Starting phenix.real_space_refine on Sat Mar 16 13:04:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/03_2024/8ixk_35794.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/03_2024/8ixk_35794.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/8ixk_35794/03_2024/8ixk_35794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/03_2024/8ixk_35794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/03_2024/8ixk_35794.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/03_2024/8ixk_35794.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 55 5.16 5 C 9720 2.51 5 N 2335 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14790 Number of models: 1 Model: "" Number of chains: 25 Chain: "R" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1091 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "S" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "Z" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 850 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "A" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1091 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "B" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "D" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "E" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 850 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "F" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1091 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "G" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "H" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "J" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 850 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "K" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1091 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "L" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "N" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "O" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 850 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "T" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1091 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 139} Chain: "V" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "W" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 344 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "X" Number of atoms: 329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 329 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'TRANS': 43} Chain: "Y" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 850 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Time building chain proxies: 7.61, per 1000 atoms: 0.51 Number of scatterers: 14790 At special positions: 0 Unit cell: (81.48, 80.51, 208.55, 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 55 16.00 O 2680 8.00 N 2335 7.00 C 9720 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: 6.08 Conformation dependent library (CDL) restraints added in 2.8 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3580 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 5 sheets defined 82.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'R' and resid 262 through 271 Processing helix chain 'R' and resid 276 through 312 removed outlier: 3.646A pdb=" N SER R 282 " --> pdb=" O ASN R 278 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 321 removed outlier: 4.048A pdb=" N GLY R 321 " --> pdb=" O ASP R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 322 through 330 Processing helix chain 'R' and resid 338 through 345 removed outlier: 3.572A pdb=" N GLN R 343 " --> pdb=" O ASN R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 371 through 399 removed outlier: 3.713A pdb=" N ASN R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU R 376 " --> pdb=" O ASP R 372 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 50 removed outlier: 4.333A pdb=" N THR P 46 " --> pdb=" O PHE P 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 50 Processing helix chain 'S' and resid 8 through 50 removed outlier: 4.025A pdb=" N VAL S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) Processing helix chain 'Z' and resid 6 through 58 removed outlier: 3.928A pdb=" N LEU Z 58 " --> pdb=" O LEU Z 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 69 through 77 Processing helix chain 'Z' and resid 80 through 107 removed outlier: 3.591A pdb=" N CYS Z 84 " --> pdb=" O ASN Z 80 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 110 No H-bonds generated for 'chain 'Z' and resid 108 through 110' Processing helix