Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/03_2024/6vhl_21207_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/03_2024/6vhl_21207.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/03_2024/6vhl_21207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/03_2024/6vhl_21207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/03_2024/6vhl_21207_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vhl_21207/03_2024/6vhl_21207_neut.pdb" } resolution = 3.3 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 2 5.16 5 C 742 2.51 5 N 220 2.21 5 O 226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1190 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 8 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Time building chain proxies: 1.23, per 1000 atoms: 1.03 Number of scatterers: 1190 At special positions: 0 Unit cell: (146.64, 78, 28.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 2 16.00 O 226 8.00 N 220 7.00 C 742 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: 0.33 Conformation dependent library (CDL) restraints added in 218.6 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 268 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: 0.23 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: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 393 1.34 - 1.46: 184 1.46 - 1.57: 627 1.57 - 1.69: 0 1.69 - 1.80: 2 Bond restraints: 1206 Sorted by residual: bond pdb=" N ARG F 379 " pdb=" CA ARG F 379 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.34e+00 bond pdb=" N ARG E 379 " pdb=" CA ARG E 379 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.27e+00 bond pdb=" N LYS F 370 " pdb=" CA LYS F 370 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.20e-02 6.94e+03 6.51e+00 bond pdb=" CE LYS E 370 " pdb=" NZ LYS E 370 " ideal model delta sigma weight residual 1.489 1.426 0.063 3.00e-02 1.11e+03 4.43e+00 bond pdb=" N LYS F 369 " pdb=" CA LYS F 369 " ideal model delta sigma weight residual 1.455 1.480 -0.025 1.27e-02 6.20e+03 4.03e+00 ... (remaining 1201 not shown) Histogram of bond angle deviations from ideal: 102.45 - 108.22: 79 108.22 - 113.99: 678 113.99 - 119.77: 297 119.77 - 125.54: 534 125.54 - 131.32: 20 Bond angle restraints: 1608 Sorted by residual: angle pdb=" N LYS E 369 " pdb=" CA LYS E 369 " pdb=" CB LYS E 369 " ideal model delta sigma weight residual 110.44 117.19 -6.75 1.43e+00 4.89e-01 2.23e+01 angle pdb=" N LYS F 369 " pdb=" CA LYS F 369 " pdb=" C LYS F 369 " ideal model delta sigma weight residual 110.50 105.97 4.53 1.41e+00 5.03e-01 1.03e+01 angle pdb=" CA GLY E 367 " pdb=" C GLY E 367 " pdb=" N ASN E 368 " ideal model delta sigma weight residual 116.69 110.25 6.44 2.04e+00 2.40e-01 9.96e+00 angle pdb=" C THR E 377 " pdb=" N PHE E 378 " pdb=" CA PHE E 378 " ideal model delta sigma weight residual 122.67 126.92 -4.25 1.47e+00 4.63e-01 8.37e+00 angle pdb=" C THR F 377 " pdb=" N PHE F 378 " pdb=" CA PHE F 378 " ideal model delta sigma weight residual 122.67 126.91 -4.24 1.47e+00 4.63e-01 8.33e+00 ... (remaining 1603 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 12.67: 592 12.67 - 25.32: 86 25.32 - 37.98: 27 37.98 - 50.64: 17 50.64 - 63.29: 6 Dihedral angle restraints: 728 sinusoidal: 304 harmonic: 424 Sorted by residual: dihedral pdb=" C GLU F 380 " pdb=" N GLU F 380 " pdb=" CA GLU F 380 " pdb=" CB GLU F 380 " ideal model delta harmonic sigma weight residual -122.60 -132.58 9.98 0 2.50e+00 1.60e-01 1.59e+01 dihedral pdb=" C GLU E 380 " pdb=" N GLU E 380 " pdb=" CA GLU E 380 " pdb=" CB GLU E 380 " ideal model delta harmonic sigma weight residual -122.60 -132.47 9.87 0 2.50e+00 1.60e-01 1.56e+01 dihedral pdb=" N GLU F 380 " pdb=" C GLU F 380 " pdb=" CA GLU F 380 " pdb=" CB GLU F 380 " ideal model delta harmonic sigma weight residual 122.80 132.04 -9.24 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 725 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.084: 147 0.084 - 0.167: 26 0.167 - 0.249: 3 0.249 - 0.332: 0 0.332 - 0.415: 2 Chirality restraints: 178 Sorted by residual: chirality pdb=" CA GLU F 380 " pdb=" N GLU F 380 " pdb=" C GLU F 380 " pdb=" CB GLU F 380 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" CA GLU E 380 " pdb=" N GLU E 380 " pdb=" C GLU E 380 " pdb=" CB GLU E 380 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" CA PHE E 378 " pdb=" N PHE E 378 " pdb=" C PHE E 378 " pdb=" CB PHE E 378 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 175 not shown) Planarity restraints: 206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 367 " -0.024 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C GLY E 367 " 0.088 2.00e-02 2.50e+03 pdb=" O GLY E 367 " -0.035 2.00e-02 2.50e+03 pdb=" N ASN E 368 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 367 " 