TRP F 92 Details of bonding type rmsd covalent geometry : bond 0.00745 (16056) covalent geometry : angle 0.93026 (21708) hydrogen bonds : bond 0.04532 ( 60) hydrogen bonds : angle 6.62698 ( 180) *********************** 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 145 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 69 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: H 101 ASN cc_start: 0.7330 (p0) cc_final: 0.6429 (t0) REVERT: J 31 TYR cc_start: 0.6340 (OUTLIER) cc_final: 0.5857 (p90) REVERT: L 31 TYR cc_start: 0.6652 (OUTLIER) cc_final: 0.5914 (p90) outliers start: 76 outliers final: 29 residues processed: 139 average time/residue: 0.1102 time to fit residues: 23.4809 Evaluate side-chains 93 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 66 THR 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 66 THR Chi-restraints excluded: chain E residue 11 VAL 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 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 89 optimal weight: 10.0000 chunk 99 optimal weight: 40.0000 chunk 98 optimal weight: 10.0000 chunk 200 optimal weight: 40.0000 chunk 82 optimal weight: 50.0000 chunk 69 optimal weight: 30.0000 chunk 57 optimal weight: 0.0970 chunk 180 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 125 optimal weight: 9.9990 chunk 202 optimal weight: 40.0000 overall best weight: 7.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 88 GLN E 133 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.067248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.062046 restraints weight = 146359.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.063184 restraints weight = 93380.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.064036 restraints weight = 64070.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.064599 restraints weight = 46041.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.065142 restraints weight = 35759.942| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3280 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= 0.143 Angle : 0.703 14.547 21708 Z= 0.357 Chirality : 0.043 0.151 2268 Planarity : 0.004 0.034 2952 Dihedral : 6.506 24.807 2224 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 2.13 % Allowed : 10.95 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.00 (0.15), residues: 2040 helix: -1.30 (0.44), residues: 120 sheet: -2.31 (0.16), residues: 792 loop : -4.52 (0.13), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 41 TYR 0.022 0.002 TYR I 118 PHE 0.014 0.001 PHE F 44 TRP 0.013 0.003 TRP J 92 Details of bonding type rmsd covalent geometry : bond 0.00326 (16056) covalent geometry : angle 0.70323 (21708) hydrogen bonds : bond 0.03780 ( 60) hydrogen bonds : angle 6.13274 ( 180) *********************** 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 127 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 PHE cc_start: 0.7070 (m-80) cc_final: 0.6429 (m-80) REVERT: E 101 ASN cc_start: 0.7108 (p0) cc_final: 0.6605 (t0) REVERT: H 101 ASN cc_start: 0.7115 (p0) cc_final: 0.6424 (t0) REVERT: I 101 ASN cc_start: 0.7188 (p0) cc_final: 0.6214 (t0) REVERT: J 31 TYR cc_start: 0.6288 (OUTLIER) cc_final: 0.5846 (p90) REVERT: L 31 TYR cc_start: 0.6584 (OUTLIER) cc_final: 0.6008 (p90) REVERT: L 101 ASN cc_start: 0.7123 (p0) cc_final: 0.6332 (t0) outliers start: 35 outliers final: 18 residues processed: 122 average time/residue: 0.1358 time to fit residues: 23.9937 Evaluate side-chains 93 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 143 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 143 ILE Chi-restraints excluded: chain E residue 31 TYR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 143 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 K residue 11 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 137 optimal weight: 40.0000 chunk 178 optimal weight: 7.9990 chunk 200 optimal weight: 0.0370 chunk 116 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 43 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 196 optimal weight: 8.9990 chunk 140 optimal weight: 20.0000 chunk 89 optimal weight: 3.9990 overall best weight: 6.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 165 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 = 0.3825 r_free = 0.3825 target = 0.068543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.063195 restraints weight = 144025.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.064327 restraints weight = 91895.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.065183 restraints weight = 63180.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.065738 restraints weight = 45865.