chain 'A' and resid 263 through 271 Processing helix chain 'A' and resid 276 through 312 removed outlier: 3.646A pdb=" N SER A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP A 294 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 removed outlier: 4.047A pdb=" N GLY A 321 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.572A pdb=" N GLN A 343 " --> pdb=" O ASN A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 399 removed outlier: 3.713A pdb=" N ASN A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU A 376 " --> pdb=" O ASP A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 50 removed outlier: 4.333A pdb=" N THR B 46 " --> pdb=" O PHE B 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 50 Processing helix chain 'D' and resid 8 through 50 removed outlier: 4.025A pdb=" N VAL D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 58 removed outlier: 3.928A pdb=" N LEU E 58 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 77 Processing helix chain 'E' and resid 80 through 107 removed outlier: 3.591A pdb=" N CYS E 84 " --> pdb=" O ASN E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'F' and resid 263 through 271 Processing helix chain 'F' and resid 276 through 312 removed outlier: 3.646A pdb=" N SER F 282 " --> pdb=" O ASN F 278 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP F 294 " --> pdb=" O SER F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 321 removed outlier: 4.048A pdb=" N GLY F 321 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 330 Processing helix chain 'F' and resid 338 through 345 removed outlier: 3.572A pdb=" N GLN F 343 " --> pdb=" O ASN F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 399 removed outlier: 3.713A pdb=" N ASN F 375 " --> pdb=" O CYS F 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 50 removed outlier: 4.333A pdb=" N THR G 46 " --> pdb=" O PHE G 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 50 Processing helix chain 'I' and resid 8 through 50 removed outlier: 4.025A pdb=" N VAL I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 6 through 58 removed outlier: 3.927A pdb=" N LEU J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 77 Processing helix chain 'J' and resid 80 through 107 removed outlier: 3.591A pdb=" N CYS J 84 " --> pdb=" O ASN J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'K' and resid 263 through 271 Processing helix chain 'K' and resid 276 through 312 removed outlier: 3.646A pdb=" N SER K 282 " --> pdb=" O ASN K 278 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP K 294 " --> pdb=" O SER K 290 " (cutoff:3.500A) Processing helix chain 'K' and resid 317 through 321 removed outlier: 4.048A pdb=" N GLY K 321 " --> pdb=" O ASP K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 322 through 330 Processing helix chain 'K' and resid 338 through 345 removed outlier: 3.573A pdb=" N GLN K 343 " --> pdb=" O ASN K 340 " (cutoff:3.500A) Processing helix chain 'K' and resid 371 through 399 removed outlier: 3.713A pdb=" N ASN K 375 " --> pdb=" O CYS K 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU K 376 " --> pdb=" O ASP K 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 6 through 50 removed outlier: 4.333A pdb=" N THR L 46 " --> pdb=" O PHE L 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 50 Processing helix chain 'N' and resid 8 through 50 removed outlier: 4.025A pdb=" N VAL N 31 " --> pdb=" O ALA N 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 58 removed outlier: 3.927A pdb=" N LEU O 58 " --> pdb=" O LEU O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 77 Processing helix chain 'O' and resid 80 through 107 removed outlier: 3.591A pdb=" N CYS O 84 " --> pdb=" O ASN O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 108 through 110 No H-bonds generated for 'chain 'O' and resid 108 through 110' Processing helix chain 'T' and resid 263 through 271 Processing helix chain 'T' and resid 276 through 312 removed outlier: 3.646A pdb=" N SER T 282 " --> pdb=" O ASN T 278 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP T 294 " --> pdb=" O SER T 290 " (cutoff:3.500A) Processing helix chain 'T' and resid 317 through 321 removed outlier: 4.048A pdb=" N GLY T 321 " --> pdb=" O ASP T 318 " (cutoff:3.500A) Processing helix chain 'T' and resid 322 through 330 Processing helix chain 'T' and resid 338 through 345 removed outlier: 3.572A pdb=" N GLN T 343 " --> pdb=" O ASN T 340 " (cutoff:3.500A) Processing helix chain 'T' and resid 371 through 399 removed outlier: 3.713A