Starting phenix.real_space_refine on Mon Sep 23 11:31:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/09_2024/8ik7_35505.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/09_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_35505/09_2024/8ik7_35505.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/09_2024/8ik7_35505.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/09_2024/8ik7_35505.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ik7_35505/09_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. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 1.02, per 1000 atoms: 0.69 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 156.7 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: 0.48 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: 0.41 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: 0.00 - 6.95: 1863 6.95 - 13.90: 69 13.90 - 20.84: 21 20.84 - 27.79: 8 27.79 - 34.74: 7 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 Time spend for trying shortcut: 0.00 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: 2.950 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.830 Find NCS groups from input model: 0.090 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.700 ------------------------------------------------------------------------------- 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 : 0.145 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: 0.0670 time to fit residues: 3.1751 Evaluate side-chains 19 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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: 9.9990 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 ** F 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 215 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.247 1512 Z= 2.423 Angle : 2.484 18.865 1968 Z= 1.380 Chirality : 0.145 0.354 120 Planarity : 0.017 0.047 312 Dihedral : 15.123 44.608 192 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 64.25 Ramachandran Plot: Outliers : 6.55 % Allowed : 39.29 % Favored : 54.17 % Rotamer: Outliers : 15.83 % Allowed : 24.17 % Favored : 60.00 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 6.25 % 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: -7.12 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.42 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.062 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 30 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 11 time to evaluate : 0.154 Fit side-chains REVERT: G 210 PHE cc_start: 0.4766 (OUTLIER) cc_final: 0.3811 (p90) REVERT: V 210 PHE cc_start: 0.9398 (OUTLIER) cc_final: 0.8771 (t80) REVERT: H 214 ASP cc_start: 0.6770 (m-30) cc_final: 0.6214 (m-30) REVERT: W 215 ASN cc_start: 0.9238 (OUTLIER) cc_final: 0.8347 (t0) outliers start: 19 outliers final: 14 residues processed: 26 average time/residue: 0.0640 time to fit residues: 2.1709 Evaluate side-chains 27 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 10 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C 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 210 PHE Chi-restraints excluded: chain G 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 V residue 210 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 210 PHE 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=4.50 ------------------------------------------------------------------------------- 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** ** 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: 0.8375 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.254 1512 Z= 2.420 Angle : 2.440 18.744 1968 Z= 1.364 Chirality : 0.149 0.380 120 Planarity : 0.015 0.050 312 Dihedral : 15.804 47.055 192 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 68.54 Ramachandran Plot: Outliers : 2.98 % Allowed : 49.40 % Favored : 47.62 % Rotamer: Outliers : 20.83 % Allowed : 25.00 % Favored : 54.17 % 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: -7.50 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.72 (0.29), 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 36 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 11 time to evaluate : 0.152 Fit side-chains REVERT: V 210 PHE cc_start: 0.9098 (OUTLIER) cc_final: 0.8630 (t80) REVERT: P 210 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.7105 (m-80) REVERT: H 214 ASP cc_start: 0.7291 (OUTLIER) cc_final: 0.6906 (m-30) outliers start: 25 outliers final: 18 residues processed: 33 average time/residue: 0.0649 time to fit residues: 2.7293 Evaluate side-chains 32 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 11 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 213 ASN Chi-restraints excluded: chain I residue 210 PHE 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 210 PHE Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain S residue 210 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 216 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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** ** 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: 0.8378 moved from start: 0.7572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.253 1512 Z= 2.421 Angle : 2.473 18.882 1968 Z= 1.384 Chirality : 0.151 0.398 120 Planarity : 0.014 0.053 312 Dihedral : 15.969 44.895 192 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 70.87 Ramachandran Plot: Outliers : 1.79 % Allowed : 55.36 % Favored : 42.86 % Rotamer: Outliers : 22.50 % Allowed : 30.00 % Favored : 47.50 % 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: -7.61 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.30), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.049 0.009 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 38 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 11 time to evaluate : 0.162 Fit side-chains revert: symmetry clash REVERT: V 210 PHE cc_start: 0.9077 (OUTLIER) cc_final: 0.8632 (t80) REVERT: P 210 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.7515 (p90) outliers start: 27 outliers final: 21 residues processed: 34 average time/residue: 0.0633 time to fit residues: 2.7772 Evaluate side-chains 34 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 11 time to evaluate : 0.144 ------------------------------------------------------------------------------- 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 I residue 210 PHE 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 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 P residue 210 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE Chi-restraints excluded: chain B residue 221 ASN Chi-restraints excluded: chain N residue 220 ASP Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 216 PHE 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** ** 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: 0.8380 moved from start: 0.7656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.243 1512 Z= 2.412 Angle : 2.490 19.102 1968 Z= 1.393 Chirality : 0.151 0.399 120 Planarity : 0.014 0.047 312 Dihedral : 16.039 44.795 192 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 72.04 Ramachandran Plot: Outliers : 2.38 % Allowed : 57.14 % Favored : 40.48 % Rotamer: Outliers : 25.83 % Allowed : 30.00 % Favored : 44.17 % 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: -7.67 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.84 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.048 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 42 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 11 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: V 210 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8626 (t80) REVERT: P 210 PHE cc_start: 0.8640 (OUTLIER) cc_final: 0.7502 (p90) outliers start: 31 outliers final: 24 residues processed: 36 average time/residue: 0.0647 time to fit residues: 2.9585 Evaluate side-chains 37 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 11 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain I residue 215 ASN Chi-restraints excluded: chain O residue 210 PHE Chi-restraints excluded: chain O residue 214 ASP Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain V residue 210 PHE Chi-restraints excluded: chain P residue 210 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE 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 F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 216 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- 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** ** 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: 0.8378 moved from start: 0.7713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.244 1512 Z= 2.414 Angle : 2.496 18.994 1968 Z= 1.396 Chirality : 0.151 0.401 120 Planarity : 0.014 0.048 312 Dihedral : 16.128 44.972 192 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 72.04 Ramachandran Plot: Outliers : 2.38 % Allowed : 55.95 % Favored : 41.67 % Rotamer: Outliers : 27.50 % Allowed : 29.17 % Favored : 43.33 % Cbeta Deviations : 0.83 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.38 % 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: -7.64 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.82 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.047 0.009 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 46 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 13 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: V 210 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8684 (t80) REVERT: P 210 PHE cc_start: 0.8629 (OUTLIER) cc_final: 0.7562 (p90) outliers start: 33 outliers final: 26 residues processed: 41 average time/residue: 0.0628 time to fit residues: 3.2379 Evaluate side-chains 40 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 12 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 214 ASP Chi-restraints excluded: chain I residue 210 PHE 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 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 P residue 210 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE 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 F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 216 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- 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** ** 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: 0.8380 moved from start: 0.7748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.244 1512 Z= 2.415 Angle : 2.501 19.067 1968 Z= 1.400 Chirality : 0.150 0.400 120 Planarity : 0.014 0.047 312 Dihedral : 16.212 46.644 192 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 72.43 Ramachandran Plot: Outliers : 1.79 % Allowed : 56.55 % Favored : 41.67 % Rotamer: Outliers : 26.67 % Allowed : 30.00 % Favored : 43.33 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.90 % 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: -7.66 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.83 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.047 0.009 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 44 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 12 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: V 210 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8683 (t80) REVERT: P 210 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7609 (p90) outliers start: 32 outliers final: 26 residues processed: 39 average time/residue: 0.0640 time to fit residues: 3.1563 Evaluate side-chains 40 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 12 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 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 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 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 P residue 210 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE 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 F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 216 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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** ** 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: 0.8379 moved from start: 0.7768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.244 1512 Z= 2.416 Angle : 2.498 19.026 1968 Z= 1.398 Chirality : 0.150 0.400 120 Planarity : 0.014 0.047 312 Dihedral : 16.239 48.147 192 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 73.60 Ramachandran Plot: Outliers : 2.38 % Allowed : 55.36 % Favored : 42.26 % Rotamer: Outliers : 27.50 % Allowed : 29.17 % Favored : 43.33 