Starting phenix.real_space_refine on Sat Mar 16 20:41:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/03_2024/6yeg_10792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/03_2024/6yeg_10792.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/03_2024/6yeg_10792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/03_2024/6yeg_10792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/03_2024/6yeg_10792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/03_2024/6yeg_10792.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.075 sd= 0.382 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 9852 2.51 5 N 2592 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 71": "NH1" <-> "NH2" Residue "A TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 71": "NH1" <-> "NH2" Residue "B TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 71": "NH1" <-> "NH2" Residue "D TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 71": "NH1" <-> "NH2" Residue "J TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15756 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "B" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "C" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "D" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "E" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "G" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "H" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "I" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "J" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "K" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Chain: "L" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1313 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 7, 'TRANS': 164} Time building chain proxies: 8.08, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.56 Conformation dependent library (CDL) restraints added in 3.1 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 5.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'E' and resid 75 through 83 Processing helix chain 'F' and resid 75 through 83 Processing helix chain 'G' and resid 75 through 83 Processing helix chain 'H' and resid 75 through 83 Processing helix chain 'I' and resid 75 through 83 Processing helix chain 'J' and resid 75 through 83 Processing helix chain 'K' and resid 75 through 83 Processing helix chain 'L' and resid 75 through 83 60 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 6.07 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: 101.06 - 107.64: 660 107.64 - 114.22: 8469 114.22 - 120.80: 6774 120.80 - 127.39: 5729 127.39 - 133.97: 76 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 2.440 nonbonded pdb=" OG SER H 62 " pdb=" OE1 GLN H 133 " model vdw 2.296 2.440 nonbonded pdb=" OE1 GLN H 107 " pdb=" OH TYR I 118 " model vdw 2.308 2.440 nonbonded pdb=" OG SER L 62 " pdb=" OE1 GLN L 133 " model vdw 2.309 2.440 nonbonded pdb=" OG SER G 62 " pdb=" OE1 GLN G 133 " model vdw 2.312 2.440 ... (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 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: 0.340 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: 2.680 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 39.870 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.320 ------------------------------------------------------------------------------- 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= 0.386 Angle : 1.076 13.524 21708 Z= 0.607 Chirality : 0.054 0.182 2268 Planarity : 0.006 0.041 2952 Dihedral : 12.040 80.677 5916 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.39 % Favored : 84.36 % Rotamer: Outliers : 0.85 % Allowed : 5.47 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.15), residues: 2040 helix: -3.75 (0.31), residues: 192 sheet: -2.48 (0.15), residues: 804 loop : -4.69 (0.14), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP L 92 PHE 0.032 0.003 PHE F 160 TYR 0.024 0.003 TYR I 158 ARG 0.008 0.001 ARG K 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 VAL cc_start: 0.7681 (m) cc_final: 0.7304 (m) REVERT: B 101 ASN cc_start: 0.5449 (p0) cc_final: 0.5030 (t0) REVERT: D 37 VAL cc_start: 0.7698 (m) cc_final: 0.7320 (m) REVERT: E 37 VAL cc_start: 0.7736 (m) cc_final: 0.7452 (m) REVERT: E 101 ASN cc_start: 0.5454 (p0) cc_final: 0.5177 (t0) REVERT: F 101 ASN cc_start: 0.5448 (p0) cc_final: 0.5189 (t0) REVERT: G 101 ASN cc_start: 0.5857 (p0) cc_final: 0.4866 (t0) REVERT: H 101 ASN cc_start: 0.5501 (p0) cc_final: 0.5057 (t0) REVERT: I 37 VAL cc_start: 0.7586 (m) cc_final: 0.7341 (m) REVERT: I 101 ASN cc_start: 0.5776 (p0) cc_final: 0.5144 (t0) REVERT: J 101 ASN cc_start: 0.6225 (p0) cc_final: 0.5368 (t0) REVERT: K 37 VAL cc_start: 0.7752 (m) cc_final: 0.7348 (m) REVERT: L 37 VAL cc_start: 0.7566 (m) cc_final: 0.7259 (m) REVERT: L 101 ASN cc_start: 0.5897 (p0) cc_final: 0.5229 (t0) outliers start: 14 outliers final: 6 residues processed: 195 average time/residue: 0.2998 time to fit residues: 84.5523 Evaluate side-chains 98 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 143 ILE Chi-restraints excluded: chain K residue 143 ILE Chi-restraints excluded: chain L residue 143 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 40.0000 chunk 154 optimal weight: 40.0000 chunk 85 optimal weight: 30.0000 chunk 52 optimal weight: 40.0000 chunk 104 optimal weight: 40.0000 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 6.9990 chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 40.0000 chunk 185 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 133 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN E 133 GLN ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 140 ASN I 140 ASN J 140 ASN K 133 GLN K 140 ASN L 140 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6086 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16056 Z= 0.235 Angle : 0.692 14.282 21708 Z= 0.348 Chirality : 0.043 0.126 2268 Planarity : 0.004 0.037 2952 Dihedral : 6.922 48.334 2232 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.77 % Favored : 86.23 % Rotamer: Outliers : 4.38 % Allowed : 7.48 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.98 (0.15), residues: 2040 helix: -1.96 (0.41), residues: 120 sheet: -2.08 (0.16), residues: 804 loop : -4.63 (0.13), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP C 92 PHE 0.017 0.002 PHE A 160 TYR 0.020 0.002 TYR I 118 ARG 0.003 0.001 ARG B 116 *********************** 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 168 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 96 time to evaluate : 1.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.5863 (p0) cc_final: 0.5158 (t0) REVERT: E 101 ASN cc_start: 0.5413 (p0) cc_final: 0.5091 (t0) REVERT: G 7 MET cc_start: 0.6394 (mmm) cc_final: 0.6164 (mmm) REVERT: H 101 ASN cc_start: 0.5756 (p0) cc_final: 0.5040 (t0) REVERT: J 7 MET cc_start: 0.6923 (mmm) cc_final: 0.6592 (mmm) REVERT: L 101 ASN cc_start: 0.5949 (p0) cc_final: 0.5048 (t0) outliers start: 72 outliers final: 29 residues processed: 163 average time/residue: 0.2856 time to fit residues: 68.8889 Evaluate side-chains 117 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 88 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 143 ILE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 66 THR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 34 ASP 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 34 ASP 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 66 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 60.0000 chunk 57 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 126 optimal weight: 20.0000 chunk 51 optimal weight: 50.0000 chunk 185 optimal weight: 6.9990 chunk 200 optimal weight: 50.0000 chunk 165 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 overall best weight: 8.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 133 GLN F 88 GLN F 165 GLN J 133 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16056 Z= 0.220 Angle : 0.671 13.561 21708 Z= 0.335 Chirality : 0.042 0.118 2268 Planarity : 0.004 0.033 2952 Dihedral : 6.288 25.426 2226 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Rotamer: Outliers : 2.80 % Allowed : 9.73 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.15), residues: 2040 helix: -0.59 (0.45), residues: 120 sheet: -1.99 (0.16), residues: 804 loop : -4.50 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 92 PHE 0.013 0.001 PHE F 44 TYR 0.019 0.002 TYR J 118 ARG 0.003 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 86 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 MET cc_start: 0.6659 (OUTLIER) cc_final: 0.6441 (mmm) REVERT: D 41 ARG cc_start: 0.6604 (ttp-170) cc_final: 0.6292 (tmt170) REVERT: E 101 ASN cc_start: 0.5480 (p0) cc_final: 0.5125 (t0) REVERT: F 7 MET cc_start: 0.6819 (mmm) cc_final: 0.6549 (mmm) REVERT: H 101 ASN cc_start: 0.5878 (p0) cc_final: 0.5141 (t0) REVERT: J 7 MET cc_start: 0.6870 (mmm) cc_final: 0.6569 (mmm) REVERT: L 101 ASN cc_start: 0.5808 (p0) cc_final: 0.5167 (t0) outliers start: 46 outliers final: 23 residues processed: 127 average time/residue: 0.2994 time to fit residues: 55.6341 Evaluate side-chains 104 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 80 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 44 PHE Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 66 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 66 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 50.0000 chunk 139 