Starting phenix.real_space_refine on Thu Sep 26 23:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/09_2024/8ixk_35794.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/09_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_35794/09_2024/8ixk_35794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/09_2024/8ixk_35794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/09_2024/8ixk_35794.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ixk_35794/09_2024/8ixk_35794.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.97, per 1000 atoms: 0.61 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 - 3.00 Amino acid : True - 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: 3.99 Conformation dependent library (CDL) restraints added in 1.9 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: 1.14 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: 4.28 Time building geometry restraints manager: 4.60 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: 0.00 - 1.40: 19199 1.40 - 2.80: 987 2.80 - 4.20: 189 4.20 - 5.60: 40 5.60 - 7.00: 15 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 3.040 nonbonded pdb=" OG SER R 351 " pdb=" O LEU E 77 " model vdw 2.310 3.040 nonbonded pdb=" O LEU Z 77 " pdb=" OG SER T 351 " model vdw 2.312 3.040 nonbonded pdb=" OG SER F 351 " pdb=" O LEU O 77 " model vdw 2.319 3.040 nonbonded pdb=" OG SER K 351 " pdb=" O LEU Y 77 " model vdw 2.325 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 0.580 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.740 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- 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 : 1.427 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: 0.2458 time to fit residues: 139.3313 Evaluate side-chains 309 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 304 time to evaluate : 1.687 ------------------------------------------------------------------------------- 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: 0.5980 chunk 136 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 163 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 350 GLN ** E 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0883 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= 0.159 Angle : 0.440 5.226 20430 Z= 0.238 Chirality : 0.034 0.120 2365 Planarity : 0.003 0.030 2550 Dihedral : 4.358 39.117 2065 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.89 % Allowed : 7.56 % Favored : 90.55 % 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: 4.83 (0.18), residues: 1900 helix: 3.70 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.60 (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 0.023 0.001 TYR M 24 ARG 0.002 0.000 ARG F 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 367 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 338 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: R 263 MET cc_start: 0.5743 (tpp) cc_final: 0.5514 (tpp) REVERT: A 263 MET cc_start: 0.5850 (tpp) cc_final: 0.5516 (tpt) REVERT: A 404 LYS cc_start: 0.6343 (OUTLIER) cc_final: 0.6086 (pttp) REVERT: C 24 TYR cc_start: 0.8945 (m-10) cc_final: 0.8623 (m-80) REVERT: E 109 ASP cc_start: 0.8394 (t0) cc_final: 0.8071 (t0) REVERT: G 44 LYS cc_start: 0.8280 (tptt) cc_final: 0.7950 (ttmm) REVERT: H 24 TYR cc_start: 0.8999 (m-10) cc_final: 0.8760 (m-10) REVERT: K 404 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5909 (pttp) REVERT: L 44 LYS cc_start: 0.8364 (tptt) cc_final: 0.8055 (ttmt) REVERT: W 24 TYR cc_start: 0.8961 (m-10) cc_final: 0.8642 (m-80) outliers start: 29 outliers final: 22 residues processed: 358 average time/residue: 0.2563 time to fit residues: 138.0937 Evaluate side-chains 339 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 315 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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 A residue 404 LYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain C residue 46 THR 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: 3.9990 chunk 50 optimal weight: 0.0270 chunk 136 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 176 optimal weight: 0.9990 chunk 145 optimal weight: 20.0000 chunk 162 optimal weight: 0.0020 chunk 55 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 overall best weight: 0.5048 ------------------------------------------------------------------------------- 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** E 51 ASN F 343 GLN F 350 GLN T 399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15095 Z= 0.131 Angle : 0.420 8.577 20430 Z= 0.226 Chirality : 0.034 0.162 2365 Planarity : 0.003 0.029 2550 Dihedral : 4.190 40.195 2057 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.69 % Allowed : 11.01 % Favored : 87.30 % 