Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql1_14060/03_2024/7ql1_14060.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql1_14060/03_2024/7ql1_14060.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql1_14060/03_2024/7ql1_14060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql1_14060/03_2024/7ql1_14060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql1_14060/03_2024/7ql1_14060.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ql1_14060/03_2024/7ql1_14060.pdb" } resolution = 3.34 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= 0.001 sd= 0.006 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 3 5.16 5 C 1053 2.51 5 N 303 2.21 5 O 312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1671 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "C" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 557 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Time building chain proxies: 1.40, per 1000 atoms: 0.84 Number of scatterers: 1671 At special positions: 0 Unit cell: (78.516, 85.786, 39.258, 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 3 16.00 O 312 8.00 N 303 7.00 C 1053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 315.2 milliseconds 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 384 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 307 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.749A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.543A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 330 removed outlier: 5.864A pdb=" N GLY A 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N HIS D 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY D 326 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN C 327 " --> pdb=" O GLY D 326 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.307A pdb=" N GLU C 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N SER D 341 " --> pdb=" O GLU C 338 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS C 340 " --> pdb=" O SER D 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.512A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.497A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 360 through 362 removed outlier: 6.431A pdb=" N THR A 361 " --> pdb=" O HIS D 362 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 371 through 377 removed outlier: 6.964A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU D 376 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS C 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) 27 hydrogen bonds defined for protein. 81 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: 0.40 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 477 1.33 - 1.45: 204 1.45 - 1.57: 1014 1.57 - 1.68: 0 1.68 - 1.80: 3 Bond restraints: 1698 Sorted by residual: bond pdb=" CZ ARG A 349 " pdb=" NH2 ARG A 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.75e+00 bond pdb=" CB THR C 361 " pdb=" OG1 THR C 361 " ideal model delta sigma weight residual 1.433 1.389 0.044 1.60e-02 3.91e+03 7.42e+00 bond pdb=" CB THR A 361 " pdb=" OG1 THR A 361 " ideal model delta sigma weight residual 1.433 1.391 0.042 1.60e-02 3.91e+03 7.01e+00 bond pdb=" CZ ARG C 349 " pdb=" NH2 ARG C 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.94e+00 bond pdb=" CZ ARG D 349 " pdb=" NH2 ARG D 349 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.81e+00 ... (remaining 1693 not shown) Histogram of bond angle deviations from ideal: 102.25 - 107.42: 129 107.42 - 112.59: 748 112.59 - 117.76: 407 117.76 - 122.93: 776 122.93 - 128.10: 214 Bond angle restraints: 2274 Sorted by residual: angle pdb=" CA ASP D 314 " pdb=" CB ASP D 314 " pdb=" CG ASP D 314 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.49e+01 angle pdb=" CA ASP C 314 " pdb=" CB ASP C 314 " pdb=" CG ASP C 314 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.88e+01 angle pdb=" CB HIS A 329 " pdb=" CG HIS A 329 " pdb=" CD2 HIS A 329 " ideal model delta sigma weight residual 131.20 124.98 6.22 1.30e+00 5.92e-01 2.29e+01 angle pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " pdb=" CD2 HIS A 374 " ideal model delta sigma weight residual 131.20 125.03 6.17 1.30e+00 5.92e-01 2.25e+01 angle pdb=" C LYS C 311 " pdb=" CA LYS C 311 " pdb=" CB LYS C 311 " ideal model delta sigma weight residual 111.11 117.00 -5.89 1.28e+00 6.10e-01 2.11e+01 ... (remaining 2269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.53: 798 8.53 - 17.06: 162 17.06 - 25.59: 42 25.59 - 34.12: 21 34.12 - 42.65: 9 Dihedral angle restraints: 1032 sinusoidal: 429 harmonic: 603 Sorted by residual: dihedral pdb=" CA ASP C 314 " pdb=" C ASP C 314 " pdb=" N LEU C 315 " pdb=" CA