Starting phenix.real_space_refine on Sun Mar 10 14:16:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjq_4566/03_2024/6qjq_4566_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjq_4566/03_2024/6qjq_4566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjq_4566/03_2024/6qjq_4566.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjq_4566/03_2024/6qjq_4566.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjq_4566/03_2024/6qjq_4566_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qjq_4566/03_2024/6qjq_4566_neut.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 774 2.51 5 N 222 2.21 5 O 216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 1218 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 207 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "B" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 207 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "C" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 207 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "E" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "F" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 199 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Time building chain proxies: 0.97, per 1000 atoms: 0.80 Number of scatterers: 1218 At special positions: 0 Unit cell: (95.68, 61.36, 39.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 216 8.00 N 222 7.00 C 774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 186.1 milliseconds 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 306 through 308 removed outlier: 6.000A pdb=" N VAL A 306 " --> pdb=" O GLN C 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 313 through 314 removed outlier: 7.144A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 317 through 319 removed outlier: 6.422A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 328 removed outlier: 7.276A pdb=" N ILE B 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 306 through 310 removed outlier: 6.521A pdb=" N VAL D 306 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL E 309 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 308 " --> pdb=" O VAL E 309 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.912A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 321 through 329 removed outlier: 7.188A pdb=" N CYS D 322 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N LEU E 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N SER D 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ASN E 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY D 326 " --> pdb=" O ASN E 327 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N HIS E 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N ILE D 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) removed outlier: 8.878A pdb=" N CYS D 322 " --> pdb=" O GLY F 323 " (cutoff:3.500A) removed outlier: 10.297A pdb=" N LEU F 325 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N SER D 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N ASN F 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY D 326 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS F 329 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE D 328 " --> pdb=" O HIS F 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 15 hydrogen bonds defined for protein. 45 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: 0.24 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 336 1.34 - 1.46: 145 1.46 - 1.57: 695 1.57 - 1.69: 54 1.69 - 1.80: 6 Bond restraints: 1236 Sorted by residual: bond pdb=" CA LYS B 311 " pdb=" C LYS B 311 " ideal model delta sigma weight residual 1.525 1.582 -0.057 1.04e-02 9.25e+03 3.02e+01 bond pdb=" CA LYS A 311 " pdb=" C LYS A 311 " ideal model delta sigma weight residual 1.525 1.582 -0.057 1.04e-02 9.25e+03 3.02e+01 bond pdb=" CA LYS C 311 " pdb=" C LYS C 311 " ideal model delta sigma weight residual 1.525 1.581 -0.057 1.04e-02 9.25e+03 2.98e+01 bond pdb=" CA ILE F 328 " pdb=" CB ILE F 328 " ideal model delta sigma weight residual 1.537 1.598 -0.061 1.17e-02 7.31e+03 2.70e+01 bond pdb=" CA ILE D 328 " pdb=" CB ILE D 328 " ideal model delta sigma weight residual 1.537 1.598 -0.061 1.17e-02 7.31e+03 2.68e+01 ... (remaining 1231 not shown) Histogram of bond angle deviations from ideal: 103.32 - 108.92: 82 108.92 - 114.52: 734 114.52 - 120.11: 276 120.11 - 125.71: 546 125.71 - 131.31: 18 Bond angle restraints: 1656 Sorted by residual: angle pdb=" N LYS C 317 " pdb=" CA LYS C 317 " pdb=" C LYS C 317 " ideal model delta sigma weight residual 108.02 114.05 -6.03 1.75e+00 3.27e-01 1.19e+01 angle pdb=" N LYS A 317 " pdb=" CA LYS A 317 " pdb=" C LYS A 317 " ideal model delta sigma weight residual 108.02 114.05 -6.03 1.75e+00 3.27e-01 1.19e+01 angle pdb=" N LYS B 317 " pdb=" CA LYS B 317 " pdb=" C LYS B 317 " ideal model delta sigma weight residual 108.02 114.03 -6.01 1.75e+00 3.27e-01 1.18e+01 angle pdb=" N LYS D 311 " pdb=" CA LYS D 311 " pdb=" C LYS D 311 " ideal model delta sigma weight residual 108.21 113.85 -5.64 2.00e+00 2.50e-01 7.95e+00 angle pdb=" N LYS F 311 " pdb=" CA LYS F 311 " pdb=" C LYS F 311 " ideal model delta sigma weight residual 108.21 113.84 -5.63 2.00e+00 2.50e-01 7.91e+00 ... (remaining 1651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.33: 648 10.33 - 20.66: 42 20.66 - 30.98: 33 30.98 - 41.31: 9 41.31 - 51.64: 12 Dihedral angle restraints: 744 sinusoidal: 294 harmonic: 450 Sorted by residual: dihedral pdb=" C LYS D 311 " pdb=" N LYS D 311 " pdb=" CA LYS D 311 " pdb=" CB LYS D 311 " ideal model delta harmonic sigma weight residual -122.60 -130.30 7.70 0 2.50e+00 1.60e-01 9.48e+00 dihedral pdb=" C LYS F 311 " pdb=" N LYS F 311 " pdb=" CA LYS F 311 " pdb=" CB LYS F 311 " ideal model delta harmonic sigma weight residual -122.60 -130.24 7.64 0 2.50e+00 1.60e-01 9.34e+00 dihedral pdb=" C LYS E 311 " pdb=" N LYS E 311 " pdb=" CA LYS E 311 " pdb=" CB LYS E 311 " ideal model delta