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.066264 restraints weight = 36026.542| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6786 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16056 Z= 0.125 Angle : 0.652 12.670 21708 Z= 0.330 Chirality : 0.042 0.123 2268 Planarity : 0.004 0.029 2952 Dihedral : 5.938 23.394 2220 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.38 % Favored : 86.62 % Rotamer: Outliers : 2.80 % Allowed : 13.44 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.81 (0.15), residues: 2040 helix: -0.52 (0.46), residues: 120 sheet: -2.21 (0.16), residues: 780 loop : -4.44 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 93 TYR 0.018 0.002 TYR I 118 PHE 0.012 0.001 PHE F 44 TRP 0.011 0.002 TRP G 92 Details of bonding type rmsd covalent geometry : bond 0.00288 (16056) covalent geometry : angle 0.65234 (21708) hydrogen bonds : bond 0.03312 ( 60) hydrogen bonds : angle 5.71135 ( 180) *********************** 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 134 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 88 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 ASP cc_start: 0.7068 (m-30) cc_final: 0.6765 (m-30) REVERT: D 44 PHE cc_start: 0.7048 (m-80) cc_final: 0.6438 (m-80) REVERT: E 101 ASN cc_start: 0.7205 (p0) cc_final: 0.6670 (t0) REVERT: F 34 ASP cc_start: 0.6559 (m-30) cc_final: 0.6334 (m-30) REVERT: H 101 ASN cc_start: 0.7200 (p0) cc_final: 0.6482 (t0) REVERT: I 101 ASN cc_start: 0.7243 (p0) cc_final: 0.6235 (t0) REVERT: J 31 TYR cc_start: 0.6169 (OUTLIER) cc_final: 0.5724 (p90) REVERT: L 31 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5891 (p90) REVERT: L 101 ASN cc_start: 0.7183 (p0) cc_final: 0.6354 (t0) outliers start: 46 outliers final: 28 residues processed: 128 average time/residue: 0.1340 time to fit residues: 24.9778 Evaluate side-chains 113 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 83 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 143 ILE 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 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 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 43 LEU 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 J residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 37 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 47 optimal weight: 9.9990 chunk 11 optimal weight: 50.0000 chunk 138 optimal weight: 30.0000 chunk 90 optimal weight: 6.9990 chunk 67 optimal weight: 40.0000 chunk 46 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 50.0000 chunk 112 optimal weight: 50.0000 chunk 98 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 overall best weight: 10.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN E 133 GLN ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.067822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.062462 restraints weight = 143767.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.063587 restraints weight = 92013.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.064464 restraints weight = 63482.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.064966 restraints weight = 45507.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.065498 restraints weight = 35767.228| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16056 Z= 0.163 Angle : 0.685 14.294 21708 Z= 0.345 Chirality : 0.043 0.119 2268 Planarity : 0.004 0.027 2952 Dihedral : 6.122 23.116 2220 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.75 % Favored : 85.25 % Rotamer: Outliers : 3.53 % Allowed : 13.87 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.79 (0.16), residues: 2040 helix: -0.21 (0.47), residues: 120 sheet: -2.30 (0.17), residues: 780 loop : -4.37 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 93 TYR 0.020 0.002 TYR I 118 PHE 0.015 0.002 PHE F 44 TRP 0.012 0.002 TRP E 92 Details of bonding type rmsd covalent geometry : bond 0.00380 (16056) covalent geometry : angle 0.68531 (21708) hydrogen bonds : bond 0.03327 ( 60) hydrogen bonds : angle 5.56075 ( 180) *********************** 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 138 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 80 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ASP cc_start: 0.6950 (m-30) cc_final: 0.6737 (m-30) REVERT: D 34 ASP cc_start: 0.7141 (m-30) cc_final: 0.6885 (m-30) REVERT: E 101 ASN cc_start: 0.7178 (p0) cc_final: 0.6702 (t0) REVERT: F 34 ASP cc_start: 0.6876 (m-30) cc_final: 0.6654 (m-30) REVERT: H 101 ASN cc_start: 0.7241 (p0) cc_final: 0.6512 (t0) REVERT: I 61 ASP cc_start: 0.5458 (m-30) cc_final: 0.5141 (m-30) REVERT: I 101 ASN cc_start: 0.7341 (p0) cc_final: 0.6267 (t0) REVERT: J 31 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5784 (p90) REVERT: K 101 ASN cc_start: 0.6725 (OUTLIER) cc_final: 0.6491 (p0) REVERT: L 31 TYR cc_start: 0.6274 (OUTLIER) cc_final: 0.5906 (p90) REVERT: L 101 ASN cc_start: 0.7287 (p0) cc_final: 0.6416 (t0) outliers start: 58 outliers final: 39 residues processed: 131 average time/residue: 0.1321 time to fit residues: 25.5682 Evaluate side-chains 118 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 76 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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 A residue 143 ILE 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 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 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 F residue 53 ILE Chi-restraints excluded: chain F residue 143 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 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 J residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 37 VAL 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 54 LEU 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 23 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 152 optimal weight: 30.0000 chunk 74 optimal weight: 7.9990 chunk 68 optimal weight: 50.0000 chunk 161 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 5.9990 chunk 147 optimal weight: 30.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3818 r_free = 0.3818 target = 0.068377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.062928 restraints weight = 142876.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.064055 restraints weight = 91458.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.064852 restraints weight = 63235.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.065395 restraints weight = 46738.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.065917 restraints weight = 37277.097| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16056 Z= 0.124 Angle : 0.639 12.870 21708 Z= 0.319 Chirality : 0.042 0.153 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.762 23.172 2220 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 3.28 % Allowed : 14.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.72 (0.16), residues: 2040 helix: 0.16 (0.48), residues: 120 sheet: -2.29 (0.17), residues: 780 loop : -4.34 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 93 TYR 0.020 0.002 TYR L 118 PHE 0.011 0.001 PHE F 44 TRP 0.010 0.002 TRP K 92 Details of bonding type rmsd covalent geometry : bond 0.00290 (16056) covalent geometry : angle 0.63922 (21708) hydrogen bonds : bond 0.03113 ( 60) hydrogen bonds : angle 5.44367 ( 180) *********************** 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 133 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 79 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 ASP cc_start: 0.7025 (m-30) cc_final: 0.6765 (m-30) REVERT: E 34 ASP cc_start: 0.6668 (m-30) cc_final: 0.6407 (m-30) REVERT: E 101 ASN cc_start: 0.7138 (p0) cc_final: 0.6647 (t0) REVERT: F 34 ASP cc_start: 0.6685 (m-30) cc_final: 0.6428 (m-30) REVERT: H 101 ASN cc_start: 0.7273 (p0) cc_final: 0.6622 (t0) REVERT: I 61 ASP cc_start: 0.5588 (m-30) cc_final: 0.5226 (m-30) REVERT: I 101 ASN cc_start: 0.7353 (p0) cc_final: 0.6361 (t0) REVERT: J 31 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.5766 (p90) REVERT: L 31 TYR cc_start: 0.6225 (OUTLIER) cc_final: 0.5847 (p90) REVERT: L 101 ASN cc_start: 0.7304 (p0) cc_final: 0.6503 (t0) outliers start: 54 outliers final: 33 residues processed: 128 average time/residue: 0.1235 time to fit residues: 23.4135 Evaluate side-chains 109 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 74 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 143 ILE Chi-restraints excluded: chain B residue 37 VAL 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 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 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 143 ILE 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 J residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR 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 143 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 53 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 151 optimal weight: 0.0370 chunk 109 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 97 optimal weight: 40.0000 chunk 93 optimal weight: 30.0000 chunk 145 optimal weight: 50.0000 chunk 121 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 81 optimal weight: 50.0000 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 20.0000 overall best weight: 9.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3805 r_free = 0.3805 target = 0.068101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.062663 restraints weight = 142031.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.063775 restraints weight = 90536.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.064669 restraints weight = 62513.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.065167 restraints weight = 45312.