pdb=" N ASN T 375 " --> pdb=" O CYS T 371 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU T 376 " --> pdb=" O ASP T 372 " (cutoff:3.500A) Processing helix chain 'V' and resid 6 through 50 removed outlier: 4.333A pdb=" N THR V 46 " --> pdb=" O PHE V 42 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 50 Processing helix chain 'X' and resid 8 through 50 removed outlier: 4.025A pdb=" N VAL X 31 " --> pdb=" O ALA X 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 6 through 58 removed outlier: 3.928A pdb=" N LEU Y 58 " --> pdb=" O LEU Y 54 " (cutoff:3.500A) Processing helix chain 'Y' and resid 69 through 77 Processing helix chain 'Y' and resid 80 through 107 removed outlier: 3.591A pdb=" N CYS Y 84 " --> pdb=" O ASN Y 80 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 110 No H-bonds generated for 'chain 'Y' and resid 108 through 110' Processing sheet with id=AA1, first strand: chain 'R' and resid 358 through 359 Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359 Processing sheet with id=AA3, first strand: chain 'F' and resid 358 through 359 Processing sheet with id=AA4, first strand: chain 'K' and resid 358 through 359 Processing sheet with id=AA5, first strand: chain 'T' and resid 358 through 359 1331 hydrogen bonds defined for protein. 3903 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: 4.53 Time building geometry restraints manager: 6.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3729 1.34 - 1.45: 2823 1.45 - 1.57: 8448 1.57 - 1.69: 0 1.69 - 1.81: 95 Bond restraints: 15095 Sorted by residual: bond pdb=" N VAL Y 55 " pdb=" CA VAL Y 55 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.74e+00 bond pdb=" N VAL E 55 " pdb=" CA VAL E 55 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.73e+00 bond pdb=" N VAL Z 55 " pdb=" CA VAL Z 55 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.57e+00 bond pdb=" N VAL J 55 " pdb=" CA VAL J 55 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.45e+00 bond pdb=" N VAL O 55 " pdb=" CA VAL O 55 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.21e-02 6.83e+03 8.35e+00 ... (remaining 15090 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.49: 293 106.49 - 113.37: 8220 113.37 - 120.25: 5658 120.25 - 127.13: 6174 127.13 - 134.01: 85 Bond angle restraints: 20430 Sorted by residual: angle pdb=" N LYS V 43 " pdb=" CA LYS V 43 " pdb=" C LYS V 43 " ideal model delta sigma weight residual 113.12 106.84 6.28 1.25e+00 6.40e-01 2.52e+01 angle pdb=" N LYS G 43 " pdb=" CA LYS G 43 " pdb=" C LYS G 43 " ideal model delta sigma weight residual 113.12 106.84 6.28 1.25e+00 6.40e-01 2.52e+01 angle pdb=" N LYS L 43 " pdb=" CA LYS L 43 " pdb=" C LYS L 43 " ideal model delta sigma weight residual 113.12 106.86 6.26 1.25e+00 6.40e-01 2.51e+01 angle pdb=" N LYS P 43 " pdb=" CA LYS P 43 " pdb=" C LYS P 43 " ideal model delta sigma weight residual 113.12 106.86 6.26 1.25e+00 6.40e-01 2.51e+01 angle pdb=" N LYS B 43 " pdb=" CA LYS B 43 " pdb=" C LYS B 43 " ideal model delta sigma weight residual 113.12 106.87 6.25 1.25e+00 6.40e-01 2.50e+01 ... (remaining 20425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.95: 7690 12.95 - 25.90: 795 25.90 - 38.85: 275 38.85 - 51.81: 60 51.81 - 64.76: 10 Dihedral angle restraints: 8830 sinusoidal: 3250 harmonic: 5580 Sorted by residual: dihedral pdb=" CA ILE Y 76 " pdb=" C ILE Y 76 " pdb=" N LEU Y 77 " pdb=" CA LEU Y 77 " ideal model delta harmonic sigma weight residual -180.00 -164.07 -15.93 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE Z 76 " pdb=" C ILE Z 76 " pdb=" N LEU Z 77 " pdb=" CA LEU Z 77 " ideal model delta harmonic sigma weight residual -180.00 -164.12 -15.88 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ILE J 76 " pdb=" C ILE J 76 " pdb=" N LEU J 77 " pdb=" CA LEU J 77 " ideal model delta harmonic sigma weight residual -180.00 -164.13 -15.87 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 8827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1703 0.038 - 0.076: 458 0.076 - 0.114: 134 0.114 - 0.152: 56 0.152 - 0.190: 14 Chirality restraints: 2365 Sorted by residual: chirality pdb=" CA ILE X 22 " pdb=" N ILE X 22 " pdb=" C ILE X 22 " pdb=" CB ILE X 22 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CA ILE D 22 " pdb=" N ILE D 22 " pdb=" C ILE D 22 " pdb=" CB ILE D 22 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA ILE S 22 " pdb=" N ILE S 22 " pdb=" C ILE S 22 " pdb=" CB ILE S 22 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.95e-01 ... (remaining 2362 