optimal weight: 8.9990 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 0.0040 chunk 197 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN E 165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6059 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16056 Z= 0.163 Angle : 0.602 12.334 21708 Z= 0.298 Chirality : 0.041 0.160 2268 Planarity : 0.003 0.029 2952 Dihedral : 5.668 23.500 2220 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 1.70 % Allowed : 12.10 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.16), residues: 2040 helix: 0.34 (0.46), residues: 120 sheet: -1.81 (0.16), residues: 804 loop : -4.43 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 92 PHE 0.008 0.001 PHE F 160 TYR 0.014 0.001 TYR J 118 ARG 0.003 0.000 ARG L 116 *********************** 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 121 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 ASN cc_start: 0.5378 (p0) cc_final: 0.5141 (t0) REVERT: F 7 MET cc_start: 0.6815 (mmm) cc_final: 0.6578 (mmm) REVERT: H 101 ASN cc_start: 0.5872 (p0) cc_final: 0.5220 (t0) REVERT: I 101 ASN cc_start: 0.5900 (p0) cc_final: 0.5233 (t0) REVERT: J 7 MET cc_start: 0.6768 (mmm) cc_final: 0.6560 (mmm) REVERT: L 101 ASN cc_start: 0.5782 (p0) cc_final: 0.5219 (t0) outliers start: 28 outliers final: 14 residues processed: 115 average time/residue: 0.3165 time to fit residues: 52.9847 Evaluate side-chains 97 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 44 PHE Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain L residue 11 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 20.0000 chunk 111 optimal weight: 30.0000 chunk 2 optimal weight: 7.9990 chunk 146 optimal weight: 0.6980 chunk 81 optimal weight: 20.0000 chunk 168 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 20.0000 chunk 49 optimal weight: 0.0050 overall best weight: 6.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6096 moved from start: 0.3568 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= 0.184 Angle : 0.605 12.719 21708 Z= 0.299 Chirality : 0.041 0.164 2268 Planarity : 0.003 0.026 2952 Dihedral : 5.624 22.509 2220 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.65 % Favored : 87.35 % Rotamer: Outliers : 2.19 % Allowed : 12.96 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.16), residues: 2040 helix: 0.58 (0.44), residues: 120 sheet: -1.80 (0.17), residues: 804 loop : -4.37 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 92 PHE 0.013 0.001 PHE D 44 TYR 0.015 0.002 TYR B 118 ARG 0.002 0.001 ARG I 116 *********************** 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 120 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 84 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 41 ARG cc_start: 0.6393 (ttp-170) cc_final: 0.6189 (tmt170) REVERT: E 101 ASN cc_start: 0.5486 (p0) cc_final: 0.5171 (t0) REVERT: F 7 MET cc_start: 0.6917 (mmm) cc_final: 0.6681 (mmm) REVERT: H 101 ASN cc_start: 0.5988 (p0) cc_final: 0.5241 (t0) REVERT: L 101 ASN cc_start: 0.5831 (p0) cc_final: 0.5170 (t0) outliers start: 36 outliers final: 24 residues processed: 115 average time/residue: 0.3232 time to fit residues: 53.5255 Evaluate side-chains 94 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 70 time to evaluate : 2.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain C residue 11 VAL 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 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 153 VAL 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 K residue 11 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 54 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 9.9990 chunk 177 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 197 optimal weight: 10.0000 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 65 optimal weight: 30.0000 chunk 103 optimal weight: 30.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16056 Z= 0.179 Angle : 0.595 12.782 21708 Z= 0.293 Chirality : 0.041 0.131 2268 Planarity : 0.003 0.027 2952 Dihedral : 5.494 22.278 2220 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.55 % Favored : 87.45 % Rotamer: Outliers : 3.47 % Allowed : 12.71 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.16), residues: 2040 helix: 0.81 (0.43), residues: 120 sheet: -1.73 (0.17), residues: 792 loop : -4.28 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 92 PHE 0.009 0.001 PHE F 44 TYR 0.017 0.002 TYR H 13 ARG 0.002 0.000 ARG C 116 *********************** 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 125 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 68 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 101 ASN cc_start: 0.5438 (p0) cc_final: 0.5164 (t0) REVERT: F 7 MET cc_start: 