Starting phenix.real_space_refine on Wed Jan 17 11:33:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk6_14039/01_2024/7qk6_14039.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk6_14039/01_2024/7qk6_14039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk6_14039/01_2024/7qk6_14039.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk6_14039/01_2024/7qk6_14039.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk6_14039/01_2024/7qk6_14039.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qk6_14039/01_2024/7qk6_14039.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 744 2.51 5 N 213 2.21 5 O 228 1.98 5 H 1278 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 314": "OD1" <-> "OD2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 314": "OD1" <-> "OD2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 2469 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 823 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Time building chain proxies: 1.37, per 1000 atoms: 0.55 Number of scatterers: 2469 At special positions: 0 Unit cell: (74.881, 64.703, 31.261, 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 6 16.00 O 228 8.00 N 213 7.00 C 744 6.00 H 1278 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.85 Conformation dependent library (CDL) restraints added in 461.5 milliseconds 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 288 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 7 sheets defined 0.0% alpha, 42.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 277 through 278 removed outlier: 6.444A pdb=" N ILE B 277 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283 removed outlier: 6.764A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 290 removed outlier: 6.925A pdb=" N VAL A 287 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN B 288 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL B 287 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LYS C 290 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER B 289 " --> pdb=" O LYS C 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.516A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.422A pdb=" N VAL B 306 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL A 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 313 through 314 removed outlier: 7.001A pdb=" N VAL B 313 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 317 through 327 removed outlier: 6.838A pdb=" N SER A 324 " --> pdb=" O GLY B 323 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 325 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY A 326 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASN B 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLY C 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N CYS B 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU C 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N SER B 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ASN C 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N GLY B 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) 12 hydrogen bonds defined for protein. 36 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: 0.74 Time building geometry restraints manager: 1.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.90 - 1.09: 510 1.09 - 1.27: 963 1.27 - 1.45: 254 1.45 - 1.64: 745 1.64 - 1.82: 6 Bond restraints: 2478 Sorted by residual: bond pdb=" N HIS C 299 " pdb=" H HIS C 299 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS B 299 " pdb=" HE1 HIS B 299 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N LYS A 290 " pdb=" H LYS A 290 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N CYS C 322 " pdb=" H CYS C 322 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLN C 288 " pdb=" H GLN C 288 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 2473 not shown) Histogram of bond angle deviations from ideal: 97.15 - 103.39: 17 103.39 - 109.63: 2020 109.63 - 115.87: 1309 115.87 - 122.11: 931 122.11 - 128.36: 256 Bond angle restraints: 4533 Sorted by residual: angle pdb=" N GLY B 326 " pdb=" CA GLY B 326 " pdb=" C GLY B 326 " ideal model delta sigma weight residual 110.69 117.71 -7.02 1.33e+00 5.65e-01 2.78e+01 angle pdb=" CA VAL B 287 " pdb=" C VAL B 287 " pdb=" N GLN B 288 " ideal model delta sigma weight residual 116.40 121.99 -5.59 1.12e+00 7.97e-01 2.49e+01 angle pdb=" CA VAL C 287 " pdb=" C VAL C 287 " pdb=" N GLN C 288 " ideal model delta sigma weight residual 116.40 121.96 -5.56 1.12e+00 7.97e-01 2.47e+01 angle pdb=" N GLY A 326 " pdb=" CA GLY A 326 " pdb=" C GLY A 326 " ideal model delta sigma weight residual 110.69 116.73 -6.04 1.33e+00 5.65e-01 2.06e+01 angle pdb=" OD1 ASN C 279 " pdb=" CG ASN C 279 " pdb=" ND2 ASN C 279 " ideal model delta sigma weight residual 122.60 118.42 4.18 1.00e+00 1.00e+00 1.75e+01 ... (remaining 4528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.30: 986 13.30 - 26.60: 66 26.60 - 39.90: 18 39.90 - 53.20: 5 53.20 - 66.50: 29 Dihedral angle restraints: 1104 sinusoidal: 633 harmonic: 471 Sorted by residual: dihedral pdb=" CA GLN C 276 " pdb=" C GLN C 276 " pdb=" N ILE C 277 " pdb=" CA ILE C 277 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLN A 276 " pdb=" C GLN A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta harmonic sigma weight residual 180.00 154.86 