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE G 42 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.89e+00 pdb=" C PHE G 42 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE G 42 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS G 43 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE P 42 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C PHE P 42 " 0.045 2.00e-02 2.50e+03 pdb=" O PHE P 42 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS P 43 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 42 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C PHE L 42 " -0.045 2.00e-02 2.50e+03 pdb=" O PHE L 42 " 0.017 2.00e-02 2.50e+03 pdb=" N LYS L 43 " 0.015 2.00e-02 2.50e+03 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 4514 2.83 - 3.35: 15464 3.35 - 3.86: 24676 3.86 - 4.38: 27622 4.38 - 4.90: 47499 Nonbonded interactions: 119775 Sorted by model distance: nonbonded pdb=" OG SER A 351 " pdb=" O LEU J 77 " model vdw 2.310 2.440 nonbonded pdb=" OG SER R 351 " pdb=" O LEU E 77 " model vdw 2.310 2.440 nonbonded pdb=" O LEU Z 77 " pdb=" OG SER T 351 " model vdw 2.312 2.440 nonbonded pdb=" OG SER F 351 " pdb=" O LEU O 77 " model vdw 2.319 2.440 nonbonded pdb=" OG SER K 351 " pdb=" O LEU Y 77 " model vdw 2.325 2.440 ... (remaining 119770 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 'F' selection = chain 'K' selection = chain 'R' selection = chain 'T' } ncs_group { reference = (chain 'B' and resid 7 through 50) selection = (chain 'C' and resid 7 through 50) selection = chain 'D' selection = (chain 'G' and resid 7 through 50) selection = (chain 'H' and resid 7 through 50) selection = chain 'I' selection = (chain 'L' and resid 7 through 50) selection = (chain 'M' and resid 7 through 50) selection = chain 'N' selection = (chain 'P' and resid 7 through 50) selection = (chain 'Q' and resid 7 through 50) selection = chain 'S' selection = (chain 'V' and resid 7 through 50) selection = (chain 'W' and resid 7 through 50) selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 3.700 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.190 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.005 0.047 15095 Z= 0.332 Angle : 0.709 7.000 20430 Z= 0.496 Chirality : 0.043 0.190 2365 Planarity : 0.003 0.030 2550 Dihedral : 12.446 64.757 5250 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.65 % Allowed : 0.52 % Favored : 98.83 % 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: 4.29 (0.18), residues: 1900 helix: 3.34 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.38 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP H 26 PHE 0.016 0.002 PHE J 43 TYR 0.011 0.001 TYR J 57 ARG 0.001 0.000 ARG F 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 370 time to evaluate : 1.552 Fit side-chains revert: symmetry clash REVERT: R 404 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.5829 (pttp) REVERT: A 316 THR cc_start: 0.8104 (p) cc_final: 0.7882 (p) REVERT: A 404 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.5875 (mmmt) REVERT: C 24 TYR cc_start: 0.8971 (m-80) cc_final: 0.8705 (m-10) REVERT: E 109 ASP cc_start: 0.8385 (t0) cc_final: 0.8060 (t0) REVERT: F 290 SER cc_start: 0.9354 (t) cc_final: 0.9018 (p) REVERT: F 316 THR cc_start: 0.8166 (p) cc_final: 0.7892 (p) REVERT: F 395 SER cc_start: 0.8431 (m) cc_final: 0.8124 (m) REVERT: G 44 LYS cc_start: 0.8187 (tptt) cc_final: 0.7951 (ttmm) REVERT: H 24 TYR cc_start: 0.9000 (m-80) cc_final: 0.8779 (m-10) REVERT: T 404 LYS cc_start: 0.6747 (OUTLIER) cc_final: 0.6311 (mmmt) REVERT: V 44 LYS cc_start: 0.8218 (tptt) cc_final: 0.7843 (ttmm) REVERT: W 24 TYR cc_start: 0.8984 (m-80) cc_final: 0.8657 (m-80) outliers start: 10 outliers final: 2 residues processed: 380 average time/residue: 0.2419 time to fit residues: 137.8071 Evaluate side-chains 309 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 304 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 404 LYS Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain F residue 404 LYS Chi-restraints excluded: chain K residue 404 LYS Chi-restraints excluded: chain T residue 404 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 274 ASN R 350 GLN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 350 GLN E 51 ASN E 74 GLN F 350 GLN J 51 ASN J 74 GLN O 51 ASN T 350 GLN Y 51 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 15095 Z= 0.152 Angle : 0.433 5.567 20430 Z= 0.234 Chirality : 0.034 0.115 2365 Planarity : 0.003 0.030 2550 Dihedral : 4.468 39.894 2065 