Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo7_19846/08_2024/9eo7_19846.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo7_19846/08_2024/9eo7_19846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo7_19846/08_2024/9eo7_19846.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo7_19846/08_2024/9eo7_19846.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo7_19846/08_2024/9eo7_19846.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eo7_19846/08_2024/9eo7_19846.cif" } resolution = 2.8 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 372 2.51 5 N 109 2.21 5 O 112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 595 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 595 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 77, 588 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} bond proxies already assigned to first conformer: 588 Time building chain proxies: 1.19, per 1000 atoms: 2.00 Number of scatterers: 595 At special positions: 0 Unit cell: (70.864, 84.048, 23.072, 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 112 8.00 N 109 7.00 C 372 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 336.2 milliseconds 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 136 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: 0.25 Creating SS restraints... No hydrogen bonds defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.00 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 154 1.34 - 1.46: 145 1.46 - 1.58: 303 1.58 - 1.70: 0 1.70 - 1.82: 3 Bond restraints: 605 Sorted by residual: bond pdb=" C GLN A 336 " pdb=" N BVAL A 337 " ideal model delta sigma weight residual 1.331 1.406 -0.075 1.27e-02 6.20e+03 3.52e+01 bond pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 1.354 1.296 0.058 1.10e-02 8.26e+03 2.75e+01 bond pdb=" CG HIS A 362 " pdb=" CD2 HIS A 362 " ideal model delta sigma weight residual 1.354 1.300 0.054 1.10e-02 8.26e+03 2.37e+01 bond pdb=" CA SER A 316 " pdb=" CB SER A 316 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.66e-02 3.63e+03 7.04e+00 bond pdb=" CE1 HIS A 330 " pdb=" NE2 HIS A 330 " ideal model delta sigma weight residual 1.321 1.295 0.026 1.00e-02 1.00e+04 6.66e+00 ... (remaining 600 not shown) Histogram of bond angle deviations from ideal: 102.18 - 108.53: 77 108.53 - 114.88: 301 114.88 - 121.22: 261 121.22 - 127.57: 167 127.57 - 133.92: 4 Bond angle restraints: 810 Sorted by residual: angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 111.73 120.08 -8.35 1.42e+00 4.96e-01 3.46e+01 angle pdb=" CB HIS A 330 " pdb=" CG HIS A 330 " pdb=" CD2 HIS A 330 " ideal model delta sigma weight residual 131.20 125.05 6.15 1.30e+00 5.92e-01 2.24e+01 angle pdb=" CB HIS A 330 " pdb=" CG HIS A 330 " pdb=" ND1 HIS A 330 " ideal model delta sigma weight residual 122.70 129.39 -6.69 1.50e+00 4.44e-01 1.99e+01 angle pdb=" CA THR A 361 " pdb=" CB THR A 361 " pdb=" OG1 THR A 361 " ideal model delta sigma weight residual 109.60 103.04 6.56 1.50e+00 4.44e-01 1.91e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 115.84 -5.15 1.33e+00 5.65e-01 1.50e+01 ... (remaining 805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.86: 263 7.86 - 15.71: 70 15.71 - 23.57: 20 23.57 - 31.43: 12 31.43 - 39.28: 5 Dihedral angle restraints: 370 sinusoidal: 155 harmonic: 215 Sorted by residual: dihedral pdb=" C ARG A 349 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta harmonic sigma weight residual -122.60 -135.14 12.54 0 2.50e+00 1.60e-01 2.52e+01 dihedral pdb=" CA SER A 352 " pdb=" C SER A 352 " pdb=" N LYS A 353 " pdb=" CA LYS A 353 " ideal model delta harmonic sigma weight residual 180.00 158.32 21.68 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ARG A 379 " pdb=" C ARG A 379 " pdb=" N GLU A 380 " pdb=" CA GLU A 380 " ideal model delta harmonic sigma weight residual 180.00 158.51 21.49 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 367 not shown) Histogram of chiral volume deviations from ideal: 0.002 - 0.077: 46 0.077 - 0.151: 36 0.151 - 0.226: 7 0.226 - 0.300: 0 0.300 - 0.375: 1 Chirality restraints: 90 Sorted by residual: chirality pdb=" CA ARG A 349 " pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CB ARG A 349 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA AMET A 337 " pdb=" N AMET A 337 " pdb=" C AMET A 337 " pdb=" CB AMET A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA ASP A 358 " pdb=" N ASP A 358 " pdb=" C ASP A 358 " pdb=" CB ASP A 358 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 87 not shown) Planarity restraints: 104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 336 " -0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLN A 336 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN A 336 " -0.018 2.00e-02 2.50e+03 pdb=" N BVAL A 337 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C ARG A 349 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG A 349 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 350 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.028 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR A 310 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " 0.004 2.00e-02 2.50e+03 ... (remaining 101 not shown) Histogram of nonbonded interaction distances: 2.58 - 3.05: 308 3.05 - 3.51: 481 3.51 - 3.97: 687 3.97 - 4.44: 515 4.44 - 4.90: 1012 Nonbonded interactions: 3003 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" OG SER A 316 " model vdw 2.583 3.040 nonbonded pdb=" O GLY A 334 " pdb=" CA GLY A 335 " model vdw 2.662 2.752 nonbonded pdb=" OD2 ASP A 314 " pdb=" NZ LYS A 370 " model vdw 2.667 3.120 nonbonded pdb=" N ASN A 368 " pdb=" O ASN A 368 " model vdw 2.668 2.496 nonbonded pdb=" O LEU A 325 " pdb=" CA GLY A 326 " model vdw 2.674 2.752 ... (remaining 2998 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.870 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 10.180 Find NCS groups from input model: 0.000 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:13.