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.065664 restraints weight = 35732.516| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16056 Z= 0.152 Angle : 0.668 13.906 21708 Z= 0.332 Chirality : 0.042 0.126 2268 Planarity : 0.004 0.038 2952 Dihedral : 5.889 23.008 2220 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.92 % Favored : 86.08 % Rotamer: Outliers : 3.28 % Allowed : 15.02 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.70 (0.16), residues: 2040 helix: 0.08 (0.47), residues: 120 sheet: -2.28 (0.17), residues: 780 loop : -4.30 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 41 TYR 0.019 0.002 TYR L 118 PHE 0.011 0.001 PHE F 44 TRP 0.011 0.002 TRP K 92 Details of bonding type rmsd covalent geometry : bond 0.00356 (16056) covalent geometry : angle 0.66777 (21708) hydrogen bonds : bond 0.03121 ( 60) hydrogen bonds : angle 5.35447 ( 180) *********************** 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 129 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 75 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 ASP cc_start: 0.7037 (m-30) cc_final: 0.6790 (m-30) REVERT: E 34 ASP cc_start: 0.6779 (m-30) cc_final: 0.6521 (m-30) REVERT: E 101 ASN cc_start: 0.7099 (p0) cc_final: 0.6505 (t0) REVERT: H 101 ASN cc_start: 0.7260 (p0) cc_final: 0.6595 (t0) REVERT: I 61 ASP cc_start: 0.5562 (m-30) cc_final: 0.5116 (m-30) REVERT: I 101 ASN cc_start: 0.7369 (p0) cc_final: 0.6334 (t0) REVERT: J 31 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5804 (p90) REVERT: K 101 ASN cc_start: 0.6684 (OUTLIER) cc_final: 0.6469 (p0) REVERT: L 31 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.5884 (p90) REVERT: L 101 ASN cc_start: 0.7245 (p0) cc_final: 0.6409 (t0) outliers start: 54 outliers final: 42 residues processed: 125 average time/residue: 0.1279 time to fit residues: 23.3753 Evaluate side-chains 112 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 67 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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 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 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 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 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE 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 J residue 11 VAL Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 54 LEU 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 66 THR Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 101 ASN 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 37 VAL Chi-restraints excluded: chain L residue 53 ILE Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 52 optimal weight: 50.0000 chunk 129 optimal weight: 50.0000 chunk 175 optimal weight: 0.0770 chunk 190 optimal weight: 40.0000 chunk 99 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 10 optimal weight: 50.0000 chunk 145 optimal weight: 50.0000 chunk 194 optimal weight: 7.9990 chunk 183 optimal weight: 7.9990 chunk 22 optimal weight: 50.0000 overall best weight: 4.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN E 88 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.068966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.063405 restraints weight = 142299.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.064533 restraints weight = 91558.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.065433 restraints weight = 64027.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.065943 restraints weight = 46580.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.066451 restraints weight = 36906.491| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16056 Z= 0.107 Angle : 0.624 12.264 21708 Z= 0.308 Chirality : 0.042 0.128 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.491 22.763 2220 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.86 % Favored : 88.14 % Rotamer: Outliers : 2.92 % Allowed : 15.75 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.61 (0.16), residues: 2040 helix: 0.45 (0.49), residues: 120 sheet: -2.22 (0.17), residues: 780 loop : -4.29 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 116 TYR 0.019 0.002 TYR F 118 PHE 0.008 0.001 PHE K 28 TRP 0.010 0.002 TRP K 92 Details of bonding type rmsd covalent geometry : bond 0.00251 (16056) covalent geometry : angle 0.62359 (21708) hydrogen bonds : bond 0.02934 ( 60) hydrogen bonds : angle 5.27224 ( 180) *********************** 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 115 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 67 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 34 ASP cc_start: 0.6919 (m-30) cc_final: 0.6674 (m-30) REVERT: E 101 ASN cc_start: 0.7099 (p0) cc_final: 0.6514 (t0) REVERT: F 7 MET