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/9eoe_19852/08_2024/9eoe_19852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoe_19852/08_2024/9eoe_19852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoe_19852/08_2024/9eoe_19852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoe_19852/08_2024/9eoe_19852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoe_19852/08_2024/9eoe_19852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eoe_19852/08_2024/9eoe_19852.cif" } resolution = 2.3 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= 0.003 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 ASP 314": "OD1" <-> "OD2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" 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: 1.22, per 1000 atoms: 2.05 Number of scatterers: 595 At special positions: 0 Unit cell: (87.344, 71.688, 21.424, 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: 1.44 Conformation dependent library (CDL) restraints added in 216.6 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: 0.23 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: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 116 1.32 - 1.44: 125 1.44 - 1.56: 361 1.56 - 1.68: 0 1.68 - 1.80: 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 1.382 -0.052 1.43e-02 4.89e+03 1.30e+01 bond pdb=" CA SER A 341 " pdb=" CB SER A 341 " ideal model delta sigma weight residual 1.533 1.486 0.047 1.90e-02 2.77e+03 6.12e+00 bond pdb=" C BVAL A 337 " pdb=" N GLU A 338 " ideal model delta sigma weight residual 1.332 1.298 0.033 1.35e-02 5.49e+03 6.05e+00 bond pdb=" CA SER A 324 " pdb=" CB SER A 324 " ideal model delta sigma weight residual 1.528 1.490 0.038 1.66e-02 3.63e+03 5.29e+00 bond pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " ideal model delta sigma weight residual 1.497 1.468 0.029 1.40e-02 5.10e+03 4.19e+00 ... (remaining 600 not shown) Histogram of bond angle deviations from ideal: 102.38 - 108.32: 56 108.32 - 114.25: 302 114.25 - 120.19: 227 120.19 - 126.12: 217 126.12 - 132.05: 8 Bond angle restraints: 810 Sorted by residual: angle pdb=" C ILE A 354 " pdb=" CA ILE A 354 " pdb=" CB ILE A 354 " ideal model delta sigma weight residual 110.28 117.03 -6.75 1.58e+00 4.01e-01 1.83e+01 angle pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta sigma weight residual 112.09 118.32 -6.23 1.54e+00 4.22e-01 1.64e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 115.87 -5.18 1.33e+00 5.65e-01 1.52e+01 angle pdb=" CA HIS A 329 " pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " ideal model delta sigma weight residual 113.80 110.39 3.41 1.00e+00 1.00e+00 1.17e+01 angle pdb=" CA GLY A 333 " pdb=" C GLY A 333 " pdb=" O GLY A 333 " ideal model delta sigma weight residual 121.58 118.61 2.97 9.00e-01 1.23e+00 1.09e+01 ... (remaining 805 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.31: 323 14.31 - 28.60: 37 28.60 - 42.89: 4 42.89 - 57.19: 2 57.19 - 71.48: 4 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 -136.21 13.61 0 2.50e+00 1.60e-01 2.97e+01 dihedral pdb=" C ILE A 354 " pdb=" N ILE A 354 " pdb=" CA ILE A 354 " pdb=" CB ILE A 354 " ideal model delta harmonic sigma weight residual -122.00 -133.59 11.59 0 2.50e+00 1.60e-01 2.15e+01 dihedral pdb=" N ARG A 349 " pdb=" C ARG A 349 " pdb=" CA ARG A 349 " pdb=" CB ARG A 349 " ideal model delta harmonic sigma weight residual 122.80 133.23 -10.43 0 2.50e+00 1.60e-01 1.74e+01 ... (remaining 367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 69 0.097 - 0.194: 16 0.194 - 0.291: 3 0.291 - 0.388: 1 0.388 - 0.485: 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 2.03 0.49 2.00e-01 2.50e+01 5.89e+00 chirality pdb=" CA ILE A 354 " pdb=" N ILE A 354 " pdb=" C ILE A 354 " pdb=" CB ILE A 354 " both_signs ideal model delta sigma weight residual False 2.43 2.14 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CB ILE A 354 " pdb=" CA ILE A 354 " pdb=" CG1 ILE A 354 " pdb=" CG2 ILE A 354 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 87 not shown) Planarity restraints: 104 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 349 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.20e+00 pdb=" C ARG A 349 " 0.043 2.00e-02 2.50e+03 pdb=" O ARG A 349 " -0.017 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=" CA LYS A 311 " -0.011 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C LYS A 311 " 0.036 2.00e-02 2.50e+03 pdb=" O LYS A 311 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 312 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 336 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C GLN A 336 " 0.034 2.00e-02 2.50e+03 pdb=" O GLN A 336 " -0.013 2.00e-02 2.50e+03 pdb=" N BVAL A 337 " -0.011 2.00e-02 2.50e+03 ... (remaining 101 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.08: 324 3.08 - 3.53: 488 3.53 - 3.99: 652 3.99 - 4.44: 563 4.44 - 4.90: 980 Nonbonded interactions: 3007 Sorted by model distance: nonbonded pdb=" N SER A 356 " pdb=" O SER A 356 " model vdw 2.621 2.496 nonbonded pdb=" O LEU A 325 " pdb=" CA GLY A 326 " model vdw 2.672 2.752 nonbonded pdb=" O LYS A 331 " pdb=" CB LYS A 331 " model vdw 2.690 2.752 nonbonded pdb=" N ASN A 368 " pdb=" O ASN A 368 " model vdw 2.697 2.496 nonbonded pdb=" N CYS A 322 " pdb=" O CYS A 322 " model vdw 2.699 2.496 ... (remaining 3002 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: 2.