Starting phenix.real_space_refine on Sun Dec 10 21:29:37 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/12_2023/6yeg_10792.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/12_2023/6yeg_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_10792/12_2023/6yeg_10792.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/12_2023/6yeg_10792.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/12_2023/6yeg_10792.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yeg_10792/12_2023/6yeg_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 8.40, per 1000 atoms: 0.53 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: 6.14 Conformation dependent library (CDL) restraints added in 3.0 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3600 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 5.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 75 through 83 Processing helix chain 'B' and resid 75 through 83 Processing helix chain 'C' and resid 75 through 83 Processing helix chain 'D' and resid 75 through 83 Processing helix chain 'E' and resid 75 through 83 Processing helix chain 'F' and resid 75 through 83 Processing helix chain 'G' and resid 75 through 83 Processing helix chain 'H' and resid 75 through 83 Processing helix chain 'I' and resid 75 through 83 Processing helix chain 'J' and resid 75 through 83 Processing helix chain 'K' and resid 75 through 83 Processing helix chain 'L' and resid 75 through 83 60 hydrogen bonds defined for protein. 180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 6.60 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 2.670 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 40.500 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.550 ------------------------------------------------------------------------------- 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 : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 195 average time/residue: 0.3076 time to fit residues: 86.8081 Evaluate side-chains 90 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1359 time to fit residues: 3.9407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 GLN ** F 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 140 ASN H 140 ASN I 140 ASN J 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: 0.6087 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16056 Z= 0.239 Angle : 0.691 14.368 21708 Z= 0.349 Chirality : 0.042 0.125 2268 Planarity : 0.004 0.037 2952 Dihedral : 6.472 22.493 2220 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 4.08 % Allowed : 7.85 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.15), residues: 2040 helix: -1.83 (0.41), residues: 120 sheet: -2.09 (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 L 92 PHE 0.017 0.002 PHE A 160 TYR 0.021 0.002 TYR I 118 ARG 0.003 0.001 ARG L 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 160 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 93 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 26 residues processed: 155 average time/residue: 0.2963 time to fit residues: 67.6243 Evaluate side-chains 108 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 82 time to evaluate : 1.733 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1303 time to fit residues: 8.6681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 50.0000 chunk 57 optimal weight: 20.0000 chunk 154 optimal weight: 30.0000 chunk 126 optimal weight: 30.0000 chunk 51 optimal weight: 50.0000 chunk 185 optimal weight: 3.9990 chunk 200 optimal weight: 50.0000 chunk 165 optimal weight: 5.9990 chunk 184 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN F 88 GLN J 133 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6062 moved from start: 0.2876 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= 0.187 Angle : 0.644 12.708 21708 Z= 0.320 Chirality : 0.041 0.119 2268 Planarity : 0.003 0.032 2952 Dihedral : 6.020 24.100 2220 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.60 % Favored : 87.40 % Rotamer: Outliers : 1.52 % Allowed : 9.55 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.62 (0.16), residues: 2040 helix: -0.40 (0.45), residues: 120 sheet: -1.92 (0.16), residues: 804 loop : -4.48 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 92 PHE 0.010 0.001 PHE F 160 TYR 0.016 0.002 TYR J 118 ARG 0.003 0.001 ARG I 116 *********************** 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 113 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 88 time to evaluate : 1.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 3 residues processed: 108 average time/residue: 0.3415 time to fit residues: 53.5684 Evaluate side-chains 84 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 1.906 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1476 time to fit residues: 3.4976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 7.9990 chunk 139 optimal weight: 40.0000 chunk 96 optimal weight: 50.0000 chunk 20 optimal weight: 8.9990 chunk 88 optimal weight: 40.0000 chunk 124 optimal weight: 0.5980 chunk 186 optimal weight: 20.0000 chunk 197 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 176 optimal weight: 20.0000 chunk 53 optimal weight: 0.