Starting phenix.real_space_refine on Thu Jul 18 16:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/07_2024/8ik7_35505.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/07_2024/8ik7_35505.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/07_2024/8ik7_35505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/07_2024/8ik7_35505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/07_2024/8ik7_35505.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/07_2024/8ik7_35505.cif" } resolution = 3.69 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= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 912 2.51 5 N 264 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 1488 Number of models: 1 Model: "" Number of chains: 24 Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "L" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "M" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "K" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "G" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "I" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "U" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "O" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "R" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "V" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "P" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "S" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "X" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "N" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "W" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "Q" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Chain: "T" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 62 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 0.98, per 1000 atoms: 0.66 Number of scatterers: 1488 At special positions: 0 Unit cell: (126.16, 90.47, 24.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 312 8.00 N 264 7.00 C 912 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: 1.79 Conformation dependent library (CDL) restraints added in 428.0 milliseconds 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 312 1.28 - 1.35: 240 1.35 - 1.41: 288 1.41 - 1.47: 221 1.47 - 1.54: 451 Bond restraints: 1512 Sorted by residual: bond pdb=" CA PHE B 222 " pdb=" CB PHE B 222 " ideal model delta sigma weight residual 1.529 1.484 0.045 1.63e-02 3.76e+03 7.64e+00 bond pdb=" CA PHE N 216 " pdb=" C PHE N 216 " ideal model delta sigma weight residual 1.532 1.514 0.019 9.60e-03 1.09e+04 3.84e+00 bond pdb=" CB PHE U 216 " pdb=" CG PHE U 216 " ideal model delta sigma weight residual 1.502 1.461 0.041 2.30e-02 1.89e+03 3.24e+00 bond pdb=" CB PHE W 216 " pdb=" CG PHE W 216 " ideal model delta sigma weight residual 1.502 1.461 0.041 2.30e-02 1.89e+03 3.10e+00 bond pdb=" CA ASN D 215 " pdb=" CB ASN D 215 " ideal model delta sigma weight residual 1.530 1.506 0.025 1.50e-02 4.44e+03 2.71e+00 ... (remaining 1507 not shown) Histogram of bond angle deviations from ideal: 77.33 - 91.74: 13 91.74 - 106.14: 88 106.14 - 120.54: 1127 120.54 - 134.95: 735 134.95 - 149.35: 5 Bond angle restraints: 1968 Sorted by residual: angle pdb=" N GLY Q 211 " pdb=" CA GLY Q 211 " pdb=" C GLY Q 211 " ideal model delta sigma weight residual 112.49 141.77 -29.28 1.21e+00 6.83e-01 5.86e+02 angle pdb=" N GLY T 211 " pdb=" CA GLY T 211 " pdb=" C GLY T 211 " ideal model delta sigma weight residual 114.61 149.35 -34.74 1.49e+00 4.50e-01 5.44e+02 angle pdb=" N GLY R 211 " pdb=" CA GLY R 211 " pdb=" C GLY R 211 " ideal model delta sigma weight residual 114.10 148.75 -34.65 1.51e+00 4.39e-01 5.26e+02 angle pdb=" N ASN I 215 " pdb=" CA ASN I 215 " pdb=" CB ASN I 215 " ideal model delta sigma weight residual 110.47 77.33 33.14 1.66e+00 3.63e-01 3.98e+02 angle pdb=" N ASP I 214 " pdb=" CA ASP I 214 " pdb=" C ASP I 214 " ideal model delta sigma weight residual 109.59 78.79 30.80 1.61e+00 3.86e-01 3.66e+02 ... (remaining 1963 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 7.86: 453 7.86 - 15.71: 140 15.71 - 23.56: 49 23.56 - 31.41: 19 31.41 - 39.25: 11 Dihedral angle restraints: 672 sinusoidal: 240 harmonic: 432 Sorted by residual: dihedral pdb=" N ASN I 215 " pdb=" C ASN I 215 " pdb=" CA ASN I 215 " pdb=" CB ASN I 215 " ideal model delta harmonic sigma weight residual 122.80 83.55 39.25 0 2.50e+00 1.60e-01 2.47e+02 dihedral pdb=" C PHE B 222 " pdb=" N PHE B 222 " pdb=" CA PHE B 222 " pdb=" CB PHE B 222 " ideal model delta harmonic sigma weight residual -122.60 -157.09 34.49 0 2.50e+00 1.60e-01 1.90e+02 dihedral pdb=" C PHE C 216 " pdb=" N PHE C 216 " pdb=" CA PHE C 216 " pdb=" CB PHE C 216 " ideal model delta harmonic sigma weight residual -122.60 -156.80 34.20 0 2.50e+00 1.60e-01 1.87e+02 ... (remaining 669 not shown) Histogram of chiral volume deviations from ideal: 0.008 - 0.308: 97 0.308 - 0.609: 13 0.609 - 0.910: 6 0.910 - 1.210: 1 1.210 - 1.511: 3 Chirality restraints: 120 Sorted by residual: chirality