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.95 % Allowed : 7.62 % Favored : 90.42 % 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: 4.87 (0.18), residues: 1900 helix: 3.74 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.59 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Q 26 PHE 0.016 0.001 PHE O 43 TYR 0.022 0.001 TYR M 24 ARG 0.002 0.000 ARG K 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 334 time to evaluate : 1.727 Fit side-chains revert: symmetry clash REVERT: R 263 MET cc_start: 0.5657 (tpp) cc_final: 0.5421 (tpp) REVERT: A 263 MET cc_start: 0.5849 (tpp) cc_final: 0.5518 (tpt) REVERT: C 24 TYR cc_start: 0.8947 (m-10) cc_final: 0.8614 (m-80) REVERT: E 109 ASP cc_start: 0.8392 (t0) cc_final: 0.8068 (t0) REVERT: G 44 LYS cc_start: 0.8281 (tptt) cc_final: 0.7956 (ttmm) REVERT: H 24 TYR cc_start: 0.8998 (m-10) cc_final: 0.8760 (m-10) REVERT: K 404 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.6084 (pttp) REVERT: L 44 LYS cc_start: 0.8363 (tptt) cc_final: 0.8057 (ttmt) REVERT: W 24 TYR cc_start: 0.8960 (m-10) cc_final: 0.8635 (m-80) outliers start: 30 outliers final: 23 residues processed: 355 average time/residue: 0.2393 time to fit residues: 127.8748 Evaluate side-chains 333 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 309 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 404 LYS Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 404 LYS Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 176 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN F 343 GLN F 350 GLN T 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15095 Z= 0.207 Angle : 0.436 8.328 20430 Z= 0.236 Chirality : 0.034 0.162 2365 Planarity : 0.003 0.033 2550 Dihedral : 4.359 40.883 2053 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.41 % Allowed : 10.62 % Favored : 86.97 % 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: 4.80 (0.18), residues: 1900 helix: 3.75 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.47 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 110 PHE 0.015 0.001 PHE O 43 TYR 0.014 0.001 TYR M 24 ARG 0.002 0.000 ARG T 378 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 310 time to evaluate : 1.627 Fit side-chains REVERT: A 263 MET cc_start: 0.5901 (tpp) cc_final: 0.5553 (tpt) REVERT: B 44 LYS cc_start: 0.8521 (tptt) cc_final: 0.8091 (ttmt) REVERT: C 24 TYR cc_start: 0.8950 (m-10) cc_final: 0.8661 (m-80) REVERT: E 109 ASP cc_start: 0.8425 (t0) cc_final: 0.8122 (t0) REVERT: G 44 LYS cc_start: 0.8336 (tptt) cc_final: 0.8017 (ttmt) REVERT: H 24 TYR cc_start: 0.9008 (m-10) cc_final: 0.8755 (m-10) REVERT: K 274 ASN cc_start: 0.7429 (OUTLIER) cc_final: 0.7162 (p0) REVERT: L 44 LYS cc_start: 0.8434 (tptt) cc_final: 0.8089 (ttmt) REVERT: M 24 TYR cc_start: 0.8970 (m-80) cc_final: 0.8752 (m-80) REVERT: W 24 TYR cc_start: 0.8973 (m-10) cc_final: 0.8638 (m-80) outliers start: 37 outliers final: 28 residues processed: 331 average time/residue: 0.2387 time to fit residues: 118.4544 Evaluate side-chains 339 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 310 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 31 VAL Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 396 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 350 GLN F 350 GLN T 350 GLN T 399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15095 Z= 0.197 Angle : 0.426 7.737 20430 Z= 0.231 Chirality : 0.034 0.126 2365 Planarity : 0.003 0.034 2550 Dihedral : 4.267 41.333 2045 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.28 % Allowed : 13.22 % Favored : 84.50 % 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: 4.74 (0.18), residues: 1900 helix: 3.73 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.36 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 110 PHE 0.015 0.001 PHE J 43 TYR 0.012 0.001 TYR M 24 ARG 0.002 0.000 ARG T 402 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 310 time to evaluate : 1.573 Fit side-chains REVERT: R 263 MET cc_start: 0.5380 (tpp) cc_final: 0.4998 (tpp) REVERT: P 44 LYS cc_start: 0.8439 (tptt) cc_final: 0.8073 (ttpt) REVERT: B 44 LYS cc_start: 0.8493 (tptt) cc_final: 0.8131 (ttmt) REVERT: C 24 TYR cc_start: 0.8951 (m-10) cc_final: 0.8638 (m-80) REVERT: E 109 ASP cc_start: 0.8441 (t0) cc_final: 0.8151 (t0) REVERT: G 44 LYS cc_start: 0.8357 (tptt) cc_final: 0.8035 (ttmt) REVERT: H 24 TYR cc_start: 0.9016 (m-10) cc_final: 0.8737 (m-10) REVERT: K 274 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.7116 (p0) REVERT: L 44 LYS cc_start: 0.8431 (tptt) cc_final: 