LEU C 315 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 151.69 28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLN C 336 " pdb=" C GLN C 336 " pdb=" N VAL C 337 " pdb=" CA VAL C 337 " ideal model delta harmonic sigma weight residual 180.00 151.75 28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 1029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 96 0.049 - 0.097: 67 0.097 - 0.146: 50 0.146 - 0.194: 30 0.194 - 0.243: 15 Chirality restraints: 258 Sorted by residual: chirality pdb=" CA LYS C 311 " pdb=" N LYS C 311 " pdb=" C LYS C 311 " pdb=" CB LYS C 311 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA LYS C 343 " pdb=" N LYS C 343 " pdb=" C LYS C 343 " pdb=" CB LYS C 343 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 255 not shown) Planarity restraints: 288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 310 " -0.095 2.00e-02 2.50e+03 5.25e-02 5.51e+01 pdb=" CG TYR D 310 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR D 310 " 0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR D 310 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR D 310 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR D 310 " 0.034 2.00e-02 2.50e+03 pdb=" CZ TYR D 310 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 310 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " -0.073 2.00e-02 2.50e+03 4.12e-02 3.40e+01 pdb=" CG TYR C 310 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.036 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " -0.058 2.00e-02 2.50e+03 2.98e-02 1.78e+01 pdb=" CG TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.039 2.00e-02 2.50e+03 ... (remaining 285 not shown) Histogram of nonbonded interaction distances: 2.65 - 3.10: 1125 3.10 - 3.55: 1466 3.55 - 4.00: 2463 4.00 - 4.45: 2760 4.45 - 4.90: 4982 Nonbonded interactions: 12796 Sorted by model distance: nonbonded pdb=" N GLY A 366 " pdb=" O GLY A 366 " model vdw 2.654 2.496 nonbonded pdb=" O LEU D 325 " pdb=" CA GLY D 326 " model vdw 2.655 2.752 nonbonded pdb=" N GLY D 366 " pdb=" O GLY D 366 " model vdw 2.656 2.496 nonbonded pdb=" O PRO C 332 " pdb=" OG SER D 356 " model vdw 2.656 2.440 nonbonded pdb=" NZ LYS D 370 " pdb=" OE1 GLU D 372 " model vdw 2.663 2.520 ... (remaining 12791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.670 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.220 Find NCS groups from input model: 0.100 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 0.044 1698 Z= 0.722 Angle : 2.010 7.476 2274 Z= 1.340 Chirality : 0.103 0.243 258 Planarity : 0.013 0.056 288 Dihedral : 11.062 42.647 648 Min Nonbonded Distance : 2.654 Molprobity Statistics. All-atom Clashscore : 0.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: -3.09 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS C 362 PHE 0.031 0.012 PHE A 378 TYR 0.095 0.035 TYR D 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.183 Fit side-chains REVERT: A 347 LYS cc_start: 0.8985 (mttt) cc_final: 0.8328 (pttm) REVERT: A 348 ASP cc_start: 0.8712 (t0) cc_final: 0.7898 (p0) REVERT: A 356 SER cc_start: 0.8863 (p) cc_final: 0.8517 (p) REVERT: C 349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7848 (mmp-170) REVERT: C 370 LYS cc_start: 0.8476 (tttt) cc_final: 0.8120 (tttt) REVERT: D 321 LYS cc_start: 0.8436 (mttt) cc_final: 0.8173 (mtpt) REVERT: D 347 LYS cc_start: 0.9016 (mttt) cc_final: 0.8763 (mptt) REVERT: D 370 LYS cc_start: 0.8664 (tttt) cc_final: 0.8380 (tttm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2784 time to fit residues: 26.3386 Evaluate side-chains 74 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.173 ------------------------------------------------------------------------------- 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: 8.9990 chunk 15 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 368 ASN C 359 ASN C 362 HIS D 327 ASN D 359 ASN D 362 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1698 Z= 0.219 Angle : 0.722 6.467 2274 Z= 0.367 Chirality : 0.052 0.144 258 Planarity : 0.004 0.037 288 Dihedral : 7.135 25.138 222 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.08 % Allowed : 17.19 % Favored : 80.73 % 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 (0.43), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 330 PHE 0.008 0.002 PHE C 346 TYR 0.008 0.002 TYR D 310 ARG 0.003 0.001 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.211 Fit side-chains REVERT: A 347 LYS cc_start: 0.9232 (mttt) cc_final: 0.8579 (pttm) REVERT: A 348 ASP cc_start: 0.8627 (t0) cc_final: 0.7163 (p0) REVERT: A 356 SER cc_start: 0.8708 (p) cc_final: 0.8301 (p) REVERT: C 311 