Starting phenix.real_space_refine on Thu Nov 14 03:33:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/11_2024/8ore_17121.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/11_2024/8ore_17121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/11_2024/8ore_17121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/11_2024/8ore_17121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/11_2024/8ore_17121.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/11_2024/8ore_17121.cif" } resolution = 2.5 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= 0.004 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: 5 Type Number sf(0) Gaussians S 3 5.16 5 C 1110 2.51 5 N 327 2.21 5 O 330 1.98 5 H 1845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3615 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.39, per 1000 atoms: 0.66 Number of scatterers: 3615 At special positions: 0 Unit cell: (82.84, 81.75, 37.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 O 330 8.00 N 327 7.00 C 1110 6.00 H 1845 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 250.6 milliseconds 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.612A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 361 removed outlier: 6.938A pdb=" N SER B 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER C 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 62 hydrogen bonds defined for protein. 186 hydrogen bond angles 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: 1.01 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 1842 1.11 - 1.29: 297 1.29 - 1.46: 490 1.46 - 1.63: 1010 1.63 - 1.81: 3 Bond restraints: 3642 Sorted by residual: bond pdb=" N GLY A 366 " pdb=" H GLY A 366 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 HIS A 362 " pdb=" HE1 HIS A 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS B 362 " pdb=" HE1 HIS B 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU C 315 " pdb=" H LEU C 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 315 " pdb=" H LEU B 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3637 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 5360 2.37 - 4.75: 912 4.75 - 7.12: 334 7.12 - 9.50: 32 9.50 - 11.87: 4 Bond angle restraints: 6642 Sorted by residual: angle pdb=" C LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta sigma weight residual 111.14 119.05 -7.91 1.39e+00 5.18e-01 3.24e+01 angle pdb=" C LEU B 325 " pdb=" CA LEU B 325 " pdb=" CB LEU B 325 " ideal model delta sigma weight residual 111.40 118.42 -7.02 1.29e+00 6.01e-01 2.96e+01 angle pdb=" N PRO B 364 " pdb=" CA PRO B 364 " pdb=" C PRO B 364 " ideal model delta sigma weight residual 113.57 120.57 -7.00 1.31e+00 5.83e-01 2.86e+01 angle pdb=" CB HIS B 362 " pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 131.20 124.91 6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 118.61 -4.81 1.00e+00 1.00e+00 2.31e+01 ... (remaining 6637 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.53: 1439 13.53 - 27.06: 117 27.06 - 40.59: 35 40.59 - 54.12: 28 54.12 - 67.65: 52 Dihedral angle restraints: 1671 sinusoidal: 960 harmonic: 711 Sorted by residual: dihedral pdb=" C LEU A 325 " pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta harmonic sigma weight residual -122.60 -138.99 16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C VAL B 363 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " pdb=" CB VAL B 363 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.54 14.54 0 2.50e+00 1.60e-01 3.38e+01 ... (remaining 1668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 200 0.120 - 0.240: 40 0.240 - 0.360: 16 0.360 - 0.479: 9 0.479 - 0.599: 2 Chirality restraints: 267 Sorted by residual: chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 264 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.099 2.00e-02 2.50e+03 4.00e-02 4.80e+01 pdb=" CG PHE A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 346 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 346 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 346 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 346 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 346 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.076 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" CG PHE B 346 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.030 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" N GLU B 342 " 0.095 2.00e-02 2.50e+03 pdb=" CA GLU B 342 " -0.027 2.00e-02 2.50e+03 pdb=" H GLU B 342 " -0.038 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 317 2.21 - 2.81: 6754 2.81 - 3.40: 9317 3.40 - 4.00: 12465 4.00 - 4.60: 17899 Nonbonded interactions: 46752 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.611 2.450 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.636 2.450 nonbonded pdb=" HG1 THR A 377 " pdb=" OE1 GLU A 380 " model vdw 1.650 2.450 nonbonded pdb=" HG1 THR C 377 " pdb=" OE2 GLU C 380 " model vdw 1.662 2.450 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.675 2.450 ... (remaining 46747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 0.910 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.410 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 : 0.011 0.052 1797 Z= 0.718 Angle : 2.085 10.566 2400 Z= 1.353 Chirality : 0.140 0.599 267 Planarity : 0.011 0.065 306 Dihedral : 10.934 54.560 696 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Cbeta Deviations : 3.48 % 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 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS C 362 PHE 0.055 0.024 PHE B 378 TYR 0.040 0.012 TYR B 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8330 (t0) cc_final: 0.8073 (t0) REVERT: A 349 ARG cc_start: 0.8027 (ttp-170) cc_final: 0.7794 (ttp-110) REVERT: B 314 ASP cc_start: 0.8198 (t0) cc_final: 0.7914 (t0) REVERT: B 317 LYS cc_start: 0.7959 (ptmt) cc_final: 0.7384 (ptpp) REVERT: B 347 LYS cc_start: 0.8635 (mttt) cc_final: 0.8389 (mttp) REVERT: C 307 GLN cc_start: 0.7873 (tt0) cc_final: 0.7448 (tt0) REVERT: C 338 GLU cc_start: 0.8150 (tt0) cc_final: 0.7887 (tt0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 2.6768 time to fit residues: 222.6515 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN A 368 ASN A 374 HIS B 307 GLN B 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1797 Z= 0.181 Angle : 0.697 4.506 2400 Z= 0.358 Chirality : 0.055 0.151 267 Planarity : 0.004 0.036 306 Dihedral : 7.165 22.681 237 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.98 % Allowed : 20.40 % Favored : 74.63 % 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: -2.23 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.009 0.002 PHE A 378 TYR 0.006 0.002 TYR B 310 ARG 0.007 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 SER cc_start: 0.8622 (m) cc_final: 0.8382 (p) REVERT: A 345 ASP cc_start: 0.8207 (t0) cc_final: 0.7899 (t0) REVERT: A 372 GLU cc_start: 0.6800 (OUTLIER) cc_final: 0.6556 (mt-10) REVERT: B 314 ASP cc_start: 0.8337 (t0) cc_final: 0.8090 (t0) REVERT: B 317 LYS cc_start: 0.7807 (ptmt) cc_final: 0.7261 (ptpp) REVERT: B 319 THR cc_start: 0.8172 (m) cc_final: 0.7663 (p) REVERT: C 380 GLU cc_start: 0.5490 (mt-10) cc_final: 0.5137 (mt-10) outliers start: 10 outliers final: 3 residues processed: 65 average time/residue: 2.4090 time to fit residues: 159.1604 Evaluate side-chains 51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 372 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN C 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1797 Z= 0.184 Angle : 0.644 5.350 2400 Z= 0.327 Chirality : 0.053 0.151 267 Planarity : 0.004 0.042 306 Dihedral : 6.373 20.171 237 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 2.99 % Allowed : 24.38 % Favored : 72.64 % 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: -2.13 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 329 PHE 0.012 0.002 PHE A 378 TYR 0.007 0.001 TYR C 310 ARG 0.008 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8163 (t0) cc_final: 0.7886 (t0) REVERT: B 319 THR cc_start: 0.8187 (m) cc_final: 0.7610 (p) REVERT: B 345 ASP cc_start: 0.7774 (t0) cc_final: 0.7317 (t70) outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 2.0425 time to fit residues: 112.6448 Evaluate side-chains 51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.4980 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 336 GLN B 374 HIS C 307 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 1797 Z= 0.181 Angle : 0.612 4.491 2400 Z= 0.310 Chirality : 0.053 0.144 267 Planarity : 0.004 0.040 306 Dihedral : 6.097 20.313 237 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.48 % Allowed : 24.38 % Favored : 71.14 % 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: -2.17 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.012 0.002 PHE A 378 TYR 0.006 0.001 TYR C 310 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.308 Fit side-chains REVERT: A 345 ASP cc_start: 0.8167 (t0) cc_final: 0.7891 (t0) REVERT: A 372 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6660 (tt0) REVERT: B 319 THR cc_start: 0.8191 (m) cc_final: 0.7640 (p) REVERT: B 345 ASP cc_start: 0.7713 (t0) cc_final: 0.7281 (t70) outliers start: 9 outliers final: 5 residues processed: 52 average time/residue: 2.0984 time to fit residues: 111.2878 Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 359 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1797 Z= 0.172 Angle : 0.588 4.512 2400 Z= 0.295 Chirality : 0.052 0.137 267 Planarity : 0.004 0.038 306 Dihedral : 5.745 18.648 237 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 3.98 % Allowed : 24.88 % Favored : 71.14 % 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: -2.08 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.010 0.002 PHE C 378 TYR 0.005 0.001 TYR C 310 ARG 0.005 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8180 (t0) cc_final: 0.7911 (t0) REVERT: A 372 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7140 (tt0) REVERT: B 319 THR cc_start: 0.8249 (m) cc_final: 0.7724 (p) REVERT: B 345 ASP cc_start: 0.7711 (t0) cc_final: 0.7159 (t70) REVERT: C 345 ASP cc_start: 0.7885 (t0) cc_final: 0.7397 (t70) REVERT: C 349 ARG cc_start: 0.8036 (ttp-110) cc_final: 0.7330 (mtp180) outliers start: 8 outliers final: 6 residues processed: 52 average time/residue: 2.0677 time to fit residues: 109.7238 Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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: 0.7632 moved from start: 0.6112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 1797 Z= 0.193 Angle : 0.603 4.506 2400 Z= 0.301 Chirality : 0.052 0.144 267 Planarity : 0.004 0.040 306 Dihedral : 5.713 21.095 237 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.98 % Allowed : 25.37 % Favored : 70.65 % 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: -2.14 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 374 PHE 0.009 0.002 PHE C 378 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8172 (t0) cc_final: 0.7913 (t0) REVERT: B 319 THR cc_start: 0.8312 (m) cc_final: 0.7786 (p) REVERT: B 