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** B 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 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: 0.6034 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16056 Z= 0.161 Angle : 0.601 12.036 21708 Z= 0.297 Chirality : 0.041 0.166 2268 Planarity : 0.003 0.029 2952 Dihedral : 5.599 23.354 2220 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.91 % Favored : 88.09 % Rotamer: Outliers : 0.79 % Allowed : 10.95 % Favored : 88.26 % 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: -4.42 (0.16), residues: 2040 helix: 0.40 (0.45), residues: 120 sheet: -1.81 (0.17), residues: 804 loop : -4.42 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP J 92 PHE 0.008 0.001 PHE F 160 TYR 0.014 0.001 TYR J 118 ARG 0.002 0.000 ARG I 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 100 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 97 average time/residue: 0.3577 time to fit residues: 49.8306 Evaluate side-chains 76 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 1.885 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1986 time to fit residues: 2.7680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 50.0000 chunk 2 optimal weight: 8.9990 chunk 146 optimal weight: 50.0000 chunk 81 optimal weight: 6.9990 chunk 168 optimal weight: 50.0000 chunk 136 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 100 optimal weight: 7.9990 chunk 176 optimal weight: 30.0000 chunk 49 optimal weight: 30.0000 overall best weight: 14.7994 ------------------------------------------------------------------------------- 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** ** E 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN K 50 ASN ** 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: 0.6239 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16056 Z= 0.321 Angle : 0.724 15.213 21708 Z= 0.363 Chirality : 0.043 0.131 2268 Planarity : 0.004 0.027 2952 Dihedral : 6.451 22.247 2220 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 19.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.62 % Favored : 83.38 % Rotamer: Outliers : 2.43 % Allowed : 12.10 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.16), residues: 2040 helix: 0.34 (0.41), residues: 108 sheet: -1.87 (0.17), residues: 792 loop : -4.35 (0.14), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 92 PHE 0.021 0.002 PHE H 44 TYR 0.021 0.003 TYR B 118 ARG 0.005 0.001 ARG L 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 110 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 70 time to evaluate : 2.022 Fit side-chains outliers start: 40 outliers final: 19 residues processed: 107 average time/residue: 0.3256 time to fit residues: 51.1360 Evaluate side-chains 74 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 55 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1483 time to fit residues: 7.6534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 38 optimal weight: 0.0970 chunk 115 optimal weight: 30.0000 chunk 48 optimal weight: 1.9990 chunk 197 optimal weight: 50.0000 chunk 163 optimal weight: 20.0000 chunk 91 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 65 optimal weight: 0.3980 chunk 103 optimal weight: 7.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 133 GLN F 88 GLN ** J 47 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6054 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16056 Z= 0.142 Angle : 0.598 12.129 21708 Z= 0.293 Chirality : 0.041 0.134 2268 Planarity : 0.003 0.030 2952 Dihedral : 5.526 23.903 2220 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 1.03 % Allowed : 12.41 % Favored : 86.56 % 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: -4.23 (0.16), residues: 2040 helix: 0.97 (0.45), residues: 120 sheet: -1.71 (0.17), residues: 792 loop : -4.30 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 92 PHE 0.007 0.001 PHE H 28 TYR 0.015 0.001 TYR G 118 ARG 0.002 0.000 ARG L 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 92 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 2 residues processed: 91 average time/residue: 0.3417 time to fit residues: 45.2794 Evaluate side-chains 59 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1971 time to fit residues: 3.1267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.2980 chunk 112 optimal weight: 9.9990 chunk 144 optimal weight: 30.0000 chunk 111 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 196 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 119 optimal weight: 50.0000 chunk 90 optimal weight: 7.9990 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.6108 moved from start: 0.4181 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= 0.175 Angle : 0.607 12.591 21708 Z= 0.296 Chirality : 0.041 0.129 2268 Planarity : 0.003 0.029 2952 Dihedral : 5.517 21.989 2220 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 0.67 % Allowed : 13.44 % Favored : 85.89 % 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: -4.15 (0.16), residues: 2040 helix: 0.91 (0.44), residues: 120 sheet: -1.64 (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 0.010 0.001 PHE H 44 TYR 0.015 0.002 TYR D 13 ARG 0.004 0.000 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 62 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 61 average time/residue: 0.4052 time to fit residues: 35.0570 Evaluate side-chains 48 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 1.784 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1365 time to fit residues: 3.3217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 117 optimal weight: 0.0010 chunk 59 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 133 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 18 optimal weight: 40.0000 chunk 154 optimal weight: 0.5980 chunk 178 optimal weight: 40.0000 overall best weight: 1.