Starting phenix.real_space_refine (version: dev) on Fri Feb 17 05:46:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/02_2023/6hrf_0260.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/02_2023/6hrf_0260.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/02_2023/6hrf_0260.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/02_2023/6hrf_0260.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/02_2023/6hrf_0260.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hrf_0260/02_2023/6hrf_0260.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.008 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 Process input model Symmetric amino acids flipped Residue "A ARG 379": "NH1" <-> "NH2" Residue "B ARG 379": "NH1" <-> "NH2" Residue "C ARG 379": "NH1" <-> "NH2" Residue "D ARG 379": "NH1" <-> "NH2" Residue "E ARG 379": "NH1" <-> "NH2" Residue "F ARG 379": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3522 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "D" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "E" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "F" Number of atoms: 587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 587 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 2.45, per 1000 atoms: 0.70 Number of scatterers: 3522 At special positions: 0 Unit cell: (115.44, 118.56, 37.44, 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 666 8.00 N 648 7.00 C 2202 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: 1.38 Conformation dependent library (CDL) restraints added in 558.5 milliseconds 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 804 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 18 sheets defined 0.0% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 305 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.632A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 318 through 322 removed outlier: 7.197A pdb=" N THR A 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N CYS C 322 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS A 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR C 319 " --> pdb=" O SER E 320 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N CYS E 322 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 329 through 330 removed outlier: 6.810A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N HIS C 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 341 Processing sheet with id=AA6, first strand: chain 'A' and resid 351 through 353 removed outlier: 6.691A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLN C 351 " --> pdb=" O SER E 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359 removed outlier: 7.330A pdb=" N SER A 356 " --> pdb=" O LEU C 357 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N ASN C 359 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ASP A 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N SER C 356 " --> pdb=" O LEU E 357 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ASN E 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ASP C 358 " --> pdb=" O ASN E 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 371 Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 6.549A pdb=" N LYS A 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N PHE C 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR A 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LYS C 375 " --> pdb=" O LEU E 376 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE E 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR C 377 " --> pdb=" O PHE E 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 305 through 310 Processing sheet with id=AB2, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.558A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL D 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 318 through 322 removed outlier: 7.138A pdb=" N THR B 319 " --> pdb=" O SER D 320 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N CYS D 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR D 319 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N CYS F 322 " --> pdb=" O THR D 319 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS D 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 329 through 330 removed outlier: 6.873A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N HIS D 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 339 through 341 removed outlier: 3.550A pdb=" N LYS B 340 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER D 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER F 341 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 351 through 353 removed outlier: 6.764A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N GLN D 351 " --> pdb=" O SER F 352 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'B' and resid 356 through 359 removed outlier: 7.381A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER D 356 " --> pdb=" O LEU F 357 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN F 359 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP D 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 369 through 371 Processing sheet with id=AB9, first strand: chain 'B' and resid 374 through 378 removed outlier: 6.610A pdb=" N LYS B 375 " --> pdb=" O LEU D 376 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N PHE D 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N LYS D 375 " --> pdb=" O LEU F 376 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N PHE F 378 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR D 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 33 hydrogen bonds defined for protein. 