0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C GLY F 367 " -0.058 2.00e-02 2.50e+03 pdb=" O GLY F 367 " 0.023 2.00e-02 2.50e+03 pdb=" N ASN F 368 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS E 331 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO E 332 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 332 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 332 " -0.027 5.00e-02 4.00e+02 ... (remaining 203 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 7 2.41 - 3.03: 635 3.03 - 3.66: 1387 3.66 - 4.28: 1677 4.28 - 4.90: 2417 Nonbonded interactions: 6123 Sorted by model distance: nonbonded pdb=" NZ LYS E 317 " pdb=" O GLY E 402 " model vdw 1.791 2.520 nonbonded pdb=" NZ LYS F 317 " pdb=" O GLY F 402 " model vdw 1.807 2.520 nonbonded pdb=" CE LYS F 317 " pdb=" O GLY F 402 " model vdw 1.970 3.440 nonbonded pdb=" CE LYS E 317 " pdb=" O GLY E 402 " model vdw 1.974 3.440 nonbonded pdb=" OG SER F 320 " pdb=" OD1 ASN F 368 " model vdw 2.392 2.440 ... (remaining 6118 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 'E' selection = chain 'F' } 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 individual isotropic 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: 1.030 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: 3.720 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 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 : 0.007 0.063 1206 Z= 0.362 Angle : 1.031 7.962 1608 Z= 0.579 Chirality : 0.072 0.415 178 Planarity : 0.008 0.051 206 Dihedral : 15.846 63.293 460 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.67 % Favored : 85.33 % Rotamer: Outliers : 4.48 % Allowed : 4.48 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.30 (0.40), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.79 (0.30), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.003 0.001 PHE F 346 TYR 0.007 0.003 TYR E 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 43 time to evaluate : 0.146 Fit side-chains REVERT: E 311 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8216 (mtpt) REVERT: E 349 ARG cc_start: 0.6252 (mtp-110) cc_final: 0.5829 (ptt-90) REVERT: F 375 LYS cc_start: 0.8511 (mttt) cc_final: 0.8303 (pptt) outliers start: 6 outliers final: 3 residues processed: 46 average time/residue: 0.2439 time to fit residues: 11.9175 Evaluate side-chains 34 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 30 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1206 Z= 0.164 Angle : 0.652 5.237 1608 Z= 0.328 Chirality : 0.049 0.122 178 Planarity : 0.005 0.041 206 Dihedral : 9.074 57.778 172 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 6.72 % Allowed : 12.69 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -5.10 (0.50), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.38), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.002 0.001 PHE E 346 TYR 0.002 0.001 TYR F 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.147 Fit side-chains REVERT: E 311 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8263 (mtpt) REVERT: E 349 ARG cc_start: 0.7294 (mtp-110) cc_final: 0.6454 (mmp-170) REVERT: F 327 ASN cc_start: 0.7894 (t0) cc_final: 0.7667 (t0) REVERT: F 340 LYS cc_start: 0.8236 (mmtm) cc_final: 0.7756 (mmtm) REVERT: F 372 GLU cc_start: 0.7100 (mp0) cc_final: 0.6894 (mp0) outliers start: 9 outliers final: 6 residues processed: 44 average time/residue: 0.2118 time to fit residues: 9.9534 Evaluate side-chains 39 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 6 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1206 Z= 0.197 Angle : 0.647 6.130 1608 Z= 0.322 Chirality : 0.046 0.118 178 Planarity : 0.005 0.042 206 Dihedral : 8.856 58.689 168 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 9.70 % Allowed : 16.42 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.56), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.43), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 329 PHE 0.005 0.001 PHE F 378 TYR 0.002 0.001 TYR F 310 ARG 0.003 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.159 Fit side-chains REVERT: E 311 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8140 (mmtt) REVERT: E 349 ARG cc_start: 0.7324 (mtp-110) cc_final: 0.6209 (mmp-170) REVERT: F 310 TYR cc_start: 0.7615 (t80) cc_final: 0.5604 (p90) REVERT: F 327 ASN cc_start: 0.8035 (t0) cc_final: 0.7579 (t0) REVERT: F 349 ARG cc_start: 0.5213 (ptt-90) cc_final: 0.4545 (mmp-170) REVERT: F 372 GLU cc_start: 0.7211 (mp0) cc_final: 0.6877 (mp0) outliers start: 13 outliers final: 10 residues processed: 48 average time/residue: 0.1672 time to fit residues: 8.7420 Evaluate side-chains 52 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 311 LYS Chi-restraints excluded: chain E residue 324 