pdb=" CA PHE B 222 " pdb=" N PHE B 222 " pdb=" C PHE B 222 " pdb=" CB PHE B 222 " both_signs ideal model delta sigma weight residual False 2.51 1.00 1.51 2.00e-01 2.50e+01 5.71e+01 chirality pdb=" CA PHE C 216 " pdb=" N PHE C 216 " pdb=" C PHE C 216 " pdb=" CB PHE C 216 " both_signs ideal model delta sigma weight residual False 2.51 1.17 1.34 2.00e-01 2.50e+01 4.50e+01 chirality pdb=" CA PHE H 216 " pdb=" N PHE H 216 " pdb=" C PHE H 216 " pdb=" CB PHE H 216 " both_signs ideal model delta sigma weight residual False 2.51 1.17 1.34 2.00e-01 2.50e+01 4.49e+01 ... (remaining 117 not shown) Planarity restraints: 312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE I 210 " 0.013 2.00e-02 2.50e+03 1.51e-02 4.01e+00 pdb=" CG PHE I 210 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE I 210 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE I 210 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE I 210 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE I 210 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE I 210 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 214 " -0.006 2.00e-02 2.50e+03 1.13e-02 1.29e+00 pdb=" C ASP H 214 " 0.020 2.00e-02 2.50e+03 pdb=" O ASP H 214 " -0.007 2.00e-02 2.50e+03 pdb=" N ASN H 215 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 216 " -0.006 2.00e-02 2.50e+03 8.06e-03 1.14e+00 pdb=" CG PHE L 216 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 PHE L 216 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE L 216 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE L 216 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE L 216 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE L 216 " -0.001 2.00e-02 2.50e+03 ... (remaining 309 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 47 2.53 - 3.12: 1307 3.12 - 3.71: 1620 3.71 - 4.31: 2246 4.31 - 4.90: 3071 Nonbonded interactions: 8291 Sorted by model distance: nonbonded pdb=" O ASN P 213 " pdb=" OD1 ASP P 214 " model vdw 1.936 3.040 nonbonded pdb=" O ASN R 213 " pdb=" OD1 ASN R 213 " model vdw 1.964 3.040 nonbonded pdb=" O ASP I 214 " pdb=" OD1 ASP I 214 " model vdw 2.032 3.040 nonbonded pdb=" N ASP I 214 " pdb=" O ASP I 214 " model vdw 2.042 2.496 nonbonded pdb=" N ASN F 215 " pdb=" O ASN F 215 " model vdw 2.082 2.496 ... (remaining 8286 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } 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: 2.830 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: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.000 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 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 : 0.009 0.045 1512 Z= 0.428 Angle : 3.746 34.741 1968 Z= 2.184 Chirality : 0.340 1.511 120 Planarity : 0.003 0.015 312 Dihedral : 10.510 35.419 432 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 29.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 22.50 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.31), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.49 (0.24), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE I 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 0.156 Fit side-chains REVERT: R 214 ASP cc_start: 0.8528 (p0) cc_final: 0.8303 (m-30) REVERT: P 210 PHE cc_start: 0.8334 (p90) cc_final: 0.6844 (t80) REVERT: A 222 PHE cc_start: 0.7226 (m-80) cc_final: 0.4813 (p90) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0650 time to fit residues: 3.1174 Evaluate side-chains 19 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 10.0000 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 213 ASN ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.6808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.268 1512 Z= 2.448 Angle : 2.526 18.624 1968 Z= 1.425 Chirality : 0.146 0.369 120 Planarity : 0.017 0.051 312 Dihedral : 14.699 41.227 192 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 77.49 Ramachandran Plot: Outliers : 8.93 % Allowed : 39.88 % Favored : 51.19 % Rotamer: Outliers : 27.50 % Allowed : 22.50 % Favored : 50.00 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 4.69 % 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: -7.28 (0.37), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.55 (0.28), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.060 0.010 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 13 time to evaluate : 0.159 Fit side-chains REVERT: P 210 PHE cc_start: 0.8304 (p90) cc_final: 0.6859 (t80) REVERT: J 215 ASN cc_start: 0.9016 (OUTLIER) cc_final: 0.8511 (p0) REVERT: H 214 ASP cc_start: 0.6802 (m-30) cc_final: 0.6273 (m-30) outliers start: 33 outliers final: 23 residues processed: 42 average time/residue: 0.0660 time to fit residues: 3.4765 Evaluate side-chains 37 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 13 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain W residue 214 ASP Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.7414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.275 