345 ASP cc_start: 0.7698 (t0) cc_final: 0.7149 (t70) REVERT: C 345 ASP cc_start: 0.7881 (t0) cc_final: 0.7411 (t70) REVERT: C 349 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7291 (mtp180) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 2.0546 time to fit residues: 104.8118 Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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: 0.7646 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1797 Z= 0.214 Angle : 0.612 4.674 2400 Z= 0.307 Chirality : 0.052 0.146 267 Planarity : 0.004 0.042 306 Dihedral : 5.676 20.276 237 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.48 % Allowed : 24.88 % Favored : 71.64 % 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: -2.12 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.010 0.002 PHE A 378 TYR 0.005 0.001 TYR C 310 ARG 0.001 0.000 ARG B 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 ASP cc_start: 0.8168 (t0) cc_final: 0.7902 (t0) REVERT: B 319 THR cc_start: 0.8263 (m) cc_final: 0.7745 (p) REVERT: B 345 ASP cc_start: 0.7679 (t0) cc_final: 0.7144 (t70) REVERT: C 345 ASP cc_start: 0.7855 (t0) cc_final: 0.7379 (t70) REVERT: C 349 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7254 (mtp180) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 2.1505 time to fit residues: 109.5961 Evaluate side-chains 55 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 LYS Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 377 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 351 GLN Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 0.3980 chunk 1 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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: 0.7602 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 1797 Z= 0.161 Angle : 0.584 4.208 2400 Z= 0.289 Chirality : 0.051 0.127 267 Planarity : 0.004 0.037 306 Dihedral : 5.407 19.606 237 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.99 % Allowed : 25.37 % Favored : 71.64 % 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: -2.16 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.003 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.283 Fit side-chains REVERT: B 315 LEU cc_start: 0.8442 (mp) cc_final: 0.8179 (mm) REVERT: B 319 THR cc_start: 0.8325 (m) cc_final: 0.7833 (p) REVERT: B 345 ASP cc_start: 0.7673 (t0) cc_final: 0.7112 (t70) REVERT: C 345 ASP cc_start: 0.7864 (t0) cc_final: 0.7394 (t70) REVERT: C 349 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7291 (mtp180) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 2.1698 time to fit residues: 110.4843 Evaluate side-chains 51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1797 Z= 0.201 Angle : 0.604 4.535 2400 Z= 0.301 Chirality : 0.052 0.144 267 Planarity : 0.004 0.037 306 Dihedral : 5.491 19.845 237 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.49 % Allowed : 26.87 % Favored : 71.64 % 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: -2.11 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.009 0.002 PHE A 378 TYR 0.005 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7892 (tp30) REVERT: B 319 THR cc_start: 0.8319 (m) cc_final: 0.7802 (p) REVERT: B 345 ASP cc_start: 0.7624 (t0) cc_final: 0.7113 (t70) REVERT: C 345 ASP cc_start: 0.7851 (t0) cc_final: 0.7369 (t70) REVERT: C 349 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7324 (mtp180) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 2.3101 time to fit residues: 117.5268 Evaluate side-chains 51 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 chunk 2 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1797 Z= 0.160 Angle : 0.588 4.149 2400 Z= 0.289 Chirality : 0.051 0.124 267 Planarity : 0.003 0.035 306 Dihedral : 5.232 18.888 237 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 27.36 % Favored : 71.14 % 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: -2.12 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 330 PHE 0.007 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 372 GLU cc_start: 0.8133 (mm-30) cc_final: 0.7863 (tp30) REVERT: B 315 LEU cc_start: 0.8434 (mp) cc_final: 0.8184 (mm) REVERT: B 319 THR cc_start: 0.8317 (m) cc_final: 0.7831 (p) REVERT: B 345 ASP cc_start: 0.7617 (t0) cc_final: 0.7117 (t70) REVERT: C 345 ASP cc_start: 0.7856 (t0) cc_final: 0.7376 (t70) REVERT: C 349 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7233 (mtp180) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 2.0190 time to fit residues: 102.9026 Evaluate side-chains 53 residues out of total 201 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 349 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.150330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.131858 restraints weight = 6252.568| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 2.03 r_work: 0.3995 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3905 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 1797 Z= 0.153 Angle : 0.571 3.875 2400 Z= 0.280 Chirality : 0.051 0.121 267 Planarity : 0.003 0.033 306 Dihedral : 5.017 15.366 237 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 1.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.49 % Allowed : 27.36 % Favored : 71.14 % 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: -2.06 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.005 0.001 PHE C 378 TYR 0.004 0.001 TYR C 310 ARG 0.002 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.01 seconds wall clock time: 59 minutes 50.34 seconds (3590.34 seconds total)