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: 5.04 (0.18), residues: 1900 helix: 3.87 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.57 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Q 26 PHE 0.014 0.001 PHE Z 43 TYR 0.015 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 *********************** 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 359 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 333 time to evaluate : 1.533 Fit side-chains REVERT: P 44 LYS cc_start: 0.8388 (tptt) cc_final: 0.8005 (ttmt) REVERT: Q 24 TYR cc_start: 0.8932 (m-10) cc_final: 0.8684 (m-80) REVERT: A 263 MET cc_start: 0.5771 (tpp) cc_final: 0.5436 (tpp) REVERT: A 404 LYS cc_start: 0.6291 (OUTLIER) cc_final: 0.5956 (pttp) REVERT: B 44 LYS cc_start: 0.8481 (tptt) cc_final: 0.8025 (ttmt) REVERT: C 24 TYR cc_start: 0.8928 (m-10) cc_final: 0.8594 (m-80) REVERT: E 109 ASP cc_start: 0.8401 (t0) cc_final: 0.8068 (t0) REVERT: G 44 LYS cc_start: 0.8270 (tptt) cc_final: 0.8025 (ttmt) REVERT: H 24 TYR cc_start: 0.8987 (m-10) cc_final: 0.8732 (m-10) REVERT: I 17 SER cc_start: 0.8659 (p) cc_final: 0.8410 (p) REVERT: K 274 ASN cc_start: 0.7377 (OUTLIER) cc_final: 0.7117 (t0) REVERT: L 44 LYS cc_start: 0.8392 (tptt) cc_final: 0.8123 (ttmt) REVERT: N 17 SER cc_start: 0.8704 (p) cc_final: 0.8423 (p) REVERT: W 24 TYR cc_start: 0.8958 (m-10) cc_final: 0.8702 (m-80) outliers start: 26 outliers final: 15 residues processed: 350 average time/residue: 0.2351 time to fit residues: 123.9207 Evaluate side-chains 331 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 314 time to evaluate : 1.542 ------------------------------------------------------------------------------- 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 A residue 274 ASN Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 404 LYS Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain E residue 106 SER 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 396 THR Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR 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: 6.9990 chunk 123 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 18 optimal weight: 0.3980 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** F 343 GLN F 399 ASN O 74 GLN Y 74 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15095 Z= 0.244 Angle : 0.451 8.060 20430 Z= 0.248 Chirality : 0.035 0.121 2365 Planarity : 0.003 0.037 2550 Dihedral : 4.061 35.371 2049 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.74 % Allowed : 12.44 % Favored : 84.82 % 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: 4.63 (0.18), residues: 1900 helix: 3.63 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.41 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Y 110 PHE 0.017 0.002 PHE K 377 TYR 0.013 0.001 TYR K 386 ARG 0.002 0.000 ARG R 378 *********************** 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 372 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 330 time to evaluate : 1.670 Fit side-chains REVERT: P 44 LYS cc_start: 0.8440 (tptt) cc_final: 0.8072 (ttmt) REVERT: B 44 LYS cc_start: 0.8489 (tptt) cc_final: 0.8132 (ttmt) REVERT: C 24 TYR cc_start: 0.8957 (m-10) cc_final: 0.8603 (m-80) REVERT: G 44 LYS cc_start: 0.8337 (tptt) cc_final: 0.8030 (ttmt) REVERT: H 24 TYR cc_start: 0.9014 (m-10) cc_final: 0.8729 (m-10) REVERT: I 17 SER cc_start: 0.8750 (p) cc_final: 0.8496 (p) REVERT: L 44 LYS cc_start: 0.8442 (tptt) cc_final: 0.8104 (ttmt) REVERT: M 20 GLU cc_start: 0.7526 (pt0) cc_final: 0.7289 (pt0) REVERT: M 24 TYR cc_start: 0.8998 (m-80) cc_final: 0.8740 (m-80) REVERT: V 44 LYS cc_start: 0.8538 (tptt) cc_final: 0.8206 (ttpt) REVERT: W 24 TYR cc_start: 0.8990 (m-10) cc_final: 0.8741 (m-80) outliers start: 42 outliers final: 33 residues processed: 352 average time/residue: 0.2362 time to fit residues: 125.2444 Evaluate side-chains 348 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 315 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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 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 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 316 THR 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 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 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: 0.2980 chunk 98 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN R 399 ASN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN T 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1405 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= 0.184 Angle : 0.433 8.601 20430 Z= 0.235 Chirality : 0.035 0.138 2365 Planarity : 0.003 0.035 2550 Dihedral : 3.972 36.227 2045 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.95 % Allowed : 15.18 % Favored : 82.87 % 