SER Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 351 GLN Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 370 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 0.0470 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 12 optimal weight: 0.0040 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.0770 chunk 1 optimal weight: 0.9990 overall best weight: 0.3048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1206 Z= 0.090 Angle : 0.584 6.966 1608 Z= 0.272 Chirality : 0.046 0.115 178 Planarity : 0.004 0.031 206 Dihedral : 7.269 52.359 168 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 5.22 % Allowed : 24.63 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.59), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.45), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 329 PHE 0.003 0.001 PHE E 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.153 Fit side-chains REVERT: E 311 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8055 (mmtt) REVERT: E 349 ARG cc_start: 0.7394 (mtp-110) cc_final: 0.6314 (mmp-170) REVERT: F 327 ASN cc_start: 0.7966 (t0) cc_final: 0.7516 (t0) REVERT: F 340 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7988 (mmtm) REVERT: F 349 ARG cc_start: 0.5220 (ptt-90) cc_final: 0.4758 (mmp-170) REVERT: F 372 GLU cc_start: 0.7172 (mp0) cc_final: 0.6899 (mp0) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 0.1854 time to fit residues: 8.3917 Evaluate side-chains 45 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.0370 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.6830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1206 Z= 0.117 Angle : 0.572 5.910 1608 Z= 0.265 Chirality : 0.045 0.112 178 Planarity : 0.004 0.035 206 Dihedral : 4.798 16.893 160 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 7.46 % Allowed : 23.13 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.004 0.001 PHE F 378 TYR 0.001 0.000 TYR E 310 ARG 0.002 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 40 time to evaluate : 0.148 Fit side-chains REVERT: E 311 LYS cc_start: 0.8515 (mtpp) cc_final: 0.8090 (mmtt) REVERT: E 349 ARG cc_start: 0.7382 (mtp-110) cc_final: 0.6277 (mmp-170) REVERT: F 340 LYS cc_start: 0.8266 (mmtm) cc_final: 0.8065 (mmtm) REVERT: F 349 ARG cc_start: 0.5122 (OUTLIER) cc_final: 0.4730 (mmp-170) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 0.2003 time to fit residues: 8.8229 Evaluate side-chains 47 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 12 optimal weight: 0.0010 chunk 11 optimal weight: 0.0030 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.7025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1206 Z= 0.098 Angle : 0.596 5.907 1608 Z= 0.274 Chirality : 0.044 0.113 178 Planarity : 0.003 0.026 206 Dihedral : 4.496 17.625 160 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 8.21 % Allowed : 22.39 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.003 0.000 PHE F 378 TYR 0.001 0.000 TYR E 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.149 Fit side-chains REVERT: E 311 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8093 (mmtt) REVERT: E 349 ARG cc_start: 0.7323 (mtp-110) cc_final: 0.6275 (mmp-170) REVERT: F 343 LYS cc_start: 0.5051 (tppt) cc_final: 0.4800 (tppt) REVERT: F 349 ARG cc_start: 0.5032 (OUTLIER) cc_final: 0.4725 (mmp-170) outliers start: 11 outliers final: 9 residues processed: 39 average time/residue: 0.1726 time to fit residues: 7.3164 Evaluate side-chains 46 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 36 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain E residue 378 PHE Chi-restraints excluded: chain F residue 349 ARG Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASN Chi-restraints excluded: chain F residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 1 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1206 Z= 0.152 Angle : 0.603 5.503 1608 Z= 0.287 Chirality : 0.045 0.111 178 Planarity : 0.004 0.036 206 Dihedral : 4.872 16.919 160 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.97 % Allowed : 25.37 % Favored : 68.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 329 PHE 0.004 0.001 PHE F 378 TYR 0.002 0.001 TYR E 310 ARG 0.002 0.001 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.149 Fit side-chains REVERT: E 311 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8168 (mmtt) REVERT: E 349 ARG cc_start: 0.7357 (mtp-110) cc_final: 0.6255 (mmp-170) REVERT: F 311 LYS cc_start: 0.8841 (ttpt) cc_final: 0.8477 (mmtt) REVERT: F 349 ARG cc_start: 0.4826 (ptt-90) cc_final: 0.4535 (mmp-170) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.1987 time to fit residues: 8.5459 Evaluate side-chains 45 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 0.0370 chunk 3 optimal weight: 0.1980 chunk 9 optimal weight: 