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 9.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 0.052 605 Z= 0.611 Angle : 1.545 6.752 810 Z= 0.993 Chirality : 0.104 0.485 90 Planarity : 0.008 0.037 104 Dihedral : 14.876 71.479 234 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 4.41 % Allowed : 4.41 % Favored : 91.18 % Cbeta Deviations : 2.94 % 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: -3.08 (0.69), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.52), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS A 330 PHE 0.010 0.003 PHE A 346 TYR 0.012 0.004 TYR A 310 ARG 0.004 0.001 ARG A 349 *********************** 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 25 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 22 time to evaluate : 0.065 Fit side-chains REVERT: A 311 LYS cc_start: 0.7490 (tmtt) cc_final: 0.6954 (ttmt) REVERT: A 331 LYS cc_start: 0.7934 (mttt) cc_final: 0.7670 (mttt) REVERT: A 347 LYS cc_start: 0.8054 (ptpt) cc_final: 0.7843 (pttt) REVERT: A 351 GLN cc_start: 0.7535 (tt0) cc_final: 0.7258 (tt0) REVERT: A 353 LYS cc_start: 0.8387 (mtpt) cc_final: 0.7968 (mtpt) REVERT: A 357 LEU cc_start: 0.7823 (pp) cc_final: 0.7431 (tp) REVERT: A 369 LYS cc_start: 0.7898 (ptmt) cc_final: 0.6643 (tppt) REVERT: A 375 LYS cc_start: 0.7716 (tttt) cc_final: 0.7354 (tttm) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 1.3224 time to fit residues: 30.6335 Evaluate side-chains 21 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 4.6657 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN A 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 605 Z= 0.248 Angle : 0.938 8.407 810 Z= 0.469 Chirality : 0.058 0.173 90 Planarity : 0.006 0.046 104 Dihedral : 10.328 49.906 85 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.88 % Allowed : 17.65 % Favored : 76.47 % 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: -3.02 (0.66), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.50), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 329 PHE 0.005 0.002 PHE A 378 TYR 0.008 0.002 TYR A 310 ARG 0.003 0.001 ARG A 349 *********************** 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 23 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 19 time to evaluate : 0.074 Fit side-chains REVERT: A 314 ASP cc_start: 0.7737 (m-30) cc_final: 0.7134 (t70) REVERT: A 315 LEU cc_start: 0.7702 (mt) cc_final: 0.7472 (mm) REVERT: A 349 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6272 (ptm-80) REVERT: A 357 LEU cc_start: 0.7584 (pp) cc_final: 0.7322 (tp) REVERT: A 369 LYS cc_start: 0.7888 (ptmt) cc_final: 0.6228 (tppt) REVERT: A 375 LYS cc_start: 0.7848 (tttt) cc_final: 0.7566 (tttm) outliers start: 4 outliers final: 1 residues processed: 21 average time/residue: 1.4505 time to fit residues: 30.6782 Evaluate side-chains 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.5653 ------------------------------------------------------------------------------- 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: 0.7842 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 605 Z= 0.199 Angle : 0.817 7.436 810 Z= 0.409 Chirality : 0.055 0.148 90 Planarity : 0.006 0.049 104 Dihedral : 9.508 49.069 83 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 20.59 % Favored : 76.47 % 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: -2.90 (0.64), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.49), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.004 0.002 PHE A 378 TYR 0.009 0.002 TYR A 310 ARG 0.003 0.001 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 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.081 Fit side-chains REVERT: A 314 ASP cc_start: 0.7753 (m-30) cc_final: 0.7151 (t70) REVERT: A 315 LEU cc_start: 0.7670 (mt) cc_final: 0.7434 (mm) REVERT: A 349 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6307 (ptm-80) REVERT: A 357 LEU cc_start: 0.7602 (pp) cc_final: 0.7315 (tp) REVERT: A 369 LYS cc_start: 0.7950 (ptmt) cc_final: 0.7578 (ptpp) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 1.3809 time to fit residues: 19.5358 Evaluate side-chains 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.2980 overall best weight: 2.0983 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 605 Z= 0.143 Angle : 0.691 6.379 810 Z= 0.344 Chirality : 0.051 0.132 90 Planarity : 0.005 0.046 104 Dihedral : 8.544 43.666 83 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.41 % Allowed : 16.18 % 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: -2.53 (0.67), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.92 (0.51), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.001 