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: 3.70 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.31 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP S 26 PHE 0.014 0.001 PHE Z 43 TYR 0.010 0.001 TYR F 386 ARG 0.001 0.000 ARG F 402 *********************** 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 346 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 316 time to evaluate : 1.676 Fit side-chains REVERT: P 44 LYS cc_start: 0.8417 (tptt) cc_final: 0.8070 (ttmt) REVERT: B 44 LYS cc_start: 0.8464 (tptt) cc_final: 0.8082 (ttmt) REVERT: C 24 TYR cc_start: 0.8935 (m-10) cc_final: 0.8600 (m-80) REVERT: E 109 ASP cc_start: 0.8399 (t0) cc_final: 0.8143 (t0) REVERT: G 44 LYS cc_start: 0.8335 (tptt) cc_final: 0.8050 (ttmt) REVERT: H 24 TYR cc_start: 0.9005 (m-10) cc_final: 0.8712 (m-10) REVERT: I 17 SER cc_start: 0.8699 (p) cc_final: 0.8467 (p) REVERT: L 44 LYS cc_start: 0.8439 (tptt) cc_final: 0.8115 (ttmt) REVERT: M 20 GLU cc_start: 0.7516 (pt0) cc_final: 0.7227 (pt0) REVERT: M 24 TYR cc_start: 0.8986 (m-80) cc_final: 0.8692 (m-80) REVERT: V 44 LYS cc_start: 0.8536 (tptt) cc_final: 0.8223 (ttpt) REVERT: W 20 GLU cc_start: 0.7625 (pt0) cc_final: 0.7311 (pt0) REVERT: W 24 TYR cc_start: 0.8982 (m-10) cc_final: 0.8714 (m-80) outliers start: 30 outliers final: 24 residues processed: 336 average time/residue: 0.2406 time to fit residues: 121.4615 Evaluate side-chains 332 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 308 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 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 76 ILE Chi-restraints excluded: chain E residue 106 SER Chi-restraints excluded: chain F residue 316 THR 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 106 SER 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 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 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: 0.9980 chunk 156 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 1.9990 chunk 144 optimal weight: 0.0020 chunk 80 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.7988 ------------------------------------------------------------------------------- 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** Y 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 15095 Z= 0.146 Angle : 0.415 8.888 20430 Z= 0.225 Chirality : 0.034 0.146 2365 Planarity : 0.003 0.032 2550 Dihedral : 3.812 33.862 2045 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.69 % Allowed : 16.03 % Favored : 82.28 % 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: 4.85 (0.18), residues: 1900 helix: 3.79 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.22 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 26 PHE 0.013 0.001 PHE Z 43 TYR 0.010 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 *********************** 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 353 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 327 time to evaluate : 1.599 Fit side-chains REVERT: P 44 LYS cc_start: 0.8382 (tptt) cc_final: 0.8091 (ttpt) REVERT: Q 20 GLU cc_start: 0.7409 (pt0) cc_final: 0.7194 (pt0) REVERT: Q 24 TYR cc_start: 0.8954 (m-10) cc_final: 0.8688 (m-80) REVERT: B 44 LYS cc_start: 0.8423 (tptt) cc_final: 0.8054 (ttmt) REVERT: C 24 TYR cc_start: 0.8914 (m-10) cc_final: 0.8610 (m-80) REVERT: E 109 ASP cc_start: 0.8417 (t0) cc_final: 0.8170 (t0) REVERT: H 24 TYR cc_start: 0.8993 (m-10) cc_final: 0.8696 (m-10) REVERT: I 17 SER cc_start: 0.8681 (p) cc_final: 0.8453 (p) REVERT: J 109 ASP cc_start: 0.8475 (t0) cc_final: 0.8263 (t0) REVERT: L 44 LYS cc_start: 0.8414 (tptt) cc_final: 0.8124 (ttmt) REVERT: M 20 GLU cc_start: 0.7447 (pt0) cc_final: 0.7148 (pt0) REVERT: M 24 TYR cc_start: 0.8954 (m-80) cc_final: 0.8666 (m-80) REVERT: V 44 LYS cc_start: 0.8520 (tptt) cc_final: 0.8189 (ttpt) REVERT: W 24 TYR cc_start: 0.8957 (m-10) cc_final: 0.8715 (m-80) outliers start: 26 outliers final: 22 residues processed: 342 average time/residue: 0.2449 time to fit residues: 125.6189 Evaluate side-chains 341 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 319 time to evaluate : 3.