harmonic sigma weight residual -122.60 -130.22 7.62 0 2.50e+00 1.60e-01 9.28e+00 ... (remaining 741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 74 0.048 - 0.096: 41 0.096 - 0.145: 43 0.145 - 0.193: 20 0.193 - 0.241: 20 Chirality restraints: 198 Sorted by residual: chirality pdb=" CA ILE F 328 " pdb=" N ILE F 328 " pdb=" C ILE F 328 " pdb=" CB ILE F 328 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA VAL A 318 " pdb=" N VAL A 318 " pdb=" C VAL A 318 " pdb=" CB VAL A 318 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA VAL C 318 " pdb=" N VAL C 318 " pdb=" C VAL C 318 " pdb=" CB VAL C 318 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 195 not shown) Planarity restraints: 198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 310 " 0.010 2.00e-02 2.50e+03 1.59e-02 5.08e+00 pdb=" CG TYR A 310 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR A 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 310 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 310 " 0.010 2.00e-02 2.50e+03 1.59e-02 5.07e+00 pdb=" CG TYR B 310 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 310 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR B 310 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.010 2.00e-02 2.50e+03 1.59e-02 5.03e+00 pdb=" CG TYR C 310 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " -0.004 2.00e-02 2.50e+03 ... (remaining 195 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 445 2.98 - 3.46: 935 3.46 - 3.94: 1837 3.94 - 4.42: 1701 4.42 - 4.90: 3218 Nonbonded interactions: 8136 Sorted by model distance: nonbonded pdb=" OD1 ASN A 327 " pdb=" ND2 ASN C 327 " model vdw 2.499 2.520 nonbonded pdb=" O SER A 324 " pdb=" N LEU C 325 " model vdw 2.526 2.520 nonbonded pdb=" N LEU D 315 " pdb=" O ASP F 314 " model vdw 2.529 2.520 nonbonded pdb=" O GLY A 326 " pdb=" N ASN C 327 " model vdw 2.566 2.520 nonbonded pdb=" O PRO A 312 " pdb=" N VAL C 313 " model vdw 2.578 2.520 ... (remaining 8131 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' and resid 274 through 330) selection = (chain 'B' and resid 274 through 330) selection = (chain 'C' and resid 274 through 330) selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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 group one per residue 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: 0.880 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: 0.010 Extract box with map and model: 3.280 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 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 : 0.021 0.061 1236 Z= 1.432 Angle : 1.173 6.033 1656 Z= 0.669 Chirality : 0.112 0.241 198 Planarity : 0.009 0.031 198 Dihedral : 13.356 51.641 456 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 2.00 % Allowed : 4.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.49), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.38), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS F 329 TYR 0.039 0.010 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.165 Fit side-chains REVERT: D 325 LEU cc_start: 0.8831 (mt) cc_final: 0.8510 (mp) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.0882 time to fit residues: 4.9781 Evaluate side-chains 20 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1236 Z= 0.181 Angle : 0.687 8.396 1656 Z= 0.320 Chirality : 0.052 0.141 198 Planarity : 0.003 0.023 198 Dihedral : 4.174 17.457 162 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.39 % Allowed : 11.81 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 329 TYR 0.012 0.003 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 24 time to evaluate : 0.157 Fit side-chains REVERT: F 315 LEU cc_start: 0.9344 (mt) cc_final: 0.9011 (pt) outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.0772 time to fit residues: 2.4204 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.0670 chunk 4 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1236 Z= 0.109 Angle : 0.598 6.624 1656 Z= 0.268 Chirality : 0.050 0.132 198 Planarity : 0.002 0.018 198 Dihedral : 3.667 15.362 162 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 13.89 % 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: -3.36 (0.51), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.39), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS E 329 TYR 0.011 0.002 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.134 Fit side-chains REVERT: F 314 ASP cc_start: 0.8493 (t0) cc_final: 0.8257 (t0) REVERT: F 315 LEU cc_start: 0.9338 (mt) cc_final: 0.8878 (pt) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.0691 time to fit residues: 2.0961 Evaluate side-chains 19 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 0.1980 chunk 11 optimal weight: 9.9990 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 1236 Z= 0.162 Angle : 0.605 7.161 1656 Z= 0.273 Chirality : 0.049 0.133 198 Planarity : 0.002 0.013 198 Dihedral : 3.787 14.728 162 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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: -3.21 (0.51), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.39), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 TYR 0.011 0.002 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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: 0 poor density : 20 time to evaluate : 0.140 Fit side-chains REVERT: F 314 ASP cc_start: 0.8546 (t0) cc_final: 0.8205 (t0) REVERT: F 315 LEU cc_start: 0.9350 (mt) cc_final: 0.8882 (pt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0840 time to fit residues: 2.1174 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 8 optimal weight: 0.0980 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 1236 Z= 0.140 Angle : 0.583 6.546 1656 Z= 0.263 Chirality : 0.049 0.132 198 Planarity : 0.002 0.015 198 Dihedral : 3.645 12.076 162 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 17.36 % 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: -3.08 (0.51), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.39), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 329 TYR 0.013 0.002 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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: 0 poor density : 21 time to evaluate : 0.158 Fit side-chains REVERT: F 314 ASP cc_start: 0.8433 (t0) cc_final: 0.8015 (t0) REVERT: F 315 LEU cc_start: 0.9349 (mt) cc_final: 0.8893 (pt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.0817 time to fit residues: 2.1702 Evaluate side-chains 18 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 9 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 overall best weight: 3.