0.8104 (ttmt) REVERT: V 44 LYS cc_start: 0.8512 (tptt) cc_final: 0.8181 (ttpt) REVERT: W 24 TYR cc_start: 0.8987 (m-10) cc_final: 0.8735 (m-80) outliers start: 35 outliers final: 30 residues processed: 330 average time/residue: 0.2385 time to fit residues: 118.0419 Evaluate side-chains 332 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 301 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain T residue 396 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 350 GLN F 350 GLN O 74 GLN T 350 GLN Y 74 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15095 Z= 0.307 Angle : 0.471 7.289 20430 Z= 0.259 Chirality : 0.036 0.135 2365 Planarity : 0.003 0.039 2550 Dihedral : 4.427 44.582 2045 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.74 % Allowed : 14.92 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.40 (0.18), residues: 1900 helix: 3.48 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.24 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 110 PHE 0.018 0.002 PHE K 377 TYR 0.025 0.002 TYR M 24 ARG 0.002 0.000 ARG F 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 306 time to evaluate : 1.650 Fit side-chains REVERT: P 44 LYS cc_start: 0.8421 (tptt) cc_final: 0.8063 (ttmt) REVERT: B 40 LYS cc_start: 0.8727 (mttp) cc_final: 0.8450 (mtmm) REVERT: B 44 LYS cc_start: 0.8573 (tptt) cc_final: 0.8209 (ttmt) REVERT: C 24 TYR cc_start: 0.8975 (m-10) cc_final: 0.8607 (m-80) REVERT: E 109 ASP cc_start: 0.8495 (t0) cc_final: 0.8232 (t0) REVERT: G 44 LYS cc_start: 0.8344 (tptt) cc_final: 0.8011 (ttmt) REVERT: J 109 ASP cc_start: 0.8460 (t0) cc_final: 0.8240 (t0) REVERT: K 274 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.7157 (p0) REVERT: L 44 LYS cc_start: 0.8472 (tptt) cc_final: 0.8165 (ttmt) REVERT: V 44 LYS cc_start: 0.8542 (tptt) cc_final: 0.8230 (ttpt) REVERT: W 24 TYR cc_start: 0.8984 (m-10) cc_final: 0.8723 (m-80) outliers start: 42 outliers final: 34 residues processed: 329 average time/residue: 0.2469 time to fit residues: 122.1445 Evaluate side-chains 330 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 295 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 55 VAL Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain A residue 274 ASN Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 55 VAL Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 55 VAL Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain T residue 396 THR Chi-restraints excluded: chain V residue 36 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 36 THR Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain X residue 13 SER Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 14 optimal weight: 0.0070 chunk 57 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 274 ASN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN T 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15095 Z= 0.155 Angle : 0.431 9.023 20430 Z= 0.230 Chirality : 0.034 0.143 2365 Planarity : 0.003 0.035 2550 Dihedral : 4.287 43.257 2045 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.63 % Allowed : 16.55 % Favored : 81.82 % 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: 4.74 (0.18), residues: 1900 helix: 3.75 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.23 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP M 26 PHE 0.018 0.001 PHE R 319 TYR 0.021 0.001 TYR M 24 ARG 0.001 0.000 ARG O 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 310 time to evaluate : 1.813 Fit side-chains REVERT: P 44 LYS cc_start: 0.8399 (tptt) cc_final: 0.8068 (ttmt) REVERT: B 40 LYS cc_start: 0.8729 (mttp) cc_final: 0.8419 (mtmm) REVERT: B 44 LYS cc_start: 0.8429 (tptt) cc_final: 0.8154 (ttmt) REVERT: C 24 TYR cc_start: 0.8922 (m-10) cc_final: 0.8585 (m-80) REVERT: E 109 ASP cc_start: 0.8463 (t0) cc_final: 0.8183 (t0) REVERT: G 44 LYS cc_start: 0.8345 (tptt) cc_final: 0.8023 (ttmt) REVERT: H 24 TYR cc_start: 0.9015 (m-10) cc_final: 0.8739 (m-10) REVERT: J 109 ASP cc_start: 0.8484 (t0) cc_final: 0.8270 (t0) REVERT: K 274 ASN cc_start: 0.7343 (OUTLIER) cc_final: 0.7064 (p0) REVERT: L 44 LYS cc_start: 0.8441 (tptt) cc_final: 0.8126 (ttmt) REVERT: V 44 LYS cc_start: 0.8493 (tptt) cc_final: 0.8174 (ttpt) REVERT: W 20 GLU cc_start: 0.7650 (pt0) cc_final: 0.7337 (pt0) REVERT: W 24 TYR cc_start: 0.8979 (m-10) cc_final: 0.8715 (m-80) outliers start: 25 outliers final: 19 residues processed: 325 average time/residue: 0.2418 time to fit residues: 117.8441 Evaluate side-chains 321 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 