Starting phenix.real_space_refine on Fri May 16 12:02:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixk_35794/05_2025/8ixk_35794.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixk_35794/05_2025/8ixk_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/cci-nas-00/data/ceres_data/8ixk_35794/05_2025/8ixk_35794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixk_35794/05_2025/8ixk_35794.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixk_35794/05_2025/8ixk_35794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixk_35794/05_2025/8ixk_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-5687/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: 8.39, per 1000 atoms: 0.57 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: 3.66 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: 1.15 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: 4.18 Time building geometry restraints manager: 4.37 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: 0.630 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: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 32.700 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.290 ------------------------------------------------------------------------------- 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= 0.351 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 Details of bonding type rmsd hydrogen bonds : bond 0.11667 ( 1331) hydrogen bonds : angle 4.00277 ( 3903) covalent geometry : bond 0.00514 (15095) covalent geometry : angle 0.70866 (20430) *********************** 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 to be fit. rotamer outliers: 10 poor density : 370 time to evaluate : 1.479 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: 0.2386 time to fit residues: 135.6907 Evaluate side-chains 309 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 304 time to evaluate : 1.508 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090607 restraints weight = 20058.285| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.58 r_work: 0.2981 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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= 0.134 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 Details of bonding type rmsd hydrogen bonds : bond 0.05986 ( 1331) hydrogen bonds : angle 3.45218 ( 3903) covalent geometry : bond 0.00248 (15095) covalent geometry : angle 0.43960 (20430) *********************** 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 to be fit. rotamer outliers: 29 poor density : 338 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: R 263 MET cc_start: 0.5754 (tpp) cc_final: 0.5478 (tpp) REVERT: A 263 MET cc_start: 0.5960 (tpp) cc_final: 0.5541 (tpt) REVERT: A 404 LYS cc_start: 0.6442 (OUTLIER) cc_final: 0.5844 (pttp) REVERT: C 24 TYR cc_start: 0.9115 (m-10) cc_final: 0.8757 (m-80) REVERT: E 109 ASP cc_start: 0.8839 (t0) cc_final: 0.8586 (t0) REVERT: G 44 LYS cc_start: 0.8335 (tptt) cc_final: 0.7708 (ttmm) REVERT: H 24 TYR cc_start: 0.9158 (m-10) cc_final: 0.8867 (m-10) REVERT: K 404 LYS cc_start: 0.6496 (OUTLIER) cc_final: 0.5771 (pttp) REVERT: L 44 LYS cc_start: 0.8446 (tptt) cc_final: 0.7877 (ttmt) REVERT: T 404 LYS cc_start: 0.6398 (OUTLIER) cc_final: 0.5865 (pttp) REVERT: W 24 TYR cc_start: 0.9135 (m-10) cc_final: 0.8788 (m-80) outliers start: 29 outliers final: 22 residues processed: 358 average time/residue: 0.2507 time to fit residues: 135.8308 Evaluate side-chains 340 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 315 time to evaluate : 1.514 ------------------------------------------------------------------------------- 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 T residue 404 LYS 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 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 81 optimal weight: 0.0030 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089519 restraints weight = 20199.746| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.58 r_work: 0.2965 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15095 Z= 0.140 Angle : 0.436 8.924 20430 Z= 0.236 Chirality : 0.034 0.156 2365 Planarity : 0.003 0.033 2550 Dihedral : 4.207 36.910 2061 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.48 % Allowed : 10.49 % Favored : 87.04 % 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: 3.74 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.55 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 110 PHE 0.015 0.001 PHE Z 43 TYR 0.016 0.001 TYR M 24 ARG 0.001 0.000 ARG K 378 Details of bonding type rmsd hydrogen bonds : bond 0.05967 ( 1331) hydrogen bonds : angle 3.39517 ( 3903) covalent geometry : bond 0.00283 (15095) covalent geometry : angle 0.43622 (20430) *********************** 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 367 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 329 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: R 404 LYS cc_start: 0.5909 (OUTLIER) cc_final: 0.5384 (pttp) REVERT: A 263 MET cc_start: 0.6021 (tpp) cc_final: 0.5612 (tpp) REVERT: A 318 ASP cc_start: 0.8268 (m-30) cc_final: 0.8063 (m-30) REVERT: B 44 LYS cc_start: 0.8578 (tptt) cc_final: 0.7853 (ttmt) REVERT: C 24 TYR cc_start: 0.9119 (m-10) cc_final: 