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA GLN B 276 " pdb=" C GLN B 276 " pdb=" N ILE B 277 " pdb=" CA ILE B 277 " ideal model delta harmonic sigma weight residual 180.00 156.76 23.24 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 1101 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.062: 119 0.062 - 0.123: 43 0.123 - 0.184: 17 0.184 - 0.245: 11 0.245 - 0.307: 5 Chirality restraints: 195 Sorted by residual: chirality pdb=" CA ASN B 279 " pdb=" N ASN B 279 " pdb=" C ASN B 279 " pdb=" CB ASN B 279 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ASN A 279 " pdb=" N ASN A 279 " pdb=" C ASN A 279 " pdb=" CB ASN A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA ASN C 279 " pdb=" N ASN C 279 " pdb=" C ASN C 279 " pdb=" CB ASN C 279 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.33e+00 ... (remaining 192 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 327 " 0.067 2.00e-02 2.50e+03 6.51e-02 6.36e+01 pdb=" CG ASN A 327 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 327 " -0.036 2.00e-02 2.50e+03 pdb=" ND2 ASN A 327 " -0.077 2.00e-02 2.50e+03 pdb="HD21 ASN A 327 " -0.034 2.00e-02 2.50e+03 pdb="HD22 ASN A 327 " 0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 327 " 0.056 2.00e-02 2.50e+03 5.95e-02 5.31e+01 pdb=" CG ASN C 327 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN C 327 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN C 327 " -0.087 2.00e-02 2.50e+03 pdb="HD21 ASN C 327 " -0.015 2.00e-02 2.50e+03 pdb="HD22 ASN C 327 " 0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 327 " 0.055 2.00e-02 2.50e+03 5.78e-02 5.01e+01 pdb=" CG ASN B 327 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN B 327 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN B 327 " -0.083 2.00e-02 2.50e+03 pdb="HD21 ASN B 327 " -0.014 2.00e-02 2.50e+03 pdb="HD22 ASN B 327 " 0.093 2.00e-02 2.50e+03 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 212 2.17 - 2.78: 4323 2.78 - 3.38: 6651 3.38 - 3.99: 9009 3.99 - 4.60: 12209 Nonbonded interactions: 32404 Sorted by model distance: nonbonded pdb=" OD1 ASP A 283 " pdb=" HG SER A 285 " model vdw 1.561 1.850 nonbonded pdb=" OD1 ASP B 283 " pdb=" HG SER B 285 " model vdw 1.567 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.580 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.601 1.850 nonbonded pdb=" OD1 ASP C 283 " pdb=" HG SER C 285 " model vdw 1.619 1.850 ... (remaining 32399 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 '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: 2.700 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: 0.030 Extract box with map and model: 11.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.620 Find NCS groups from input model: 0.150 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:14.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 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 0.034 1200 Z= 0.782 Angle : 1.845 7.017 1608 Z= 1.231 Chirality : 0.095 0.307 195 Planarity : 0.009 0.040 201 Dihedral : 9.701 40.941 462 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.54), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.51 (0.41), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS A 299 TYR 0.040 0.012 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 2.2149 time to fit residues: 74.0039 Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS B 327 ASN A 299 HIS A 327 ASN C 299 HIS C 327 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1200 Z= 0.262 Angle : 0.738 5.619 1608 Z= 0.384 Chirality : 0.055 0.160 195 Planarity : 0.006 0.045 201 Dihedral : 6.862 23.899 162 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % 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: -2.24 (0.53), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.40), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS A 299 TYR 0.014 0.003 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.206 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 3.1644 time to fit residues: 70.4275 Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 13 optimal weight: 0.0770 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 overall best weight: 0.2894 ------------------------------------------------------------------------------- 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: 0.7872 moved from start: 0.4036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1200 Z= 0.156 Angle : 0.607 4.254 1608 Z= 0.312 Chirality : 0.054 0.145 195 Planarity : 0.006 0.049 201 Dihedral : 6.314 23.639 162 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 11.81 % Favored : 88.19 % 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: -2.34 (0.55), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.78 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.009 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 3.2110 time to fit residues: 71.4318 Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.7898 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 1200 Z= 0.185 Angle : 0.556 3.711 1608 Z= 0.286 Chirality : 0.054 0.143 195 Planarity : 0.005 0.043 201 Dihedral : 5.948 22.490 162 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 13.19 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.55), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.009 