301 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 274 ASN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN T 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15095 Z= 0.214 Angle : 0.444 7.910 20430 Z= 0.239 Chirality : 0.035 0.154 2365 Planarity : 0.003 0.036 2550 Dihedral : 4.236 43.230 2045 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.63 % Allowed : 17.98 % Favored : 80.39 % 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: 4.60 (0.18), residues: 1900 helix: 3.65 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.22 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 110 PHE 0.015 0.002 PHE K 377 TYR 0.027 0.001 TYR M 24 ARG 0.001 0.000 ARG R 378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 306 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: P 44 LYS cc_start: 0.8427 (tptt) cc_final: 0.8100 (ttmt) REVERT: B 40 LYS cc_start: 0.8781 (mttp) cc_final: 0.8443 (mtmm) REVERT: B 44 LYS cc_start: 0.8524 (tptt) cc_final: 0.8277 (ttmt) REVERT: C 24 TYR cc_start: 0.8932 (m-10) cc_final: 0.8617 (m-80) REVERT: E 109 ASP cc_start: 0.8489 (t0) cc_final: 0.8223 (t0) REVERT: G 44 LYS cc_start: 0.8368 (tptt) cc_final: 0.8038 (ttmt) REVERT: H 24 TYR cc_start: 0.9023 (m-10) cc_final: 0.8745 (m-10) REVERT: J 109 ASP cc_start: 0.8515 (t0) cc_final: 0.8289 (t0) REVERT: K 274 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.7008 (p0) REVERT: L 44 LYS cc_start: 0.8487 (tptt) cc_final: 0.8159 (ttmt) REVERT: V 44 LYS cc_start: 0.8541 (tptt) cc_final: 0.8248 (ttpt) REVERT: W 24 TYR cc_start: 0.8981 (m-10) cc_final: 0.8723 (m-80) outliers start: 25 outliers final: 23 residues processed: 321 average time/residue: 0.2455 time to fit residues: 117.7680 Evaluate side-chains 327 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 303 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 274 ASN Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 274 ASN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN T 350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15095 Z= 0.144 Angle : 0.429 8.237 20430 Z= 0.230 Chirality : 0.034 0.160 2365 Planarity : 0.003 0.033 2550 Dihedral : 4.107 40.726 2045 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.50 % Allowed : 18.31 % Favored : 80.20 % 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: 4.77 (0.18), residues: 1900 helix: 3.74 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.15 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 26 PHE 0.028 0.001 PHE R 319 TYR 0.025 0.001 TYR M 24 ARG 0.000 0.000 ARG O 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 327 time to evaluate : 1.645 Fit side-chains revert: symmetry clash REVERT: P 44 LYS cc_start: 0.8376 (tptt) cc_final: 0.8092 (ttpt) REVERT: Q 20 GLU cc_start: 0.7430 (pt0) cc_final: 0.7222 (pt0) REVERT: Q 24 TYR cc_start: 0.8961 (m-10) cc_final: 0.8696 (m-80) REVERT: B 40 LYS cc_start: 0.8774 (mttp) cc_final: 0.8419 (mtmm) REVERT: B 44 LYS cc_start: 0.8406 (tptt) cc_final: 0.8156 (ttmt) REVERT: C 24 TYR cc_start: 0.8910 (m-10) cc_final: 0.8602 (m-80) REVERT: E 109 ASP cc_start: 0.8469 (t0) cc_final: 0.8189 (t0) REVERT: G 44 LYS cc_start: 0.8326 (tptt) cc_final: 0.7999 (ttmt) REVERT: H 24 TYR cc_start: 0.9013 (m-10) cc_final: 0.8740 (m-10) REVERT: J 109 ASP cc_start: 0.8526 (t0) cc_final: 0.8304 (t0) REVERT: L 44 LYS cc_start: 0.8427 (tptt) cc_final: 0.8131 (ttmt) REVERT: V 44 LYS cc_start: 0.8493 (tptt) cc_final: 0.8209 (ttpt) REVERT: W 24 TYR cc_start: 0.8962 (m-10) cc_final: 0.8661 (m-80) outliers start: 23 outliers final: 19 residues processed: 340 average time/residue: 0.2393 time to fit residues: 122.0216 Evaluate side-chains 333 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 314 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 151 optimal weight: 0.0670 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN T 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 15095 Z= 0.141 Angle : 0.429 8.872 20430 Z= 0.231 Chirality : 0.034 0.168 2365 Planarity : 0.003 0.031 2550 Dihedral : 3.944 36.999 2045 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.30 % Allowed : 19.02 % Favored : 79.67 % 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: 4.81 (0.18), residues: 1900 helix: 3.78 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.12 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP Q 26 PHE 0.029 0.001 PHE R 319 TYR 0.028 0.001 TYR M 24 ARG 0.000 0.000 ARG T 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 321 time to evaluate : 1.761 Fit side-chains