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 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.076 Fit side-chains REVERT: A 314 ASP cc_start: 0.7542 (m-30) cc_final: 0.7196 (t70) REVERT: A 315 LEU cc_start: 0.7594 (mt) cc_final: 0.7365 (mm) REVERT: A 349 ARG cc_start: 0.7027 (OUTLIER) cc_final: 0.6631 (ptp90) REVERT: A 357 LEU cc_start: 0.7560 (pp) cc_final: 0.7294 (tp) REVERT: A 369 LYS cc_start: 0.7911 (ptmt) cc_final: 0.6273 (tppt) outliers start: 2 outliers final: 1 residues processed: 14 average time/residue: 1.4575 time to fit residues: 20.5894 Evaluate side-chains 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.9320 ------------------------------------------------------------------------------- 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: 0.7795 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 605 Z= 0.138 Angle : 0.668 5.914 810 Z= 0.331 Chirality : 0.051 0.129 90 Planarity : 0.005 0.044 104 Dihedral : 6.594 33.320 83 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 5.88 % Allowed : 14.71 % 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: -2.28 (0.72), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.55), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.003 0.001 PHE A 346 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.001 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 22 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.074 Fit side-chains REVERT: A 314 ASP cc_start: 0.7234 (m-30) cc_final: 0.6865 (t70) REVERT: A 315 LEU cc_start: 0.7600 (mt) cc_final: 0.7367 (mm) REVERT: A 317 LYS cc_start: 0.7366 (pttm) cc_final: 0.6893 (ptmm) REVERT: A 349 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6564 (ptp90) REVERT: A 357 LEU cc_start: 0.7544 (pp) cc_final: 0.7327 (tp) REVERT: A 369 LYS cc_start: 0.7882 (ptmt) cc_final: 0.6276 (tppt) outliers start: 3 outliers final: 1 residues processed: 19 average time/residue: 1.6401 time to fit residues: 31.4167 Evaluate side-chains 20 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.0370 chunk 6 optimal weight: 10.0000 overall best weight: 1.6447 ------------------------------------------------------------------------------- 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: 0.7789 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 0.035 605 Z= 0.125 Angle : 0.637 5.508 810 Z= 0.316 Chirality : 0.049 0.126 90 Planarity : 0.005 0.044 104 Dihedral : 6.126 28.864 83 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.41 % Allowed : 14.71 % 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: -2.20 (0.72), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.55), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.003 0.001 PHE A 346 TYR 0.006 0.002 TYR A 310 ARG 0.001 0.001 ARG A 349 *********************** 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 20 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.074 Fit side-chains REVERT: A 314 ASP cc_start: 0.7590 (m-30) cc_final: 0.7250 (t70) REVERT: A 315 LEU cc_start: 0.7619 (mt) cc_final: 0.7370 (mm) REVERT: A 317 LYS cc_start: 0.7351 (pttm) cc_final: 0.6882 (ptmm) REVERT: A 349 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6588 (ptp90) REVERT: A 369 LYS cc_start: 0.7912 (ptmt) cc_final: 0.6239 (tppt) outliers start: 2 outliers final: 1 residues processed: 18 average time/residue: 1.6204 time to fit residues: 29.3782 Evaluate side-chains 19 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 1.1983 ------------------------------------------------------------------------------- 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: 0.7777 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 605 Z= 0.108 Angle : 0.562 4.927 810 Z= 0.286 Chirality : 0.049 0.121 90 Planarity : 0.004 0.041 104 Dihedral : 5.630 24.590 83 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.41 % Allowed : 16.18 % 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: -2.07 (0.75), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.57 (0.57), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 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 20 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.065 Fit side-chains REVERT: A 314 ASP cc_start: 0.7607 (m-30) cc_final: 0.7260 (t70) REVERT: A 315 LEU cc_start: 0.7598 (mt) cc_final: 0.7350 (mm) REVERT: A 349 ARG cc_start: 0.6866 (OUTLIER) cc_final: 0.6510 (ptp90) REVERT: A 354 ILE cc_start: 0.7972 (OUTLIER) cc_final: 0.7575 (mt) REVERT: A 369 LYS cc_start: 0.7876 (ptmt) cc_final: 0.6248 (tppt) outliers start: 2 outliers final: 0 residues processed: 18 average time/residue: 1.5869 time to fit residues: 28.7656 Evaluate side-chains 20 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7748 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 605 Z= 0.094 Angle : 0.534 4.183 810 Z= 0.267 Chirality : 0.048 0.114 90 Planarity : 0.004 0.038 104 Dihedral : 4.971 17.833 83 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % 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: -1.87 (0.77), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.59), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 330 PHE 0.001 0.000 PHE A 346 TYR 0.004 0.001 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 19 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.077 Fit side-chains REVERT: A 314 ASP cc_start: 0.7549 (m-30) cc_final: 0.7220 (t70) REVERT: A 315 LEU cc_start: 0.7577 (mt) cc_final: 0.7339 (mm) REVERT: A 349 ARG cc_start: 0.6803 (ptm-80) cc_final: 0.6486 (ptp90) REVERT: A 354 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7684 (mt) REVERT: A 369 LYS cc_start: 0.7870 (ptmt) cc_final: 0.6259 (tppt) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 1.5690 time to fit residues: 28.4491 Evaluate side-chains 18 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.0470 chunk 6 optimal weight: 0.5980 overall best weight: 1.5480 ------------------------------------------------------------------------------- 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: 0.7782 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 605 Z= 0.118 Angle : 0.614 5.631 810 Z= 0.303 Chirality : 0.049 0.121 90 Planarity : 0.005 0.047 104 Dihedral : 5.515 24.417 83 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % 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: -1.88 (0.78), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.42 (0.59), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.003 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.002 0.001 ARG A 349 *********************** 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 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.070 Fit side-chains REVERT: A 314 ASP cc_start: 0.7617 (m-30) cc_final: 0.7075 (t70) REVERT: A 315 LEU cc_start: 0.7599 (mt) cc_final: 0.7336 (mm) REVERT: A 349 ARG cc_start: 0.6943 (ptm-80) cc_final: 0.6582 (ptp90) REVERT: A 354 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.7610 (mt) REVERT: A 369 LYS cc_start: 0.7907 (ptmt) cc_final: 0.6228 (tppt) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 1.4379 time to fit residues: 20.3122 Evaluate side-chains 15 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 0.0030 chunk 6 optimal weight: 9.9990 overall best weight: 0.4997 ------------------------------------------------------------------------------- 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: 0.7727 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 605 Z= 0.091 Angle : 0.548 5.056 810 Z= 0.267 Chirality : 0.047 0.110 90 Planarity : 0.005 0.045 104 Dihedral : 4.752 15.951 83 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.94 % Allowed : 16.18 % 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: -1.84 (0.78), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.60), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 330 PHE 0.001 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.000 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 19 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.074 Fit side-chains REVERT: A 314 ASP cc_start: 0.7512 (m-30) cc_final: 0.7190 (t70) REVERT: A 315 LEU cc_start: 0.7554 (mt) cc_final: 0.7325 (mm) REVERT: A 331 LYS cc_start: 0.8306 (mttt) cc_final: 0.7919 (mtpt) REVERT: A 349 ARG cc_start: 0.6833 (ptm-80) cc_final: 0.6535 (ptp90) REVERT: A 354 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7602 (mt) REVERT: A 369 LYS cc_start: 0.7850 (ptmt) cc_final: 0.6254 (tppt) outliers start: 1 outliers final: 0 residues processed: 18 average time/residue: 1.4497 time to fit residues: 26.3001 Evaluate side-chains 18 residues out of total 66 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 7 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.0000 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 overall best weight: 2.3327 ------------------------------------------------------------------------------- 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 = 0.4453 r_free = 0.4453 target = 0.211128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.188852 restraints weight = 3607.301| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 6.61 r_work: 0.4008 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4003 r_free = 0.4003 target_work(ls_wunit_k1) = 0.167 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4010 r_free = 0.4010 target_work(ls_wunit_k1) = 0.168 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.4010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 605 Z= 0.142 Angle : 0.657 6.082 810 Z= 0.326 Chirality : 0.050 0.130 90 Planarity : 0.005 0.050 104 Dihedral : 5.791 27.763 83 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % 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: -1.85 (0.79), residues: 78 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.60), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.004 0.001 PHE A 346 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 923.57 seconds wall clock time: 17 minutes 0.62 seconds (1020.62 seconds total)