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8094 (mmtm) REVERT: C 336 GLN cc_start: 0.8948 (mp10) cc_final: 0.8331 (mp10) REVERT: C 348 ASP cc_start: 0.8775 (OUTLIER) cc_final: 0.8553 (t70) REVERT: C 349 ARG cc_start: 0.8573 (mtt180) cc_final: 0.7485 (mmp-170) REVERT: D 347 LYS cc_start: 0.9075 (mttt) cc_final: 0.8678 (mmtm) REVERT: D 349 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8399 (mtp85) outliers start: 4 outliers final: 1 residues processed: 75 average time/residue: 0.2226 time to fit residues: 18.0154 Evaluate side-chains 60 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 1698 Z= 0.285 Angle : 0.677 5.904 2274 Z= 0.344 Chirality : 0.052 0.142 258 Planarity : 0.004 0.038 288 Dihedral : 6.399 20.753 222 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 16.67 % Favored : 80.21 % 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: -2.19 (0.42), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS C 330 PHE 0.005 0.002 PHE C 378 TYR 0.012 0.002 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.203 Fit side-chains REVERT: A 348 ASP cc_start: 0.8564 (t0) cc_final: 0.7058 (p0) REVERT: A 356 SER cc_start: 0.8614 (p) cc_final: 0.8123 (p) REVERT: C 311 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8077 (mmtm) REVERT: C 336 GLN cc_start: 0.8459 (mp10) cc_final: 0.7621 (mm110) REVERT: C 349 ARG cc_start: 0.8790 (mtt180) cc_final: 0.7599 (mmp-170) REVERT: C 371 ILE cc_start: 0.8690 (mm) cc_final: 0.8361 (mt) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.1515 time to fit residues: 9.8835 Evaluate side-chains 59 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN D 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1698 Z= 0.260 Angle : 0.635 5.625 2274 Z= 0.320 Chirality : 0.051 0.137 258 Planarity : 0.004 0.039 288 Dihedral : 6.064 18.590 222 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.60 % Allowed : 16.15 % Favored : 81.25 % 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 (0.43), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.012 0.002 TYR D 310 ARG 0.003 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.215 Fit side-chains REVERT: A 348 ASP cc_start: 0.8530 (t0) cc_final: 0.7490 (p0) REVERT: A 356 SER cc_start: 0.8699 (p) cc_final: 0.8165 (p) REVERT: C 311 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8077 (mmtm) REVERT: C 314 ASP cc_start: 0.8442 (m-30) cc_final: 0.8036 (t0) REVERT: C 336 GLN cc_start: 0.8680 (mp10) cc_final: 0.7747 (mm110) REVERT: C 349 ARG cc_start: 0.8769 (mtt180) cc_final: 0.7655 (mmp-170) outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.1550 time to fit residues: 9.4610 Evaluate side-chains 55 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 50 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 6 optimal weight: 0.0570 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 1698 Z= 0.295 Angle : 0.663 6.051 2274 Z= 0.334 Chirality : 0.051 0.137 258 Planarity : 0.003 0.038 288 Dihedral : 5.920 18.055 222 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.60 % Allowed : 18.75 % Favored : 78.65 % 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: -2.19 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.006 0.001 PHE D 346 TYR 0.013 0.003 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.213 Fit side-chains REVERT: A 348 ASP cc_start: 0.8561 (t0) cc_final: 0.7469 (p0) REVERT: A 356 SER cc_start: 0.8655 (p) cc_final: 0.8210 (p) REVERT: C 314 ASP cc_start: 0.8488 (m-30) cc_final: 0.8173 (t0) REVERT: C 336 GLN cc_start: 0.8842 (mp10) cc_final: 0.7868 (mm110) REVERT: C 349 ARG cc_start: 0.8854 (mtt180) cc_final: 0.7612 (mmp-170) outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 0.1327 time to fit residues: 7.5226 Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 345 ASP Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1698 Z= 0.326 Angle : 0.662 5.115 2274 Z= 0.336 Chirality : 0.051 0.136 258 Planarity : 0.004 0.038 288 Dihedral : 6.002 18.031 222 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.60 % Allowed : 21.35 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.44), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.010 0.001 PHE D 346 TYR 0.014 0.003 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.200 Fit side-chains REVERT: A 348 ASP cc_start: 0.8502 (t0) cc_final: 0.7354 (p0) REVERT: C 314 ASP cc_start: 0.8501 (m-30) cc_final: 0.8207 (t0) REVERT: C 349 ARG cc_start: 0.8799 (mtt180) cc_final: 0.7697 (mmp-170) outliers start: 5 outliers final: 5 residues processed: 51 average time/residue: 0.1278 time to fit residues: 7.5390 Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 19 optimal