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 1236 Z= 0.267 Angle : 0.633 6.567 1656 Z= 0.299 Chirality : 0.050 0.137 198 Planarity : 0.003 0.021 198 Dihedral : 4.115 12.469 162 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 18.06 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.52), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.40), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 329 TYR 0.010 0.002 TYR B 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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: 0 poor density : 20 time to evaluate : 0.155 Fit side-chains REVERT: F 315 LEU cc_start: 0.9432 (mt) cc_final: 0.8980 (pt) outliers start: 0 outliers final: 0 residues processed: 20 average time/residue: 0.0814 time to fit residues: 2.0545 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.0770 overall best weight: 2.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1236 Z= 0.180 Angle : 0.599 6.416 1656 Z= 0.278 Chirality : 0.050 0.134 198 Planarity : 0.003 0.024 198 Dihedral : 3.912 12.276 162 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % 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: -2.87 (0.53), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.006 0.002 TYR D 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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: 0 poor density : 17 time to evaluate : 0.164 Fit side-chains REVERT: F 315 LEU cc_start: 0.9435 (mt) cc_final: 0.8939 (pt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0610 time to fit residues: 1.4681 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 10 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 3 optimal weight: 0.0980 chunk 7 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 1 optimal weight: 0.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 1236 Z= 0.195 Angle : 0.618 7.455 1656 Z= 0.283 Chirality : 0.050 0.134 198 Planarity : 0.003 0.024 198 Dihedral : 3.918 12.195 162 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 0.00 % Allowed : 17.36 % 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: -2.86 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.007 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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: 0 poor density : 18 time to evaluate : 0.168 Fit side-chains REVERT: F 315 LEU cc_start: 0.9439 (mt) cc_final: 0.8956 (pt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0595 time to fit residues: 1.5196 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 6 optimal weight: 8.9990 chunk 5 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1236 Z= 0.217 Angle : 0.620 6.922 1656 Z= 0.287 Chirality : 0.050 0.134 198 Planarity : 0.003 0.025 198 Dihedral : 4.094 12.479 162 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.54), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.41), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 329 TYR 0.007 0.002 TYR A 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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: 0 poor density : 17 time to evaluate : 0.128 Fit side-chains REVERT: F 315 LEU cc_start: 0.9444 (mt) cc_final: 0.8959 (pt) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0609 time to fit residues: 1.4599 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 8 optimal weight: 0.0000 chunk 3 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 0 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1236 Z= 0.168 Angle : 0.605 6.708 1656 Z= 0.277 Chirality : 0.050 0.132 198 Planarity : 0.003 0.024 198 Dihedral : 3.872 12.286 162 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.69 % Allowed : 18.06 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.55), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 TYR 0.005 0.001 TYR E 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 300 Ramachandran restraints generated. 150 Oldfield, 0 Emsley, 150 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 : 0.165 Fit side-chains REVERT: F 315 LEU cc_start: 0.9440 (mt) cc_final: 0.8985 (pt) outliers start: 1 outliers final: 0 residues processed: 19 average time/residue: 0.0577 time to fit residues: 1.5490 Evaluate side-chains 17 residues out of total 144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 12 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 327 ASN ** 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 = 0.4022 r_free = 0.4022 target = 0.077720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.070816 restraints weight = 4777.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.072374 restraints weight = 1986.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.073376 restraints weight = 1167.891| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 1236 Z= 0.174 Angle : 0.619 7.014 1656 Z= 0.283 Chirality : 0.050 0.134 198 Planarity : 0.003 0.023 198 Dihedral : 4.086 12.566 162 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.55), residues: 150 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.42), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 329 TYR 0.005 0.001 TYR A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 722.87 seconds wall clock time: 14 minutes 56.96 seconds (896.96 seconds total)