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.90 % 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 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.80 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.046 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 45 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 12 time to evaluate : 0.132 Fit side-chains revert: symmetry clash REVERT: G 210 PHE cc_start: 0.3703 (OUTLIER) cc_final: 0.3468 (p90) REVERT: V 210 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8681 (t80) REVERT: P 210 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.7617 (p90) outliers start: 33 outliers final: 26 residues processed: 39 average time/residue: 0.0569 time to fit residues: 2.8030 Evaluate side-chains 41 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 12 time to evaluate : 0.132 ------------------------------------------------------------------------------- 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 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 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 P residue 210 PHE Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE 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 F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 216 PHE 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** ** 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: 0.8380 moved from start: 0.7782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.244 1512 Z= 2.415 Angle : 2.497 19.035 1968 Z= 1.398 Chirality : 0.150 0.401 120 Planarity : 0.014 0.046 312 Dihedral : 16.239 48.764 192 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 72.43 Ramachandran Plot: Outliers : 2.38 % Allowed : 55.95 % Favored : 41.67 % Rotamer: Outliers : 28.33 % Allowed : 28.33 % Favored : 43.33 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.90 % 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: -7.61 (0.38), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.79 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.046 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 46 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 12 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: V 210 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8680 (t80) REVERT: P 210 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.7612 (p90) outliers start: 34 outliers final: 27 residues processed: 39 average time/residue: 0.0639 time to fit residues: 3.1496 Evaluate side-chains 41 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 12 time to evaluate : 0.149 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain I residue 210 PHE 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 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 P residue 210 PHE Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE 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 F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 216 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- 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** ** 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: 0.8380 moved from start: 0.7785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.242 1512 Z= 2.415 Angle : 2.500 19.029 1968 Z= 1.400 Chirality : 0.150 0.399 120 Planarity : 0.014 0.045 312 Dihedral : 16.188 49.079 192 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 73.99 Ramachandran Plot: Outliers : 2.38 % Allowed : 55.95 % Favored : 41.67 % Rotamer: Outliers : 24.17 % Allowed : 32.50 % Favored : 43.33 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.90 % 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: -7.57 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.77 (0.30), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.046 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 41 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 12 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: V 210 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8679 (t80) REVERT: P 210 PHE cc_start: 0.8624 (OUTLIER) cc_final: 0.7620 (p90) outliers start: 29 outliers final: 26 residues processed: 36 average time/residue: 0.0644 time to fit residues: 2.9616 Evaluate side-chains 40 residues out of total 120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 12 time to evaluate : 0.155 ------------------------------------------------------------------------------- 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 214 ASP Chi-restraints excluded: chain I residue 210 PHE 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 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 P residue 210 PHE Chi-restraints excluded: chain X residue 216 PHE Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 216 PHE 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 F residue 210 PHE Chi-restraints excluded: chain H residue 214 ASP Chi-restraints excluded: chain W residue 213 ASN Chi-restraints excluded: chain W residue 216 PHE 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** ** 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 = 0.3436 r_free = 0.3436 target = 0.082044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.067500 restraints weight = 4647.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.068202 restraints weight = 3373.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.068745 restraints weight = 2771.619| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.051 0.242 1512 Z= 2.414 Angle : 2.499 19.042 1968 Z= 1.399 Chirality : 0.150 0.400 120 Planarity : 0.014 0.045 312 Dihedral : 16.206 49.001 192 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 73.21 Ramachandran Plot: Outliers : 2.38 % Allowed : 55.36 % Favored : 42.26 % Rotamer: Outliers : 27.50 % Allowed : 29.17 % Favored : 43.33 % Cbeta Deviations : 1.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 9.90 % 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: -7.57 (0.39), residues: 168 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.77 (0.29), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.046 0.009 PHE Q 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 361.26 seconds wall clock time: 7 minutes 9.82 seconds (429.82 seconds total)