weight: 0.3980 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1698 Z= 0.249 Angle : 0.625 5.225 2274 Z= 0.315 Chirality : 0.050 0.130 258 Planarity : 0.003 0.037 288 Dihedral : 5.748 17.119 222 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.60 % Allowed : 22.40 % Favored : 75.00 % 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: -2.29 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.007 0.001 PHE D 346 TYR 0.011 0.002 TYR D 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.217 Fit side-chains REVERT: A 348 ASP cc_start: 0.8547 (t0) cc_final: 0.7454 (p0) REVERT: C 314 ASP cc_start: 0.8363 (m-30) cc_final: 0.8108 (t0) REVERT: C 336 GLN cc_start: 0.8973 (mp10) cc_final: 0.8009 (mm110) REVERT: C 349 ARG cc_start: 0.8782 (mtt180) cc_final: 0.7699 (mmp-170) outliers start: 5 outliers final: 5 residues processed: 50 average time/residue: 0.1345 time to fit residues: 7.7488 Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1698 Z= 0.274 Angle : 0.633 5.152 2274 Z= 0.320 Chirality : 0.050 0.131 258 Planarity : 0.003 0.036 288 Dihedral : 5.716 16.915 222 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.60 % Allowed : 23.96 % Favored : 73.44 % 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: -2.32 (0.45), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.006 0.001 PHE D 346 TYR 0.012 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.213 Fit side-chains REVERT: A 348 ASP cc_start: 0.8633 (t0) cc_final: 0.7526 (p0) REVERT: C 314 ASP cc_start: 0.8377 (m-30) cc_final: 0.8130 (t0) REVERT: C 349 ARG cc_start: 0.8816 (mtt180) cc_final: 0.7732 (mmp-170) REVERT: D 314 ASP cc_start: 0.8774 (m-30) cc_final: 0.8029 (t0) outliers start: 5 outliers final: 5 residues processed: 50 average time/residue: 0.1358 time to fit residues: 7.8559 Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 1698 Z= 0.241 Angle : 0.625 5.259 2274 Z= 0.315 Chirality : 0.050 0.128 258 Planarity : 0.003 0.037 288 Dihedral : 5.604 16.520 222 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 23.44 % Favored : 73.44 % 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: -2.33 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.192 Fit side-chains REVERT: A 348 ASP cc_start: 0.8678 (t0) cc_final: 0.7487 (p0) REVERT: C 349 ARG cc_start: 0.8790 (mtt180) cc_final: 0.7692 (mmp-170) REVERT: D 314 ASP cc_start: 0.8742 (m-30) cc_final: 0.8016 (t0) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1074 time to fit residues: 6.2403 Evaluate side-chains 51 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1698 Z= 0.235 Angle : 0.623 5.259 2274 Z= 0.312 Chirality : 0.050 0.131 258 Planarity : 0.003 0.036 288 Dihedral : 5.496 16.342 222 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.12 % Allowed : 23.44 % Favored : 73.44 % 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: -2.35 (0.46), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.005 0.001 PHE D 346 TYR 0.010 0.002 TYR D 310 ARG 0.001 0.000 ARG A 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 426 Ramachandran restraints generated. 213 Oldfield, 0 Emsley, 213 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.207 Fit side-chains REVERT: A 348 ASP cc_start: 0.8669 (t0) cc_final: 0.7644 (p0) REVERT: A 359 ASN cc_start: 0.8455 (m110) cc_final: 0.8063 (m110) REVERT: C 349 ARG cc_start: 0.8874 (mtt180) cc_final: 0.7642 (mmp-170) REVERT: D 314 ASP cc_start: 0.8725 (m-30) cc_final: 0.8013 (t0) REVERT: D 349 ARG cc_start: 0.8828 (mtp85) cc_final: 0.7820 (mtm-85) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1591 time to fit residues: 8.9454 Evaluate side-chains 50 residues out of total 192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain D residue 375 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 20 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.127439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.110165 restraints weight = 2465.062| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 2.51 r_work: 0.3783 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1698 Z= 0.278 Angle : 0.656 6.678 2274 Z= 0.324 Chirality : 0.050 0.130 258 Planarity : 0.003 0.036 288 Dihedral : 5.517 16.649 222 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.12 % Allowed : 24.48 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.47), residues: 213 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.36), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 330 PHE 0.006 0.001 PHE D 346 TYR 0.011 0.002 TYR D 310 ARG 0.005 0.001 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 891.80 seconds wall clock time: 17 minutes 45.26 seconds (1065.26 seconds total)