1512 Z= 2.455 Angle : 2.518 18.917 1968 Z= 1.422 Chirality : 0.150 0.419 120 Planarity : 0.016 0.054 312 Dihedral : 15.589 42.068 192 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 87.23 Ramachandran Plot: Outliers : 4.17 % Allowed : 52.38 % Favored : 43.45 % Rotamer: Outliers : 39.17 % Allowed : 17.50 % Favored : 43.33 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.77 % 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: -7.48 (0.40), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.70 (0.30), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.052 0.009 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 10 time to evaluate : 0.145 Fit side-chains REVERT: G 210 PHE cc_start: 0.3885 (OUTLIER) cc_final: 0.2989 (p90) REVERT: P 210 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: J 215 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8522 (p0) REVERT: H 214 ASP cc_start: 0.6930 (OUTLIER) cc_final: 0.6520 (m-30) REVERT: W 213 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8545 (p0) REVERT: W 215 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8225 (t0) outliers start: 47 outliers final: 33 residues processed: 52 average time/residue: 0.0637 time to fit residues: 4.1234 Evaluate side-chains 51 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 12 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain S residue 210 PHE Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.7596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.278 1512 Z= 2.459 Angle : 2.523 18.952 1968 Z= 1.428 Chirality : 0.151 0.453 120 Planarity : 0.015 0.053 312 Dihedral : 15.910 45.473 192 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 91.51 Ramachandran Plot: Outliers : 3.57 % Allowed : 54.17 % Favored : 42.26 % Rotamer: Outliers : 44.17 % Allowed : 16.67 % Favored : 39.17 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.29 % 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: -7.53 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.73 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.051 0.008 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 11 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: P 210 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7623 (p90) REVERT: J 215 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8519 (p0) REVERT: W 213 ASN cc_start: 0.8847 (OUTLIER) cc_final: 0.8555 (p0) REVERT: W 215 ASN cc_start: 0.9230 (OUTLIER) cc_final: 0.8127 (t0) outliers start: 53 outliers final: 39 residues processed: 57 average time/residue: 0.0539 time to fit residues: 3.8543 Evaluate side-chains 55 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 12 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.7693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.278 1512 Z= 2.460 Angle : 2.533 19.088 1968 Z= 1.433 Chirality : 0.152 0.452 120 Planarity : 0.015 0.053 312 Dihedral : 16.127 46.343 192 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 91.12 Ramachandran Plot: Outliers : 4.17 % Allowed : 57.14 % Favored : 38.69 % Rotamer: Outliers : 42.50 % Allowed : 18.33 % Favored : 39.17 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 8.33 % 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: -7.60 (0.40), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.049 0.008 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 12 time to evaluate : 0.156 Fit side-chains revert: symmetry clash REVERT: P 210 PHE cc_start: 0.8721 (OUTLIER) cc_final: 0.7781 (p90) REVERT: J 215 ASN cc_start: 0.8956 (OUTLIER) cc_final: 0.8520 (p0) REVERT: W 213 ASN cc_start: 0.8818 (OUTLIER) cc_final: 0.8583 (p0) REVERT: W 215 ASN cc_start: 0.9229 (OUTLIER) cc_final: 0.8202 (t0) outliers start: 51 outliers final: 41 residues processed: 55 average time/residue: 0.0604 time to fit residues: 4.1368 Evaluate side-chains 58 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 13 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 213 ASN Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 213 ASN Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.7767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.279 1512 Z= 2.459 Angle : 2.537 19.002 1968 Z= 1.435 Chirality : 0.152 0.456 120 Planarity : 0.015 0.053 312 Dihedral : 16.250 46.764 192 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 91.90 Ramachandran Plot: Outliers : 4.17 % Allowed : 55.36 % Favored : 40.48 % Rotamer: Outliers : 46.67 % Allowed : 15.83 % Favored : 37.50 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.81 % 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: -7.63 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.81 (0.30), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.008 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 12 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: P 210 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.7788 (p90) REVERT: J 215 