Starting phenix.real_space_refine on Thu Dec 7 19:29:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/12_2023/8org_17123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/12_2023/8org_17123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/12_2023/8org_17123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/12_2023/8org_17123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/12_2023/8org_17123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8org_17123/12_2023/8org_17123.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1206 2.51 5 N 357 2.21 5 O 372 1.98 5 H 2025 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3966 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "A" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "C" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1322 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Time building chain proxies: 2.61, per 1000 atoms: 0.66 Number of scatterers: 3966 At special positions: 0 Unit cell: (70.8825, 92.6925, 35.9865, 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 372 8.00 N 357 7.00 C 1206 6.00 H 2025 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: 2.41 Conformation dependent library (CDL) restraints added in 488.7 milliseconds 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 11 sheets defined 0.0% alpha, 45.3% 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 278 through 283 removed outlier: 6.401A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299 removed outlier: 6.398A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310 removed outlier: 6.827A pdb=" N GLY B 304 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N GLY B 303 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N VAL C 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.459A pdb=" N ASP B 314 " --> pdb=" O LEU A 315 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N LYS A 317 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N SER B 316 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER C 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU B 315 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N VAL C 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.760A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.457A pdb=" N ASN B 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS C 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS B 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341 removed outlier: 6.392A pdb=" N VAL B 337 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LYS A 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 339 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346 Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354 Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.729A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2019 1.03 - 1.22: 6 1.22 - 1.41: 755 1.41 - 1.61: 1204 1.61 - 1.80: 6 Bond restraints: 3990 Sorted by residual: bond pdb=" CB PRO C 312 " pdb=" CG PRO C 312 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" CB PRO B 312 " pdb=" CG PRO B 312 " ideal model delta sigma weight residual 1.492 1.411 0.081 5.00e-02 4.00e+02 2.59e+00 bond pdb=" CB PRO A 312 " pdb=" CG PRO A 312 " ideal model delta sigma weight residual 1.492 1.412 0.080 5.00e-02 4.00e+02 2.56e+00 bond pdb=" CE LYS C 311 " pdb=" NZ LYS C 311 " ideal model delta sigma weight residual 1.489 1.442 0.047 3.00e-02 1.11e+03 2.41e+00 bond pdb=" CE LYS A 311 " pdb=" NZ LYS A 311 " ideal model delta sigma weight residual 1.489 1.443 0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 3985 not shown) Histogram of bond angle deviations from ideal: 102.70 - 108.45: 1562 108.45 - 114.20: 3825 114.20 - 119.94: 630 119.94 - 125.69: 1185 125.69 - 131.44: 79 Bond angle restraints: 7281 Sorted by residual: angle pdb=" CA LYS C 281 " pdb=" CB LYS C 281 " pdb=" CG LYS C 281 " ideal model delta sigma weight residual 114.10 120.92 -6.82 2.00e+00 2.50e-01 1.16e+01 angle pdb=" CA LYS A 281 " pdb=" CB LYS A 281 " pdb=" CG LYS A 281 " ideal model delta sigma weight residual 114.10 120.89 -6.79 2.00e+00 2.50e-01 1.15e+01 angle pdb=" CA LYS B 281 " pdb=" CB LYS B 281 " pdb=" CG LYS B 281 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.15e+01 angle pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 109.23 114.31 -5.08 1.55e+00 4.16e-01 1.08e+01 angle pdb=" N LYS B 281 " pdb=" CA LYS B 281 " pdb=" C LYS B 281 " ideal model delta sigma weight residual 109.23 114.30 -5.07 1.55e+00 4.16e-01 1.07e+01 ... (remaining 7276 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 1557 13.45 - 26.91: 143 26.91 - 40.36: 19 40.36 - 53.81: 12 53.81 - 67.26: 39 Dihedral angle restraints: 1770 sinusoidal: 993 harmonic: 777 Sorted by residual: dihedral pdb=" CA LEU A 357 " pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU B 357 " pdb=" C LEU B 357 " pdb=" N ASP B 358 " pdb=" CA ASP B 358 " ideal model delta harmonic sigma weight residual 180.00 155.60 24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA LEU C 357 " pdb=" C LEU C 357 " pdb=" N ASP C 358 " pdb=" CA ASP C 358 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 ... (remaining 1767 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.076: 228 0.076 - 0.152: 63 0.152 - 0.227: 3 0.227 - 