revert: symmetry clash REVERT: P 44 LYS cc_start: 0.8348 (tptt) cc_final: 0.8095 (ttpt) REVERT: Q 20 GLU cc_start: 0.7389 (pt0) cc_final: 0.7185 (pt0) REVERT: Q 24 TYR cc_start: 0.8954 (m-10) cc_final: 0.8706 (m-80) REVERT: B 44 LYS cc_start: 0.8404 (tptt) cc_final: 0.8174 (ttmt) REVERT: C 24 TYR cc_start: 0.8899 (m-10) cc_final: 0.8614 (m-80) REVERT: E 109 ASP cc_start: 0.8413 (t0) cc_final: 0.8121 (t0) REVERT: G 28 MET cc_start: 0.8395 (ttp) cc_final: 0.8135 (ttp) REVERT: G 44 LYS cc_start: 0.8288 (tptt) cc_final: 0.8062 (ttpt) REVERT: H 24 TYR cc_start: 0.9001 (m-10) cc_final: 0.8734 (m-10) REVERT: J 109 ASP cc_start: 0.8574 (t0) cc_final: 0.8337 (t0) REVERT: L 44 LYS cc_start: 0.8404 (tptt) cc_final: 0.8125 (ttmt) REVERT: V 44 LYS cc_start: 0.8464 (tptt) cc_final: 0.8232 (ttpt) REVERT: W 24 TYR cc_start: 0.8953 (m-10) cc_final: 0.8658 (m-80) outliers start: 20 outliers final: 18 residues processed: 333 average time/residue: 0.2425 time to fit residues: 121.1033 Evaluate side-chains 333 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 315 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 9.9990 chunk 104 optimal weight: 0.0980 chunk 81 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 179 optimal weight: 0.7980 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 399 ASN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 15095 Z= 0.146 Angle : 0.432 8.679 20430 Z= 0.232 Chirality : 0.035 0.192 2365 Planarity : 0.003 0.032 2550 Dihedral : 3.814 33.224 2045 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.43 % Allowed : 19.35 % Favored : 79.22 % 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: 4.78 (0.18), residues: 1900 helix: 3.76 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.06 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 26 PHE 0.032 0.001 PHE R 319 TYR 0.012 0.001 TYR W 21 ARG 0.001 0.000 ARG T 402 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 323 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: P 44 LYS cc_start: 0.8362 (tptt) cc_final: 0.8093 (ttpt) REVERT: Q 24 TYR cc_start: 0.8947 (m-10) cc_final: 0.8703 (m-80) REVERT: B 44 LYS cc_start: 0.8409 (tptt) cc_final: 0.8184 (ttmt) REVERT: C 24 TYR cc_start: 0.8892 (m-10) cc_final: 0.8629 (m-80) REVERT: E 109 ASP cc_start: 0.8448 (t0) cc_final: 0.8158 (t0) REVERT: F 263 MET cc_start: 0.6293 (tpp) cc_final: 0.6005 (tpt) REVERT: G 28 MET cc_start: 0.8369 (ttp) cc_final: 0.8127 (ttp) REVERT: G 44 LYS cc_start: 0.8284 (tptt) cc_final: 0.8065 (ttpt) REVERT: H 24 TYR cc_start: 0.8977 (m-10) cc_final: 0.8718 (m-10) REVERT: J 109 ASP cc_start: 0.8576 (t0) cc_final: 0.8338 (t0) REVERT: L 44 LYS cc_start: 0.8384 (tptt) cc_final: 0.8136 (ttmt) REVERT: V 44 LYS cc_start: 0.8469 (tptt) cc_final: 0.8225 (ttpt) REVERT: W 24 TYR cc_start: 0.8946 (m-10) cc_final: 0.8654 (m-80) REVERT: X 20 GLU cc_start: 0.8005 (pm20) cc_final: 0.7639 (pm20) outliers start: 22 outliers final: 19 residues processed: 335 average time/residue: 0.2404 time to fit residues: 120.5092 Evaluate side-chains 334 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 315 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain Z residue 76 ILE Chi-restraints excluded: chain Z residue 106 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 274 ASN Chi-restraints excluded: chain H residue 46 THR Chi-restraints excluded: chain J residue 106 SER Chi-restraints excluded: chain K residue 274 ASN Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 76 ILE Chi-restraints excluded: chain Y residue 106 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 143 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 74 GLN F 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088323 restraints weight = 20282.413| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.59 r_work: 0.2946 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15095 Z= 0.180 Angle : 0.449 8.364 20430 Z= 0.242 Chirality : 0.035 0.182 2365 Planarity : 0.003 0.033 2550 Dihedral : 3.793 31.828 2045 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.30 % Allowed : 19.48 % Favored : 79.22 % 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: 4.69 (0.18), residues: 1900 helix: 3.69 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.08 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 26 PHE 0.030 0.001 PHE R 319 TYR 0.027 0.001 TYR M 24 ARG 0.005 0.000 ARG T 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3177.18 seconds wall clock time: 58 minutes 10.35 seconds (3490.35 seconds total)