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8522 (p0) REVERT: W 213 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (p0) REVERT: W 215 ASN cc_start: 0.9245 (OUTLIER) cc_final: 0.8223 (t0) outliers start: 56 outliers final: 42 residues processed: 58 average time/residue: 0.0658 time to fit residues: 4.7554 Evaluate side-chains 58 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 12 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 214 ASP Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 213 ASN Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 213 ASN Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.7838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.279 1512 Z= 2.462 Angle : 2.536 19.100 1968 Z= 1.437 Chirality : 0.152 0.457 120 Planarity : 0.015 0.053 312 Dihedral : 16.357 51.581 192 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 91.51 Ramachandran Plot: Outliers : 4.76 % Allowed : 55.36 % Favored : 39.88 % Rotamer: Outliers : 45.83 % Allowed : 15.83 % Favored : 38.33 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.81 % 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: -7.51 (0.43), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.72 (0.33), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.008 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 13 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: G 216 PHE cc_start: 0.9027 (OUTLIER) cc_final: 0.8514 (t80) REVERT: V 210 PHE cc_start: 0.9135 (OUTLIER) cc_final: 0.8763 (t80) REVERT: P 210 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7724 (p90) REVERT: J 215 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8524 (p0) REVERT: W 213 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8593 (p0) REVERT: W 215 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8231 (t0) outliers start: 55 outliers final: 41 residues processed: 60 average time/residue: 0.0613 time to fit residues: 4.5384 Evaluate side-chains 60 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 13 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 210 PHE Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 213 ASN Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 213 ASN Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.7906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.279 1512 Z= 2.462 Angle : 2.539 19.036 1968 Z= 1.439 Chirality : 0.152 0.457 120 Planarity : 0.015 0.053 312 Dihedral : 16.387 53.470 192 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 90.73 Ramachandran Plot: Outliers : 4.17 % Allowed : 55.36 % Favored : 40.48 % Rotamer: Outliers : 45.00 % Allowed : 18.33 % Favored : 36.67 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.81 % 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: -7.55 (0.41), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.75 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.009 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 13 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: G 216 PHE cc_start: 0.9037 (OUTLIER) cc_final: 0.8581 (t80) REVERT: V 210 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8865 (t80) REVERT: P 210 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7716 (p90) REVERT: J 215 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8523 (p0) REVERT: W 215 ASN cc_start: 0.9266 (OUTLIER) cc_final: 0.8262 (t0) outliers start: 54 outliers final: 41 residues processed: 58 average time/residue: 0.0638 time to fit residues: 4.5996 Evaluate side-chains 59 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 13 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 210 PHE Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 210 PHE Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 213 ASN Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 213 ASN Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 0.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.7940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.276 1512 Z= 2.463 Angle : 2.541 19.129 1968 Z= 1.440 Chirality : 0.152 0.452 120 Planarity : 0.015 0.052 312 Dihedral : 16.387 53.594 192 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 91.51 Ramachandran Plot: Outliers : 4.17 % Allowed : 55.36 % Favored : 40.48 % Rotamer: Outliers : 45.00 % Allowed : 18.33 % Favored : 36.67 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.81 % 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: -7.59 (0.40), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.78 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.009 PHE Q 216 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 13 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: G 216 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8588 (t80) REVERT: V 210 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8813 (t80) REVERT: P 210 PHE cc_start: 0.8661 (OUTLIER) cc_final: 0.7712 (p90) REVERT: J 215 ASN cc_start: 0.8954 (OUTLIER) cc_final: 0.8527 (p0) REVERT: W 215 ASN cc_start: 0.9257 (OUTLIER) cc_final: 0.8237 (t0) outliers start: 54 outliers final: 40 residues processed: 59 average time/residue: 0.0634 time to fit residues: 4.6301 Evaluate side-chains 59 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 14 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 210 PHE Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 213 ASN Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 213 ASN Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.275 1512 Z= 2.461 Angle : 2.551 19.107 1968 Z= 1.446 Chirality : 0.152 0.452 120 Planarity : 0.015 0.051 312 Dihedral : 16.315 53.531 192 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 92.29 Ramachandran Plot: Outliers : 4.76 % Allowed : 55.36 % Favored : 39.88 % Rotamer: Outliers : 40.83 % Allowed : 22.50 % Favored : 36.67 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.81 % 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: -7.62 (0.40), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.81 (0.31), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.009 PHE Q 216 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 336 Ramachandran restraints generated. 168 Oldfield, 0 Emsley, 168 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 13 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: G 216 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8580 (t80) REVERT: V 210 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8813 (t80) REVERT: P 210 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7712 (p90) REVERT: J 215 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8527 (p0) REVERT: W 215 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.8231 (t0) outliers start: 49 outliers final: 39 residues processed: 57 average time/residue: 0.0617 time to fit residues: 4.3777 Evaluate side-chains 57 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 13 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 ASN Chi-restraints excluded: chain L residue 219 ASN Chi-restraints excluded: chain L residue 221 ASN Chi-restraints excluded: chain M residue 219 ASN Chi-restraints excluded: chain K residue 214 ASP Chi-restraints excluded: chain K residue 215 ASN Chi-restraints excluded: chain G residue 213 ASN Chi-restraints excluded: chain G residue 216 PHE Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 213 ASN Chi-restraints excluded: chain I residue 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain U residue 214 ASP Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 213 ASN Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain O residue 215 ASN Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 210 PHE Chi-restraints excluded: chain V residue 213 ASN Chi-restraints excluded: chain V residue 215 ASN Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain S residue 213 ASN Chi-restraints excluded: chain S residue 214 ASP Chi-restraints excluded: chain X residue 213 ASN Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 213 ASN Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain E residue 213 ASN Chi-restraints excluded: chain E residue 214 ASP Chi-restraints excluded: chain A residue 219 ASN Chi-restraints excluded: chain B residue 219 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain J residue 213 ASN Chi-restraints excluded: chain J residue 215 ASN Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 213 ASN Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 215 ASN Chi-restraints excluded: chain W residue 216 PHE Chi-restraints excluded: chain Q residue 213 ASN Chi-restraints excluded: chain Q residue 215 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1 random chunks: chunk 0 optimal weight: 1.9990 overall best weight: 50.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.081707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.067335 restraints weight = 4681.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.068051 restraints weight = 3395.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.068051 restraints weight = 2792.660| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.7966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.052 0.275 1512 Z= 2.462 Angle : 2.555 19.112 1968 Z= 1.444 Chirality : 0.152 0.453 120 Planarity : 0.015 0.050 312 Dihedral : 16.338 53.779 192 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 92.29 Ramachandran Plot: Outliers : 4.76 % Allowed : 56.55 % Favored : 38.69 % Rotamer: Outliers : 38.33 % Allowed : 25.00 % Favored : 36.67 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 7.81 % 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: -7.63 (0.40), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.81 (0.30), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 0.009 PHE Q 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 382.89 seconds wall clock time: 7 minutes 37.80 seconds (457.80 seconds total)