0.303: 3 0.303 - 0.378: 3 Chirality restraints: 300 Sorted by residual: chirality pdb=" CB ILE B 360 " pdb=" CA ILE B 360 " pdb=" CG1 ILE B 360 " pdb=" CG2 ILE B 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB ILE C 360 " pdb=" CA ILE C 360 " pdb=" CG1 ILE C 360 " pdb=" CG2 ILE C 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CB ILE A 360 " pdb=" CA ILE A 360 " pdb=" CG1 ILE A 360 " pdb=" CG2 ILE A 360 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 297 not shown) Planarity restraints: 582 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 288 " -0.025 2.00e-02 2.50e+03 3.22e-02 1.55e+01 pdb=" CD GLN B 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN B 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN B 288 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN B 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN B 288 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 288 " -0.025 2.00e-02 2.50e+03 3.21e-02 1.55e+01 pdb=" CD GLN A 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 288 " 0.054 2.00e-02 2.50e+03 pdb="HE21 GLN A 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN A 288 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 288 " -0.025 2.00e-02 2.50e+03 3.20e-02 1.53e+01 pdb=" CD GLN C 288 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN C 288 " 0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN C 288 " 0.053 2.00e-02 2.50e+03 pdb="HE21 GLN C 288 " 0.001 2.00e-02 2.50e+03 pdb="HE22 GLN C 288 " -0.049 2.00e-02 2.50e+03 ... (remaining 579 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.32: 1175 2.32 - 2.89: 9040 2.89 - 3.46: 8824 3.46 - 4.03: 13749 4.03 - 4.60: 19241 Nonbonded interactions: 52029 Sorted by model distance: nonbonded pdb=" OD2 ASP C 295 " pdb=" HZ3 LYS C 311 " model vdw 1.746 1.850 nonbonded pdb=" OD2 ASP B 295 " pdb=" HZ3 LYS B 311 " model vdw 1.747 1.850 nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ3 LYS A 311 " model vdw 1.748 1.850 nonbonded pdb="HD22 ASN A 296 " pdb=" OD2 ASP A 358 " model vdw 1.764 1.850 nonbonded pdb="HD22 ASN B 296 " pdb=" OD2 ASP B 358 " model vdw 1.765 1.850 ... (remaining 52024 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 3.540 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 : 0.010 0.081 1965 Z= 0.651 Angle : 1.263 7.621 2628 Z= 0.667 Chirality : 0.075 0.378 300 Planarity : 0.005 0.032 336 Dihedral : 11.917 66.727 759 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % 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: -2.52 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.91 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.006 HIS A 299 PHE 0.012 0.005 PHE C 346 TYR 0.016 0.009 TYR A 310 ARG 0.002 0.001 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 2.4963 time to fit residues: 243.3895 Evaluate side-chains 48 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN A 286 ASN A 336 GLN A 359 ASN C 327 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1965 Z= 0.174 Angle : 0.598 4.444 2628 Z= 0.298 Chirality : 0.052 0.136 300 Planarity : 0.003 0.017 336 Dihedral : 6.582 17.367 261 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.95 % Allowed : 17.98 % Favored : 78.07 % 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: -2.68 (0.41), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.31), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 PHE 0.002 0.001 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.338 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 66 average time/residue: 1.5504 time to fit residues: 105.1471 Evaluate side-chains 57 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 0.337 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.5750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1965 Z= 0.213 Angle : 0.545 4.320 2628 Z= 0.277 Chirality : 0.051 0.127 300 Planarity : 0.003 0.025 336 Dihedral : 5.992 16.446 261 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.75 % Allowed : 22.37 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 299 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 55 average time/residue: 1.3539 time to fit residues: 76.7743 Evaluate side-chains 51 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.344 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 13 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.6081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1965 Z= 0.165 Angle : 0.491 3.691 2628 Z= 0.252 Chirality : 0.051 0.128 300 Planarity : 0.003 0.028 336 Dihedral : 5.462 15.220 261 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 0.