cc_start: 0.7453 (mmm) cc_final: 0.7116 (mmm) REVERT: H 101 ASN cc_start: 0.7135 (p0) cc_final: 0.6564 (t0) REVERT: I 101 ASN cc_start: 0.7334 (p0) cc_final: 0.6362 (t0) REVERT: J 31 TYR cc_start: 0.6229 (OUTLIER) cc_final: 0.5786 (p90) REVERT: L 31 TYR cc_start: 0.6204 (OUTLIER) cc_final: 0.5777 (p90) REVERT: L 101 ASN cc_start: 0.7303 (p0) cc_final: 0.6484 (t0) outliers start: 48 outliers final: 34 residues processed: 112 average time/residue: 0.1429 time to fit residues: 22.9994 Evaluate side-chains 99 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 0.582 ------------------------------------------------------------------------------- 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 143 ILE 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 E residue 11 VAL Chi-restraints excluded: chain E residue 31 TYR 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 143 ILE 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 89 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 89 ILE Chi-restraints excluded: chain J residue 31 TYR Chi-restraints excluded: chain J residue 54 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 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 37 VAL Chi-restraints excluded: chain L residue 53 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 44 optimal weight: 50.0000 chunk 179 optimal weight: 30.0000 chunk 201 optimal weight: 6.9990 chunk 149 optimal weight: 50.0000 chunk 36 optimal weight: 9.9990 chunk 185 optimal weight: 30.0000 chunk 193 optimal weight: 20.0000 chunk 154 optimal weight: 1.9990 chunk 33 optimal weight: 30.0000 chunk 22 optimal weight: 10.0000 chunk 162 optimal weight: 50.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3805 r_free = 0.3805 target = 0.068102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.062654 restraints weight = 142679.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.063781 restraints weight = 90987.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.064578 restraints weight = 62843.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.065122 restraints weight = 46332.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.065679 restraints weight = 36876.362| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.4550 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= 0.154 Angle : 0.682 13.962 21708 Z= 0.335 Chirality : 0.043 0.117 2268 Planarity : 0.003 0.030 2952 Dihedral : 5.757 22.631 2220 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.41 % Favored : 85.59 % Rotamer: Outliers : 2.86 % Allowed : 15.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.16), residues: 2040 helix: 0.11 (0.46), residues: 120 sheet: -2.25 (0.17), residues: 780 loop : -4.25 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 93 TYR 0.027 0.002 TYR K 13 PHE 0.010 0.001 PHE H 44 TRP 0.010 0.002 TRP K 92 Details of bonding type rmsd covalent geometry : bond 0.00359 (16056) covalent geometry : angle 0.68182 (21708) hydrogen bonds : bond 0.03076 ( 60) hydrogen bonds : angle 5.21402 ( 180) *********************** 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 115 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 68 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 34 ASP cc_start: 0.7006 (m-30) cc_final: 0.6772 (m-30) REVERT: E 101 ASN cc_start: 0.7120 (p0) cc_final: 0.6528 (t0) REVERT: H 101 ASN cc_start: 0.7241 (p0) cc_final: 0.6578 (t0) REVERT: I 101 ASN cc_start: 0.7277 (p0) cc_final: 0.6266 (t0) REVERT: J 31 TYR cc_start: 0.6253 (OUTLIER) cc_final: 0.5873 (p90) REVERT: L 31 TYR cc_start: 0.6210 (OUTLIER) cc_final: 0.5796 (p90) REVERT: L 101 ASN cc_start: 0.7253 (p0) cc_final: 0.6389 (t0) outliers start: 47 outliers final: 42 residues processed: 113 average time/residue: 0.1316 time to fit residues: 22.0153 Evaluate side-chains 108 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 64 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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 143 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 151 VAL 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 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 143 ILE 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 89 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 66 THR Chi-restraints excluded: chain I residue 89 ILE 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 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 37 VAL Chi-restraints excluded: chain L residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 80 optimal weight: 20.0000 chunk 36 optimal weight: 6.9990 chunk 181 optimal weight: 30.0000 chunk 25 optimal weight: 50.0000 chunk 99 optimal weight: 5.9990 chunk 59 optimal weight: 40.0000 chunk 162 optimal weight: 0.0770 chunk 188 optimal weight: 30.0000 chunk 51 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 overall best weight: 10.