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.289 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 3.3324 time to fit residues: 57.3523 Evaluate side-chains 16 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 12 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 0.5980 chunk 13 optimal weight: 0.0970 chunk 8 optimal weight: 0.0770 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.7887 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1200 Z= 0.140 Angle : 0.523 3.624 1608 Z= 0.268 Chirality : 0.053 0.141 195 Planarity : 0.005 0.045 201 Dihedral : 5.614 21.288 162 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 15.97 % Favored : 83.33 % 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: -2.27 (0.56), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.43), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.008 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.211 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 3.0954 time to fit residues: 68.8847 Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 8 optimal weight: 0.0050 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- 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: 0.7909 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1200 Z= 0.159 Angle : 0.507 3.568 1608 Z= 0.257 Chirality : 0.053 0.140 195 Planarity : 0.004 0.041 201 Dihedral : 5.496 19.334 162 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % 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 (0.57), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.005 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.219 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 3.1217 time to fit residues: 60.0268 Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 4 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1200 Z= 0.164 Angle : 0.494 3.559 1608 Z= 0.252 Chirality : 0.053 0.141 195 Planarity : 0.004 0.038 201 Dihedral : 5.409 18.805 162 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.69 % Allowed : 15.97 % Favored : 83.33 % 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 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 299 TYR 0.005 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.209 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 3.3324 time to fit residues: 70.7573 Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 9 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1200 Z= 0.177 Angle : 0.510 3.616 1608 Z= 0.260 Chirality : 0.054 0.141 195 Planarity : 0.004 0.036 201 Dihedral : 5.388 18.109 162 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 15.97 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.45), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 TYR 0.004 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.208 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 20 average time/residue: 2.9348 time to fit residues: 59.4651 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 9 optimal weight: 0.4980 chunk 8 optimal weight: 0.3980 chunk 5 optimal weight: 0.3980 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1200 Z= 0.147 Angle : 0.494 3.572 1608 Z= 0.251 Chirality : 0.054 0.141 195 Planarity : 0.004 0.038 201 Dihedral : 5.287 17.684 162 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % 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 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.004 0.001 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 18 time to evaluate : 0.190 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 19 average time/residue: 2.9146 time to fit residues: 56.1033 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 1200 Z= 0.168 Angle : 0.516 4.434 1608 Z= 0.259 Chirality : 0.054 0.139 195 Planarity : 0.004 0.039 201 Dihedral : 5.308 17.344 162 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % 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: -2.15 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.003 0.001 TYR A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 312 Ramachandran restraints generated. 156 Oldfield, 0 Emsley, 156 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.185 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 17 average time/residue: 2.8929 time to fit residues: 49.8371 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 15 random chunks: chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.161476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.151110 restraints weight = 3753.570| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 1.57 r_work: 0.4299 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.4229 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.4229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1200 Z= 0.146 Angle : 0.483 3.607 1608 Z= 0.244 Chirality : 0.053 0.140 195 Planarity : 0.004 0.039 201 Dihedral : 5.209 16.707 162 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.69 % Allowed : 16.67 % Favored : 82.64 % 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: -2.14 (0.58), residues: 156 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.44), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 TYR 0.004 0.001 TYR A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2835.41 seconds wall clock time: 50 minutes 40.88 seconds (3040.88 seconds total)