0.6933 (mmm) cc_final: 0.6720 (mmm) REVERT: H 101 ASN cc_start: 0.5859 (p0) cc_final: 0.5226 (t0) REVERT: L 101 ASN cc_start: 0.5831 (p0) cc_final: 0.5131 (t0) outliers start: 57 outliers final: 30 residues processed: 121 average time/residue: 0.2999 time to fit residues: 53.5723 Evaluate side-chains 89 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 59 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain E residue 11 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 31 TYR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 11 VAL 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 190 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 112 optimal weight: 40.0000 chunk 144 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 196 optimal weight: 0.0050 chunk 123 optimal weight: 9.9990 chunk 119 optimal weight: 50.0000 chunk 90 optimal weight: 30.0000 overall best weight: 7.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.4093 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= 0.199 Angle : 0.614 13.377 21708 Z= 0.302 Chirality : 0.041 0.127 2268 Planarity : 0.003 0.035 2952 Dihedral : 5.612 21.727 2220 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.14 % Favored : 86.86 % Rotamer: Outliers : 2.74 % Allowed : 13.02 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.20 (0.16), residues: 2040 helix: 0.68 (0.42), residues: 120 sheet: -1.69 (0.17), residues: 792 loop : -4.23 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 92 PHE 0.012 0.001 PHE H 44 TYR 0.021 0.002 TYR I 13 ARG 0.003 0.001 ARG H 116 *********************** 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 99 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 54 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 ASN cc_start: 0.5444 (p0) cc_final: 0.5113 (t0) REVERT: F 7 MET cc_start: 0.6942 (mmm) cc_final: 0.6716 (mmm) REVERT: H 101 ASN cc_start: 0.5870 (p0) cc_final: 0.5195 (t0) REVERT: L 101 ASN cc_start: 0.5871 (p0) cc_final: 0.5105 (t0) outliers start: 45 outliers final: 38 residues processed: 95 average time/residue: 0.3227 time to fit residues: 44.9686 Evaluate side-chains 81 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 43 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 31 TYR Chi-restraints excluded: chain D residue 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 53 ILE Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 11 VAL Chi-restraints excluded: chain L residue 37 VAL Chi-restraints excluded: chain L residue 53 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 3.9990 chunk 78 optimal weight: 50.0000 chunk 117 optimal weight: 50.0000 chunk 59 optimal weight: 8.9990 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 97 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 154 optimal weight: 0.4980 chunk 178 optimal weight: 4.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16056 Z= 0.156 Angle : 0.585 12.635 21708 Z= 0.285 Chirality : 0.040 0.130 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.339 22.462 2220 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.18 % Favored : 88.82 % Rotamer: Outliers : 2.13 % Allowed : 13.50 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.07 (0.16), residues: 2040 helix: 1.19 (0.45), residues: 120 sheet: -1.60 (0.18), residues: 792 loop : -4.21 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 92 PHE 0.007 0.001 PHE H 28 TYR 0.016 0.002 TYR D 13 ARG 0.003 0.000 ARG A 116 *********************** 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 91 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 56 time to evaluate : 1.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 ASN cc_start: 0.5364 (p0) cc_final: 0.5150 (t0) REVERT: H 101 ASN cc_start: 0.5791 (p0) cc_final: 0.5233 (t0) REVERT: L 101 ASN cc_start: 0.5706 (p0) cc_final: 0.5051 (t0) outliers start: 35 outliers final: 23 residues processed: 90 average time/residue: 0.3541 time to fit residues: 45.5485 Evaluate side-chains 75 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 52 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 53 ILE 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 E residue 151 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 153 VAL 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 173 THR Chi-restraints excluded: chain J residue 11 VAL 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 53 ILE Chi-restraints excluded: chain L residue 11 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 188 optimal weight: 40.0000 chunk 171 optimal weight: 0.2980 chunk 183 optimal weight: 40.0000 chunk 110 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 56 optimal weight: 40.0000 chunk 165 optimal weight: 