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3802 r_free = 0.3802 target = 0.068106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.062692 restraints weight = 141986.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.063800 restraints weight = 90500.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.064485 restraints weight = 62887.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.065124 restraints weight = 47688.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.065608 restraints weight = 37170.824| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16056 Z= 0.163 Angle : 0.700 14.404 21708 Z= 0.344 Chirality : 0.043 0.118 2268 Planarity : 0.004 0.029 2952 Dihedral : 5.908 23.446 2220 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 3.04 % Allowed : 15.57 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.64 (0.16), residues: 2040 helix: 0.03 (0.46), residues: 120 sheet: -2.24 (0.17), residues: 780 loop : -4.25 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 41 TYR 0.028 0.002 TYR K 13 PHE 0.012 0.001 PHE L 44 TRP 0.010 0.002 TRP K 92 Details of bonding type rmsd covalent geometry : bond 0.00380 (16056) covalent geometry : angle 0.69983 (21708) hydrogen bonds : bond 0.03163 ( 60) hydrogen bonds : angle 5.24587 ( 180) ********************** 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 108 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 58 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 101 ASN cc_start: 0.7304 (p0) cc_final: 0.6573 (t0) REVERT: J 31 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.5942 (p90) REVERT: L 31 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5797 (p90) REVERT: L 101 ASN cc_start: 0.7332 (p0) cc_final: 0.6499 (t0) outliers start: 50 outliers final: 46 residues processed: 106 average time/residue: 0.1399 time to fit residues: 21.3853 Evaluate side-chains 102 residues out of total 1644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 54 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 A residue 143 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 151 VAL 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 53 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 117 GLU 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 143 ILE 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 H residue 89 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 66 THR Chi-restraints excluded: chain I residue 89 ILE 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 J residue 173 THR 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 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 37 VAL Chi-restraints excluded: chain L residue 53 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 56 optimal weight: 50.0000 chunk 34 optimal weight: 50.0000 chunk 168 optimal weight: 0.0170 chunk 198 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 122 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 166 optimal weight: 40.0000 chunk 30 optimal weight: 10.0000 overall best weight: 7.6028 ------------------------------------------------------------------------------- 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** ** L 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 = 0.3817 r_free = 0.3817 target = 0.068545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.063063 restraints weight = 141064.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.064163 restraints weight = 90526.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.065021 restraints weight = 62918.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.065542 restraints weight = 46268.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.066083 restraints weight = 36998.278| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.4753 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= 0.133 Angle : 0.668 13.960 21708 Z= 0.328 Chirality : 0.042 0.119 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.712 23.177 2220 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 2.98 % Allowed : 15.75 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.55 (0.16), residues: 2040 helix: 0.30 (0.48), residues: 120 sheet: -2.15 (0.17), residues: 780 loop : -4.24 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 41 TYR 0.023 0.002 TYR I 13 PHE 0.010 0.001 PHE K 28 TRP 0.011 0.002 TRP K 92 Details of bonding type rmsd covalent geometry : bond 0.00312 (16056) covalent geometry : angle 0.66834 (21708) hydrogen bonds : bond 0.03032 ( 60) hydrogen bonds : angle 5.16534 ( 180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.60 seconds wall clock time: 32 minutes 39.43 seconds (1959.43 seconds total)