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 0.075 605 Z= 0.670 Angle : 1.590 8.348 810 Z= 1.025 Chirality : 0.095 0.375 90 Planarity : 0.009 0.032 104 Dihedral : 12.220 39.283 234 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.47 % Allowed : 8.82 % Favored : 89.71 % Cbeta Deviations : 1.47 % 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: -4.16 (0.58), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.44), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS A 330 PHE 0.032 0.008 PHE A 346 TYR 0.038 0.011 TYR A 310 ARG 0.004 0.001 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.064 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8763 (tmtt) cc_final: 0.8399 (ttpt) REVERT: A 343 LYS cc_start: 0.8476 (mttp) cc_final: 0.8072 (mtpp) REVERT: A 349 ARG cc_start: 0.8092 (ptp-170) cc_final: 0.7588 (ptm160) REVERT: A 375 LYS cc_start: 0.8287 (tttt) cc_final: 0.7950 (ttmp) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 1.1543 time to fit residues: 19.8158 Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 4 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.4310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN A 330 HIS A 368 ASN A 374 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 605 Z= 0.104 Angle : 0.540 5.057 810 Z= 0.273 Chirality : 0.049 0.129 90 Planarity : 0.004 0.025 104 Dihedral : 5.179 13.747 81 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 16.18 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.73), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.56), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 329 PHE 0.004 0.001 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8672 (tmtt) cc_final: 0.8428 (ttpt) REVERT: A 343 LYS cc_start: 0.8401 (mttp) cc_final: 0.8054 (mtpp) REVERT: A 348 ASP cc_start: 0.8668 (t0) cc_final: 0.7886 (m-30) REVERT: A 358 ASP cc_start: 0.8735 (p0) cc_final: 0.8286 (m-30) REVERT: A 375 LYS cc_start: 0.8251 (tttt) cc_final: 0.7889 (ttmt) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 1.3666 time to fit residues: 16.5800 Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 overall best weight: 1.1653 ------------------------------------------------------------------------------- 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: 0.8407 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 605 Z= 0.107 Angle : 0.510 4.864 810 Z= 0.254 Chirality : 0.049 0.127 90 Planarity : 0.003 0.024 104 Dihedral : 4.624 13.155 81 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.47 % Allowed : 13.24 % Favored : 85.29 % 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: -2.41 (0.78), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.83 (0.59), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8688 (tmtt) cc_final: 0.8442 (ttpt) REVERT: A 343 LYS cc_start: 0.8417 (mttp) cc_final: 0.8070 (mtpp) REVERT: A 375 LYS cc_start: 0.8264 (tttt) cc_final: 0.7902 (ttmt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 1.1131 time to fit residues: 13.5340 Evaluate side-chains 11 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 overall best weight: 1.6657 ------------------------------------------------------------------------------- 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: 0.8424 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 605 Z= 0.131 Angle : 0.523 4.860 810 Z= 0.264 Chirality : 0.049 0.132 90 Planarity : 0.003 0.020 104 Dihedral : 4.657 12.266 81 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 17.65 % Favored : 80.88 % 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: -2.10 (0.83), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8443 (ttpt) REVERT: A 342 GLU cc_start: 0.4783 (OUTLIER) cc_final: 0.3698 (mp0) REVERT: A 343 LYS cc_start: 0.8358 (mttp) cc_final: 0.8103 (mtpm) REVERT: A 375 LYS cc_start: 0.8266 (tttt) cc_final: 0.7901 (ttmp) REVERT: A 379 ARG cc_start: 0.8879 (mpt-90) cc_final: 0.6668 (ppt170) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 1.2734 time to fit residues: 18.0187 Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.6320 ------------------------------------------------------------------------------- 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: 0.8428 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 605 Z= 0.126 Angle : 0.515 4.597 810 Z= 0.258 Chirality : 0.048 0.130 90 Planarity : 0.003 0.018 104 Dihedral : 4.535 11.102 81 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.47 % Allowed : 17.65 % Favored : 80.88 % 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: -1.93 (0.83), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.46 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.002 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.066 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8730 (tmtt) cc_final: 0.8461 (ttpt) REVERT: A 375 LYS cc_start: 0.8290 (tttt) cc_final: 0.7923 (ttmp) REVERT: A 379 ARG cc_start: 0.8913 (mpt-90) cc_final: 0.6714 (ppt170) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 1.4643 time to fit residues: 17.7491 Evaluate side-chains 11 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3323 ------------------------------------------------------------------------------- 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: 0.8448 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 605 Z= 0.167 Angle : 0.548 4.751 810 Z= 0.278 Chirality : 0.049 0.138 90 Planarity : 0.003 0.018 104 Dihedral : 4.745 11.860 81 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 