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 46 THR Chi-restraints excluded: chain S residue 48 LYS 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 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 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 316 THR Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain N residue 17 SER Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 106 SER 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: 6.9990 chunk 19 optimal weight: 0.9980 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 146 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 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 350 GLN ** Z 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15095 Z= 0.217 Angle : 0.445 8.843 20430 Z= 0.242 Chirality : 0.035 0.152 2365 Planarity : 0.003 0.035 2550 Dihedral : 3.823 34.243 2045 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.08 % Allowed : 16.03 % Favored : 81.89 % 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: 4.66 (0.18), residues: 1900 helix: 3.69 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.20 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 110 PHE 0.016 0.002 PHE K 377 TYR 0.011 0.001 TYR F 386 ARG 0.001 0.000 ARG A 402 *********************** 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 351 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 319 time to evaluate : 1.587 Fit side-chains REVERT: P 44 LYS cc_start: 0.8423 (tptt) cc_final: 0.8125 (ttpt) REVERT: B 44 LYS cc_start: 0.8450 (tptt) cc_final: 0.8135 (ttmt) REVERT: C 24 TYR cc_start: 0.8933 (m-10) cc_final: 0.8617 (m-80) REVERT: E 109 ASP cc_start: 0.8461 (t0) cc_final: 0.8204 (t0) REVERT: G 28 MET cc_start: 0.8394 (ttp) cc_final: 0.8192 (ttp) REVERT: H 24 TYR cc_start: 0.9017 (m-10) cc_final: 0.8706 (m-10) REVERT: I 17 SER cc_start: 0.8734 (p) cc_final: 0.8509 (p) REVERT: J 109 ASP cc_start: 0.8493 (t0) cc_final: 0.8267 (t0) REVERT: L 44 LYS cc_start: 0.8412 (tptt) cc_final: 0.8118 (ttmt) REVERT: M 20 GLU cc_start: 0.7462 (pt0) cc_final: 0.7169 (pt0) REVERT: M 24 TYR cc_start: 0.8975 (m-80) cc_final: 0.8697 (m-80) REVERT: V 44 LYS cc_start: 0.8537 (tptt) cc_final: 0.8223 (ttpt) REVERT: W 24 TYR cc_start: 0.8970 (m-10) cc_final: 0.8710 (m-80) outliers start: 32 outliers final: 26 residues processed: 339 average time/residue: 0.2398 time to fit residues: 121.8777 Evaluate side-chains 338 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 312 time to evaluate : 1.643 ------------------------------------------------------------------------------- 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 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 E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER 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 316 THR 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 36 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: 1.9990 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.1980 chunk 85 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 136 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15095 Z= 0.140 Angle : 0.426 9.616 20430 Z= 0.230 Chirality : 0.034 0.161 2365 Planarity : 0.003 0.032 2550 Dihedral : 3.724 33.131 2045 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.56 % Allowed : 16.68 % Favored : 81.76 % 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: 4.86 (0.18), residues: 1900 helix: 3.81 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.14 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP M 26 PHE 0.011 0.001 PHE Z 43 TYR 0.009 0.001 TYR Q 21 ARG 0.001 0.000 ARG T 402 *********************** 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 346 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 322 time to evaluate : 1.693 Fit side-chains REVERT: R 263 MET cc_start: 0.5799 (tpp) cc_final: 0.5585 (tpp) REVERT: P 44 LYS cc_start: 0.8388 (tptt) cc_final: 0.8119 (ttpt) REVERT: Q 24 TYR cc_start: 0.8959 (m-10) cc_final: 0.8688 (m-80) REVERT: A 263 MET cc_start: 0.6005 (tpp) cc_final: 0.5733 (tpp) REVERT: B 44 LYS cc_start: 0.8384 (tptt) cc_final: 0.8088 (ttmt) REVERT: C 24 TYR cc_start: 0.8903 (m-10) cc_final: 0.8602 (m-80) REVERT: E 109 ASP cc_start: 0.8499 (t0) cc_final: 0.8226 (t0) REVERT: G 28 MET cc_start: 0.8357 (ttp) cc_final: 0.8157 (ttp) REVERT: H 24 TYR cc_start: 0.8984 (m-10) cc_final: 0.8682 (m-10) REVERT: J 109 ASP cc_start: 0.8518 (t0) cc_final: 0.8301 (t0) REVERT: L 44 LYS cc_start: 0.8404 (tptt) cc_final: 0.8135 (ttmt) REVERT: V 44 LYS cc_start: 0.8492 (tptt) cc_final: 0.8200 (ttpt) REVERT: W 24 TYR cc_start: 0.8960 (m-10) cc_final: 0.8680 (m-80) outliers start: 24 outliers final: 22 residues processed: 335 average time/residue: 0.2790 time to fit residues: 141.9564 Evaluate side-chains 336 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 314 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 290 SER 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 B residue 36 THR 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 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 K residue 316 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 7.9990 chunk 151 optimal weight: 0.0670 chunk 161 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 49 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 15095 Z= 0.141 Angle : 0.424 9.899 20430 Z= 0.230 Chirality : 0.034 0.165 2365 Planarity : 0.003 0.031 2550 Dihedral : 3.634 31.014 2045 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.76 % Allowed : 17.00 % Favored : 81.24 % 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: 4.91 (0.18), residues: 1900 helix: 3.85 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.16 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 26 PHE 0.012 0.001 PHE Z 43 TYR 0.024 0.001 TYR M 24 ARG 0.001 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 348 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 321 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: P 44 LYS cc_start: 0.8362 (tptt) cc_final: 0.8096 (ttpt) REVERT: Q 24 TYR cc_start: 0.8947 (m-10) cc_final: 0.8685 (m-80) REVERT: B 44 LYS cc_start: 0.8417 (tptt) cc_final: 0.8170 (ttmt) REVERT: C 24 TYR cc_start: 0.8906 (m-10) cc_final: 0.8600 (m-80) REVERT: E 109 ASP cc_start: 0.8498 (t0) cc_final: 0.8234 (t0) REVERT: H 24 TYR cc_start: 0.8972 (m-10) cc_final: 0.8677 (m-10) REVERT: J 109 ASP cc_start: 0.8551 (t0) cc_final: 0.8321 (t0) REVERT: L 44 LYS cc_start: 0.8382 (tptt) cc_final: 0.8137 (ttmt) REVERT: V 44 LYS cc_start: 0.8446 (tptt) cc_final: 0.8201 (ttpt) REVERT: W 24 TYR cc_start: 0.8946 (m-10) cc_final: 0.8670 (m-80) outliers start: 27 outliers final: 24 residues processed: 337 average time/residue: 0.2398 time to fit residues: 120.8060 Evaluate side-chains 342 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 318 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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 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 E residue 76 ILE Chi-restraints excluded: chain E residue 106 SER 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 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 170 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 165 optimal weight: 5.9990 chunk 142 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 15095 Z= 0.180 Angle : 0.449 9.994 20430 Z= 0.244 Chirality : 0.035 0.171 2365 Planarity : 0.003 0.033 2550 Dihedral : 3.634 30.922 2045 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.63 % Allowed : 17.46 % Favored : 80.91 % 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 : 0.15 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP S 26 PHE 0.014 0.001 PHE Z 43 TYR 0.028 0.001 TYR M 24 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 344 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 319 time to evaluate : 1.487 Fit side-chains REVERT: P 44 LYS cc_start: 0.8397 (tptt) cc_final: 0.8061 (ttpt) REVERT: Q 24 TYR cc_start: 0.8954 (m-10) cc_final: 0.8692 (m-80) REVERT: B 44 LYS cc_start: 0.8412 (tptt) cc_final: 0.8159 (ttmt) REVERT: C 24 TYR cc_start: 0.8915 (m-10) cc_final: 0.8613 (m-80) REVERT: E 109 ASP cc_start: 0.8527 (t0) cc_final: 0.8239 (t0) REVERT: H 24 TYR cc_start: 0.8979 (m-10) cc_final: 0.8686 (m-10) REVERT: J 109 ASP cc_start: 0.8551 (t0) cc_final: 0.8316 (t0) REVERT: L 44 LYS cc_start: 0.8386 (tptt) cc_final: 0.8130 (ttmt) REVERT: T 305 ASP cc_start: 0.7561 (t0) cc_final: 0.7207 (t0) REVERT: V 44 LYS cc_start: 0.8489 (tptt) cc_final: 0.8224 (ttpt) REVERT: W 24 TYR cc_start: 0.8949 (m-10) cc_final: 0.8670 (m-80) outliers start: 25 outliers final: 24 residues processed: 333 average time/residue: 0.2410 time to fit residues: 120.1940 Evaluate side-chains 341 residues out of total 1535 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 317 time to evaluate : 1.489 ------------------------------------------------------------------------------- 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 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 76 ILE Chi-restraints excluded: chain E residue 106 SER 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 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 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: 3.9990 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN F 399 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.118817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.089828 restraints weight = 20129.241| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.59 r_work: 0.2970 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 15095 Z= 0.159 Angle : 0.457 12.410 20430 Z= 0.243 Chirality : 0.035 0.166 2365 Planarity : 0.003 0.032 2550 Dihedral : 3.619 30.462 2045 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.63 % Allowed : 17.59 % Favored : 80.78 % 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: 4.83 (0.18), residues: 1900 helix: 3.79 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.15 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Q 26 PHE 0.012 0.001 PHE Z 43 TYR 0.028 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3263.02 seconds wall clock time: 58 minutes 58.90 seconds (3538.90 seconds total)