99 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: 0.81 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 630 1.32 - 1.44: 788 1.44 - 1.55: 2027 1.55 - 1.67: 125 1.67 - 1.79: 6 Bond restraints: 3576 Sorted by residual: bond pdb=" C LYS E 311 " pdb=" N PRO E 312 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.17e-02 7.31e+03 2.07e+01 bond pdb=" C LYS B 311 " pdb=" N PRO B 312 " ideal model delta sigma weight residual 1.333 1.386 -0.053 1.17e-02 7.31e+03 2.04e+01 bond pdb=" C LYS C 311 " pdb=" N PRO C 312 " ideal model delta sigma weight residual 1.333 1.385 -0.053 1.17e-02 7.31e+03 2.03e+01 bond pdb=" N ARG B 349 " pdb=" CA ARG B 349 " ideal model delta sigma weight residual 1.457 1.529 -0.071 1.58e-02 4.01e+03 2.03e+01 bond pdb=" C LYS A 311 " pdb=" N PRO A 312 " ideal model delta sigma weight residual 1.333 1.385 -0.053 1.17e-02 7.31e+03 2.02e+01 ... (remaining 3571 not shown) Histogram of bond angle deviations from ideal: 102.98 - 108.67: 204 108.67 - 114.37: 2082 114.37 - 120.06: 834 120.06 - 125.76: 1620 125.76 - 131.45: 42 Bond angle restraints: 4782 Sorted by residual: angle pdb=" N SER F 352 " pdb=" CA SER F 352 " pdb=" C SER F 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER E 352 " pdb=" CA SER E 352 " pdb=" C SER E 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER C 352 " pdb=" CA SER C 352 " pdb=" C SER C 352 " ideal model delta sigma weight residual 108.99 114.69 -5.70 1.57e+00 4.06e-01 1.32e+01 angle pdb=" N SER D 352 " pdb=" CA SER D 352 " pdb=" C SER D 352 " ideal model delta sigma weight residual 108.99 114.68 -5.69 1.57e+00 4.06e-01 1.31e+01 ... (remaining 4777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.36: 1896 13.36 - 26.71: 174 26.71 - 40.06: 72 40.06 - 53.41: 24 53.41 - 66.76: 12 Dihedral angle restraints: 2178 sinusoidal: 912 harmonic: 1266 Sorted by residual: dihedral pdb=" CB LYS B 353 " pdb=" CG LYS B 353 " pdb=" CD LYS B 353 " pdb=" CE LYS B 353 " ideal model delta sinusoidal sigma weight residual -60.00 -101.76 41.76 3 1.50e+01 4.44e-03 7.48e+00 dihedral pdb=" CB LYS A 353 " pdb=" CG LYS A 353 " pdb=" CD LYS A 353 " pdb=" CE LYS A 353 " ideal model delta sinusoidal sigma weight residual -60.00 -101.73 41.73 3 1.50e+01 4.44e-03 7.47e+00 dihedral pdb=" CB LYS D 353 " pdb=" CG LYS D 353 " pdb=" CD LYS D 353 " pdb=" CE LYS D 353 " ideal model delta sinusoidal sigma weight residual -60.00 -101.72 41.72 3 1.50e+01 4.44e-03 7.47e+00 ... (remaining 2175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 227 0.050 - 0.099: 142 0.099 - 0.149: 81 0.149 - 0.198: 72 0.198 - 0.248: 12 Chirality restraints: 534 Sorted by residual: chirality pdb=" CA ILE D 328 " pdb=" N ILE D 328 " pdb=" C ILE D 328 " pdb=" CB ILE D 328 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE B 328 " pdb=" N ILE B 328 " pdb=" C ILE B 328 " pdb=" CB ILE B 328 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA ILE C 328 " pdb=" N ILE C 328 " pdb=" C ILE C 328 " pdb=" CB ILE C 328 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 531 not shown) Planarity restraints: 612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 368 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C ASN E 368 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN E 368 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS E 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 368 " 0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C ASN A 368 " -0.044 2.00e-02 2.50e+03 pdb=" O ASN A 368 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS A 369 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 368 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.53e+00 pdb=" C ASN B 368 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN B 368 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS B 369 " -0.015 2.00e-02 2.50e+03 ... (remaining 609 not shown) Histogram of nonbonded interaction distances: 2.63 - 3.08: 2011 3.08 - 3.54: 3350 3.54 - 3.99: 5016 3.99 - 4.45: 4850 4.45 - 4.90: 9434 Nonbonded interactions: 24661 Sorted by model distance: nonbonded pdb=" OG SER B 316 " pdb=" NZ LYS B 370 " model vdw 2.627 2.520 nonbonded pdb=" OG SER D 316 " pdb=" NZ LYS D 370 " model vdw 2.628 2.520 nonbonded pdb=" OG SER A 316 " pdb=" NZ LYS A 370 " model vdw 2.628 2.520 nonbonded pdb=" OG SER C 316 " pdb=" NZ LYS C 370 " model vdw 2.628 2.520 nonbonded pdb=" OG SER E 316 " pdb=" NZ LYS E 370 " model vdw 2.628 2.520 ... (remaining 24656 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' 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2202 2.51 5 N 648 2.21 5 O 666 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.180 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: 4.540 Check model and map are aligned: 0.050 Process input model: 15.020 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 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 : 0.016 0.071 3576 Z= 1.101 Angle : 1.247 6.892 4782 Z= 0.750 Chirality : 0.093 0.248 534 Planarity : 0.010 0.038 612 Dihedral : 13.679 66.761 1374 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer Outliers : 0.00 % 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: -4.08 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.21), residues: 450 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.438 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.3209 time to fit residues: 51.9690 Evaluate side-chains 84 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.407 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** C 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN E 336 GLN F 362 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.4837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 3576 Z= 0.332 Angle : 0.685 5.994 4782 Z= 0.349 Chirality : 0.049 0.146 534 Planarity : 0.004 0.029 612 Dihedral : 5.206 13.686 474 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 2.74 % 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: -3.71 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.82 (0.23), residues: 450 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.523 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 105 average time/residue: 0.2502 time to fit residues: 29.9198 Evaluate side-chains 102 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.444 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0787 time to fit residues: 1.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 HIS ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.6749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 3576 Z= 0.574 Angle : 0.835 6.655 4782 Z= 0.425 Chirality : 0.052 0.143 534 Planarity : 0.006 0.075 612 Dihedral : 6.184 18.510 474 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer Outliers : 1.99 % 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: -3.74 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.22), residues: 450 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.470 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 108 average time/residue: 0.1900 time to fit residues: 24.2550 Evaluate side-chains 98 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0399 time to fit residues: 0.9048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.6940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3576 Z= 0.285 Angle : 0.684 8.215 4782 Z= 0.332 Chirality : 0.049 0.153 534 Planarity : 0.004 0.031 612 Dihedral : 5.044 13.968 474 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 2.24 % 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: -3.66 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.22), residues: 450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.497 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 101 average time/residue: 0.2034 time to fit residues: 24.1046 Evaluate side-chains 94 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 89 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0376 time to fit residues: 0.9849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 34 optimal weight: 0.0030 chunk 28 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN ** D 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 3576 Z= 0.282 Angle : 0.672 7.189 4782 Z= 0.324 Chirality : 0.048 0.155 534 Planarity : 0.004 0.026 612 Dihedral : 4.853 14.714 474 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer Outliers : 1.74 % 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: -3.69 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.21), residues: 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.471 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 94 average time/residue: 0.2033 time to fit residues: 22.5367 Evaluate side-chains 85 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.447 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0353 time to fit residues: 0.7543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 9.9990 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 HIS ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN F 336 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.7477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3576 Z= 0.313 Angle : 0.681 8.556 4782 Z= 0.330 Chirality : 0.048 0.173 534 Planarity : 0.004 0.033 612 Dihedral : 4.867 16.325 474 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer Outliers : 1.00 % 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: -3.64 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.21), residues: 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 96 time to evaluate : 0.471 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 99 average time/residue: 0.1937 time to fit residues: 22.6505 Evaluate side-chains 93 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 91 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0396 time to fit residues: 0.7635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 336 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.7641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 3576 Z= 0.292 Angle : 0.699 7.849 4782 Z= 0.339 Chirality : 0.048 0.169 534 Planarity : 0.004 0.033 612 Dihedral : 4.739 15.240 474 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer Outliers : 2.24 % 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: -3.56 (0.28), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.22), residues: 450 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 89 time to evaluate : 0.453 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 93 average time/residue: 0.1863 time to fit residues: 20.8312 Evaluate side-chains 95 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0477 time to fit residues: 1.0688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.7714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 3576 Z= 0.230 Angle : 0.657 8.217 4782 Z= 0.316 Chirality : 0.048 0.175 534 Planarity : 0.004 0.034 612 Dihedral : 4.361 14.947 474 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer Outliers : 1.00 % 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: -3.43 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 90 time to evaluate : 0.482 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 92 average time/residue: 0.1900 time to fit residues: 20.6601 Evaluate side-chains 93 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 89 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0951 time to fit residues: 1.0758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 8.9990 chunk 41 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.7971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 3576 Z= 0.444 Angle : 0.761 7.745 4782 Z= 0.378 Chirality : 0.051 0.173 534 Planarity : 0.005 0.040 612 Dihedral : 5.135 15.860 474 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer Outliers : 0.75 % 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: -3.50 (0.29), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.22), residues: 450 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 0.452 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 99 average time/residue: 0.1949 time to fit residues: 22.8275 Evaluate side-chains 94 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0350 time to fit residues: 0.8207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 3576 Z= 0.236 Angle : 0.686 7.716 4782 Z= 0.338 Chirality : 0.048 0.176 534 Planarity : 0.004 0.031 612 Dihedral : 4.396 16.089 474 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 0.25 % 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: -3.36 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.23), residues: 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 900 Ramachandran restraints generated. 450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 91 time to evaluate : 0.436 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1911 time to fit residues: 20.8513 Evaluate side-chains 91 residues out of total 402 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 90 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0443 time to fit residues: 0.7296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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 = 0.4235 r_free = 0.4235 target = 0.141534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.119377 restraints weight = 5427.029| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.88 r_work: 0.3827 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.8090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 3576 Z= 0.330 Angle : 0.720 7.621 4782 Z= 0.354 Chirality : 0.050 0.175 534 Planarity : 0.004 0.028 612 Dihedral : 4.715 15.745 474 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer Outliers : 0.50 % 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: -3.41 (0.30), residues: 450 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.23), residues: 450 =============================================================================== Job complete usr+sys time: 1278.16 seconds wall clock time: 23 minutes 51.92 seconds (1431.92 seconds total)