17.65 % Favored : 79.41 % 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: -1.84 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.004 0.001 PHE A 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 11 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8709 (tmtt) cc_final: 0.8198 (mmtt) REVERT: A 375 LYS cc_start: 0.8280 (tttt) cc_final: 0.7928 (ttmp) REVERT: A 379 ARG cc_start: 0.8928 (mpt-90) cc_final: 0.6594 (pmt170) outliers start: 2 outliers final: 1 residues processed: 13 average time/residue: 1.4482 time to fit residues: 19.0254 Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 overall best weight: 1.2983 ------------------------------------------------------------------------------- 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: 0.8415 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 605 Z= 0.109 Angle : 0.488 4.435 810 Z= 0.248 Chirality : 0.048 0.128 90 Planarity : 0.002 0.017 104 Dihedral : 4.402 10.666 81 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 19.12 % Favored : 79.41 % 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: -1.78 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.35 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.002 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8436 (ttpt) REVERT: A 348 ASP cc_start: 0.8535 (t0) cc_final: 0.7961 (m-30) REVERT: A 375 LYS cc_start: 0.8276 (tttt) cc_final: 0.7904 (ttmp) REVERT: A 379 ARG cc_start: 0.8927 (mpt-90) cc_final: 0.6628 (ppt170) outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 1.2126 time to fit residues: 15.9512 Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.6317 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 605 Z= 0.126 Angle : 0.505 4.524 810 Z= 0.256 Chirality : 0.048 0.133 90 Planarity : 0.002 0.016 104 Dihedral : 4.430 10.657 81 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 22.06 % Favored : 77.94 % 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: -1.77 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.34 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.002 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8447 (ttpt) REVERT: A 375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7908 (ttmp) REVERT: A 379 ARG cc_start: 0.8919 (mpt-90) cc_final: 0.6658 (ppt170) outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 1.2813 time to fit residues: 15.5561 Evaluate side-chains 12 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 6 optimal weight: 1.9990 overall best weight: 1.6950 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 605 Z= 0.130 Angle : 0.506 4.530 810 Z= 0.257 Chirality : 0.048 0.133 90 Planarity : 0.002 0.015 104 Dihedral : 4.425 10.488 81 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.47 % Allowed : 20.59 % Favored : 77.94 % 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: -1.76 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.002 0.001 PHE A 346 TYR 0.008 0.002 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8702 (tmtt) cc_final: 0.8449 (ttpt) REVERT: A 348 ASP cc_start: 0.8520 (t0) cc_final: 0.7963 (m-30) REVERT: A 375 LYS cc_start: 0.8315 (tttt) cc_final: 0.7932 (ttmp) REVERT: A 379 ARG cc_start: 0.8918 (mpt-90) cc_final: 0.6654 (ppt170) outliers start: 1 outliers final: 1 residues processed: 13 average time/residue: 1.1852 time to fit residues: 15.5936 Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 overall best weight: 2.9987 ------------------------------------------------------------------------------- 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: 0.8460 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 605 Z= 0.199 Angle : 0.570 4.710 810 Z= 0.291 Chirality : 0.049 0.144 90 Planarity : 0.002 0.014 104 Dihedral : 4.742 11.947 81 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 19.12 % Favored : 77.94 % 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: -1.82 (0.85), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.65), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.005 0.001 PHE A 346 TYR 0.013 0.004 TYR A 310 ARG 0.001 0.000 ARG A 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 156 Ramachandran restraints generated. 78 Oldfield, 0 Emsley, 78 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.8736 (tmtt) cc_final: 0.8230 (mmtm) REVERT: A 375 LYS cc_start: 0.8296 (tttt) cc_final: 0.7933 (ttmp) REVERT: A 379 ARG cc_start: 0.8949 (mpt-90) cc_final: 0.6751 (pmt170) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 1.2381 time to fit residues: 17.5223 Evaluate side-chains 13 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.0030 overall best weight: 2.6670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.208235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.187033 restraints weight = 6470.877| |-----------------------------------------------------------------------------| r_work (start): 0.4323 rms_B_bonded: 5.47 r_work: 0.4170 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4163 r_free = 0.4163 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4159 r_free = 0.4159 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 605 Z= 0.184 Angle : 0.558 4.691 810 Z= 0.286 Chirality : 0.048 0.141 90 Planarity : 0.002 0.013 104 Dihedral : 4.700 11.629 81 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.47 % Allowed : 20.59 % Favored : 77.94 % 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: -1.88 (0.84), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.64), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 330 PHE 0.003 0.001 PHE A 346 TYR 0.011 0.003 TYR A 310 ARG 0.001 0.000 ARG A 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 791.60 seconds wall clock time: 14 minutes 45.04 seconds (885.04 seconds total)