5.9990 chunk 173 optimal weight: 50.0000 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN H 165 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16056 Z= 0.168 Angle : 0.610 12.829 21708 Z= 0.292 Chirality : 0.041 0.126 2268 Planarity : 0.003 0.029 2952 Dihedral : 5.326 21.750 2220 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 1.82 % Allowed : 13.81 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.16), residues: 2040 helix: 1.10 (0.43), residues: 120 sheet: -1.58 (0.18), residues: 792 loop : -4.15 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 92 PHE 0.008 0.001 PHE F 44 TYR 0.016 0.002 TYR D 13 ARG 0.003 0.000 ARG J 116 *********************** 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 82 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 52 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 ASN cc_start: 0.5440 (p0) cc_final: 0.5161 (t0) REVERT: H 101 ASN cc_start: 0.5875 (p0) cc_final: 0.5247 (t0) REVERT: L 101 ASN cc_start: 0.5747 (p0) cc_final: 0.5107 (t0) outliers start: 30 outliers final: 26 residues processed: 82 average time/residue: 0.3467 time to fit residues: 40.7780 Evaluate side-chains 78 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 52 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 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 E residue 151 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 153 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 173 THR Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 173 THR Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 53 ILE Chi-restraints excluded: chain L residue 11 VAL 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 193 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 134 optimal weight: 3.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 40.0000 chunk 161 optimal weight: 40.0000 chunk 16 optimal weight: 50.0000 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 128 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16056 Z= 0.141 Angle : 0.582 12.165 21708 Z= 0.277 Chirality : 0.040 0.134 2268 Planarity : 0.003 0.027 2952 Dihedral : 5.062 22.380 2220 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 1.28 % Allowed : 14.29 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.94 (0.17), residues: 2040 helix: 1.51 (0.46), residues: 120 sheet: -1.48 (0.18), residues: 792 loop : -4.17 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 92 PHE 0.006 0.001 PHE L 28 TYR 0.011 0.001 TYR D 13 ARG 0.002 0.000 ARG J 116 ********************** 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 81 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 60 time to evaluate : 1.863 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 101 ASN cc_start: 0.5463 (p0) cc_final: 0.5132 (t0) REVERT: C 101 ASN cc_start: 0.5353 (p0) cc_final: 0.4890 (t0) REVERT: H 101 ASN cc_start: 0.5746 (p0) cc_final: 0.5236 (t0) REVERT: L 101 ASN cc_start: 0.5618 (p0) cc_final: 0.5099 (t0) outliers start: 21 outliers final: 17 residues processed: 80 average time/residue: 0.3583 time to fit residues: 41.0091 Evaluate side-chains 72 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 31 TYR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 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 E residue 151 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 173 THR 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 172 optimal weight: 50.0000 chunk 49 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 30.0000 chunk 67 optimal weight: 9.9990 chunk 166 optimal weight: 50.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN ** A 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.068888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.063279 restraints weight = 141298.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.064396 restraints weight = 91323.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.065296 restraints weight = 63500.154| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.4586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16056 Z= 0.192 Angle : 0.616 13.538 21708 Z= 0.297 Chirality : 0.041 0.122 2268 Planarity : 0.003 0.028 2952 Dihedral : 5.304 20.563 2220 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 1.40 % Allowed : 14.60 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.16), residues: 2040 helix: 1.07 (0.44), residues: 120 sheet: -1.50 (0.18), residues: 792 loop : -4.14 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 92 PHE 0.011 0.001 PHE H 44 TYR 0.018 0.002 TYR D 13 ARG 0.002 0.001 ARG C 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.29 seconds wall clock time: 42 minutes 33.40 seconds (2553.40 seconds total)