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.63 % Allowed : 20.61 % Favored : 76.75 % 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: -2.78 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 54 average time/residue: 1.3762 time to fit residues: 76.6931 Evaluate side-chains 54 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 0.331 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.1720 time to fit residues: 2.8215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN A 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1965 Z= 0.188 Angle : 0.492 3.700 2628 Z= 0.254 Chirality : 0.050 0.124 300 Planarity : 0.003 0.030 336 Dihedral : 5.369 15.005 261 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.19 % Allowed : 21.05 % Favored : 76.75 % 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: -2.75 (0.42), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 48 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 1.3962 time to fit residues: 73.4716 Evaluate side-chains 50 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1249 time to fit residues: 0.5670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1965 Z= 0.156 Angle : 0.472 3.662 2628 Z= 0.241 Chirality : 0.051 0.122 300 Planarity : 0.003 0.028 336 Dihedral : 5.066 14.690 261 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.63 % Allowed : 21.05 % Favored : 76.32 % 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: -2.71 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.32), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.001 0.000 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 49 average time/residue: 1.4079 time to fit residues: 71.1814 Evaluate side-chains 48 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.1769 time to fit residues: 0.8509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.7612 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 1965 Z= 0.183 Angle : 0.478 3.653 2628 Z= 0.244 Chirality : 0.050 0.121 300 Planarity : 0.003 0.030 336 Dihedral : 5.109 14.698 261 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.07 % Allowed : 19.30 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.43), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 49 average time/residue: 1.1096 time to fit residues: 56.1709 Evaluate side-chains 51 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.250 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 2 average time/residue: 0.1249 time to fit residues: 0.6181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.0470 chunk 10 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 1965 Z= 0.147 Angle : 0.464 3.702 2628 Z= 0.236 Chirality : 0.050 0.121 300 Planarity : 0.003 0.029 336 Dihedral : 4.933 14.550 261 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.19 % Allowed : 20.18 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.44), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.001 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 44 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 47 average time/residue: 1.3310 time to fit residues: 64.7572 Evaluate side-chains 48 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 44 time to evaluate : 0.324 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 2 average time/residue: 0.1724 time to fit residues: 0.8333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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: 0.7584 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1965 Z= 0.121 Angle : 0.449 3.854 2628 Z= 0.227 Chirality : 0.051 0.122 300 Planarity : 0.003 0.030 336 Dihedral : 4.660 14.329 261 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.75 % Allowed : 21.05 % Favored : 77.19 % 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: -2.60 (0.44), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.001 0.000 PHE A 346 TYR 0.003 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 41 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 1.3687 time to fit residues: 60.8410 Evaluate side-chains 44 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1196 time to fit residues: 0.5614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 1 optimal weight: 3.9990 chunk 13 optimal weight: 0.0670 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 0.5736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 1965 Z= 0.127 Angle : 0.457 4.011 2628 Z= 0.230 Chirality : 0.051 0.123 300 Planarity : 0.003 0.029 336 Dihedral : 4.587 14.187 261 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 22.37 % Favored : 76.75 % 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: -2.61 (0.44), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.33), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.002 0.000 PHE A 346 TYR 0.002 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 504 Ramachandran restraints generated. 252 Oldfield, 0 Emsley, 252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 1.5260 time to fit residues: 69.2588 Evaluate side-chains 43 residues out of total 228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.4298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.132564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.114941 restraints weight = 7161.517| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.87 r_work: 0.3852 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.6618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1965 Z= 0.238 Angle : 0.496 3.772 2628 Z= 0.253 Chirality : 0.049 0.118 300 Planarity : 0.003 0.032 336 Dihedral : 5.108 15.246 261 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.32 % Allowed : 22.37 % Favored : 76.32 % 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: -2.63 (0.44), residues: 252 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 330 PHE 0.003 0.001 PHE C 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3102.17 seconds wall clock time: 57 minutes 59.65 seconds (3479.65 seconds total)