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 GLN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5997 moved from start: 0.4393 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= 0.136 Angle : 0.573 11.143 21708 Z= 0.278 Chirality : 0.040 0.133 2268 Planarity : 0.003 0.030 2952 Dihedral : 5.123 23.122 2220 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 0.18 % Allowed : 13.38 % Favored : 86.44 % 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: -4.01 (0.16), residues: 2040 helix: 1.55 (0.46), residues: 120 sheet: -1.53 (0.18), residues: 792 loop : -4.22 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 92 PHE 0.006 0.001 PHE H 28 TYR 0.023 0.001 TYR D 104 ARG 0.002 0.000 ARG G 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.4015 time to fit residues: 32.4516 Evaluate side-chains 47 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 46 time to evaluate : 1.805 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1298 time to fit residues: 2.5441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 110 optimal weight: 20.0000 chunk 79 optimal weight: 40.0000 chunk 143 optimal weight: 40.0000 chunk 56 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.6084 moved from start: 0.4469 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= 0.173 Angle : 0.608 12.598 21708 Z= 0.293 Chirality : 0.040 0.125 2268 Planarity : 0.003 0.030 2952 Dihedral : 5.252 20.910 2220 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer: Outliers : 0.24 % Allowed : 14.11 % Favored : 85.64 % 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: -4.01 (0.16), residues: 2040 helix: 1.22 (0.45), residues: 120 sheet: -1.56 (0.18), residues: 792 loop : -4.16 (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 H 44 TYR 0.016 0.002 TYR D 13 ARG 0.002 0.000 ARG I 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 50 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 1.912 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 49 average time/residue: 0.3924 time to fit residues: 28.6478 Evaluate side-chains 45 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1430 time to fit residues: 2.8302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 20.0000 chunk 118 optimal weight: 50.0000 chunk 91 optimal weight: 20.0000 chunk 134 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 187 optimal weight: 50.0000 chunk 161 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 125 optimal weight: 7.9990 chunk 99 optimal weight: 0.0970 chunk 128 optimal weight: 20.0000 overall best weight: 11.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 165 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: 0.6215 moved from start: 0.4627 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= 0.265 Angle : 0.690 15.475 21708 Z= 0.337 Chirality : 0.042 0.118 2268 Planarity : 0.003 0.031 2952 Dihedral : 5.926 21.811 2220 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.26 % Favored : 85.74 % Rotamer: Outliers : 0.30 % Allowed : 14.17 % Favored : 85.52 % 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: 0.43 (0.41), residues: 120 sheet: -1.80 (0.17), residues: 804 loop : -4.12 (0.14), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 92 PHE 0.016 0.002 PHE H 44 TYR 0.029 0.002 TYR D 13 ARG 0.003 0.001 ARG A 93 ********************** 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 47 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 42 time to evaluate : 2.048 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 47 average time/residue: 0.3576 time to fit residues: 25.6570 Evaluate side-chains 40 residues out of total 1644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 1.917 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1614 time to fit residues: 3.1207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0980 chunk 149 optimal weight: 0.8980 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 162 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 29 optimal weight: 10.0000 chunk 142 optimal weight: 30.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 165 GLN I 165 GLN ** 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 = 0.3838 r_free = 0.3838 target = 0.069104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.063573 restraints weight = 142285.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.064708 restraints weight = 91804.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.065518 restraints weight = 63736.629| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4715 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= 0.159 Angle : 0.606 13.389 21708 Z= 0.292 Chirality : 0.041 0.133 2268 Planarity : 0.003 0.031 2952 Dihedral : 5.409 22.079 2220 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.78 % Favored : 89.22 % Rotamer: Outliers : 0.06 % Allowed : 14.29 % Favored : 85.64 % 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: -4.02 (0.16), residues: 2040 helix: 1.27 (0.45), residues: 120 sheet: -1.64 (0.17), residues: 792 loop : -4.11 (0.14), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 92 PHE 0.008 0.001 PHE J 28 TYR 0.014 0.002 TYR G 118 ARG 0.002 0.000 ARG J 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2229.77 seconds wall clock time: 42 minutes 38.42 seconds (2558.42 seconds total)