0.7980 chunk 4 optimal weight: 0.0670 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1206 Z= 0.095 Angle : 0.592 6.428 1608 Z= 0.269 Chirality : 0.044 0.112 178 Planarity : 0.003 0.027 206 Dihedral : 4.361 17.910 160 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.33 % Favored : 90.67 % Rotamer: Outliers : 5.22 % Allowed : 25.37 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.47), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 362 PHE 0.002 0.000 PHE F 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.148 Fit side-chains REVERT: E 311 LYS cc_start: 0.8548 (mtpp) cc_final: 0.8173 (mmtt) REVERT: E 349 ARG cc_start: 0.7277 (mtp-110) cc_final: 0.6296 (mmp-170) REVERT: F 311 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8459 (mmtt) REVERT: F 343 LYS cc_start: 0.4808 (tppt) cc_final: 0.4572 (tppt) outliers start: 7 outliers final: 5 residues processed: 41 average time/residue: 0.1990 time to fit residues: 8.7657 Evaluate side-chains 40 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 11 optimal weight: 0.0070 chunk 12 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.7457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1206 Z= 0.098 Angle : 0.574 6.126 1608 Z= 0.259 Chirality : 0.044 0.111 178 Planarity : 0.003 0.026 206 Dihedral : 4.340 15.336 160 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.48 % Allowed : 26.12 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.61), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.003 0.000 PHE F 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG E 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.143 Fit side-chains REVERT: E 311 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8187 (mmtt) REVERT: E 343 LYS cc_start: 0.5370 (tppt) cc_final: 0.5065 (tppt) REVERT: E 349 ARG cc_start: 0.7306 (mtp-110) cc_final: 0.6298 (mmp-170) REVERT: F 311 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8489 (mmtt) REVERT: F 343 LYS cc_start: 0.4995 (tppt) cc_final: 0.4747 (tppt) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 0.1592 time to fit residues: 6.5324 Evaluate side-chains 39 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.0570 chunk 3 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.5100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6905 moved from start: 0.7533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1206 Z= 0.098 Angle : 0.618 7.149 1608 Z= 0.271 Chirality : 0.044 0.111 178 Planarity : 0.002 0.022 206 Dihedral : 4.217 14.542 160 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.48 % Allowed : 26.12 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.66 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 PHE 0.003 0.000 PHE F 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG E 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.155 Fit side-chains REVERT: E 311 LYS cc_start: 0.8568 (mtpp) cc_final: 0.8206 (mmtt) REVERT: E 343 LYS cc_start: 0.5440 (tppt) cc_final: 0.5144 (tppt) REVERT: E 349 ARG cc_start: 0.7284 (mtp-110) cc_final: 0.6355 (mmp-170) REVERT: F 311 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8494 (mmtt) REVERT: F 343 LYS cc_start: 0.4951 (tppt) cc_final: 0.4733 (tppt) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.1928 time to fit residues: 7.7129 Evaluate side-chains 40 residues out of total 134 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain E residue 368 ASN Chi-restraints excluded: chain F residue 352 SER Chi-restraints excluded: chain F residue 363 VAL Chi-restraints excluded: chain F residue 368 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 14 random chunks: chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 12 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 0.2980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 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 = 0.4518 r_free = 0.4518 target = 0.152194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.141541 restraints weight = 2884.999| |-----------------------------------------------------------------------------| r_work (start): 0.4387 rms_B_bonded: 4.29 r_work: 0.4302 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1206 Z= 0.082 Angle : 0.593 6.710 1608 Z= 0.254 Chirality : 0.044 0.111 178 Planarity : 0.003 0.025 206 Dihedral : 3.857 13.668 160 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 27.61 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.60), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.46), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 362 PHE 0.001 0.000 PHE F 378 TYR 0.001 0.000 TYR F 310 ARG 0.001 0.000 ARG E 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 826.14 seconds wall clock time: 16 minutes 40.03 seconds (1000.03 seconds total)