0.8746 (m-80) REVERT: G 44 LYS cc_start: 0.8353 (tptt) cc_final: 0.7760 (ttmt) REVERT: H 24 TYR cc_start: 0.9168 (m-10) cc_final: 0.8856 (m-10) REVERT: I 17 SER cc_start: 0.8810 (p) cc_final: 0.8603 (p) REVERT: L 44 LYS cc_start: 0.8561 (tptt) cc_final: 0.7961 (ttmt) REVERT: T 404 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5881 (pttp) REVERT: W 24 TYR cc_start: 0.9138 (m-10) cc_final: 0.8772 (m-80) outliers start: 38 outliers final: 28 residues processed: 354 average time/residue: 0.2319 time to fit residues: 123.6914 Evaluate side-chains 341 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 311 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 T residue 404 LYS 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 106 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 59 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 126 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 90 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 F 343 GLN T 350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.087949 restraints weight = 20258.675| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.58 r_work: 0.2937 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1195 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= 0.148 Angle : 0.440 9.182 20430 Z= 0.238 Chirality : 0.034 0.130 2365 Planarity : 0.003 0.035 2550 Dihedral : 4.135 36.062 2057 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.80 % Allowed : 12.70 % 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: 3.71 (0.12), residues: 1525 sheet: None (None), residues: 0 loop : 0.42 (0.30), 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 0.026 0.001 TYR M 24 ARG 0.002 0.000 ARG F 378 Details of bonding type rmsd hydrogen bonds : bond 0.06064 ( 1331) hydrogen bonds : angle 3.40569 ( 3903) covalent geometry : bond 0.00314 (15095) covalent geometry : angle 0.44033 (20430) *********************** 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 368 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 325 time to evaluate : 1.641 Fit side-chains REVERT: R 404 LYS cc_start: 0.6143 (OUTLIER) cc_final: 0.5711 (pttp) REVERT: P 44 LYS cc_start: 0.8552 (tptt) cc_final: 0.7835 (ttpt) REVERT: A 263 MET cc_start: 0.5919 (tpp) cc_final: 0.5517 (tpp) REVERT: B 44 LYS cc_start: 0.8550 (tptt) cc_final: 0.7863 (ttmt) REVERT: C 24 TYR cc_start: 0.9131 (m-10) cc_final: 0.8741 (m-80) REVERT: E 109 ASP cc_start: 0.8877 (t0) cc_final: 0.8677 (t0) REVERT: G 44 LYS cc_start: 0.8407 (tptt) cc_final: 0.7797 (ttmt) REVERT: H 24 TYR cc_start: 0.9178 (m-10) cc_final: 0.8842 (m-10) REVERT: I 17 SER cc_start: 0.8778 (p) cc_final: 0.8554 (p) REVERT: L 44 LYS cc_start: 0.8532 (tptt) cc_final: 0.7944 (ttmt) REVERT: T 404 LYS cc_start: 0.6290 (OUTLIER) cc_final: 0.5543 (pttp) REVERT: V 44 LYS cc_start: 0.8585 (tptt) cc_final: 0.7962 (ttpt) REVERT: W 24 TYR cc_start: 0.9159 (m-10) cc_final: 0.8862 (m-80) outliers start: 43 outliers final: 33 residues processed: 348 average time/residue: 0.2395 time to fit residues: 125.7442 Evaluate side-chains 351 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 316 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR 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 316 THR 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 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 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 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 T residue 404 LYS 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 56 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 130 optimal weight: 0.0980 chunk 106 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089495 restraints weight = 20279.260| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.58 r_work: 0.2962 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1292 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= 0.128 Angle : 0.428 8.809 20430 Z= 0.231 Chirality : 0.034 0.133 2365 Planarity : 0.003 0.033 2550 Dihedral : 4.013 35.328 2053 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.08 % Allowed : 15.77 % Favored : 82.15 % 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: 3.74 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.30 (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 0.019 0.001 TYR M 24 ARG 0.000 0.000 ARG T 402 Details of bonding type rmsd hydrogen bonds : bond 0.05762 ( 1331) hydrogen bonds : angle 3.32390 ( 3903) covalent geometry : bond 0.00243 (15095) covalent geometry : angle 0.42755 (20430) *********************** 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 351 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 319 time to evaluate : 1.567 Fit side-chains REVERT: R 404 LYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5835 (pttp) REVERT: P 44 LYS cc_start: 0.8540 (tptt) cc_final: 0.7829 (ttmt) REVERT: A 274 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7155 (t0) REVERT: B 44 LYS cc_start: 0.8533 (tptt) cc_final: 0.7859 (ttmt) REVERT: C 24 TYR cc_start: 0.9113 (m-10) cc_final: 0.8764 (m-80) REVERT: E 109 ASP cc_start: 0.8883 (t0) cc_final: 0.8648 (t0) REVERT: G 44 LYS cc_start: 0.8391 (tptt) cc_final: 0.7786 (ttmt) REVERT: H 24 TYR cc_start: 0.9178 (m-10) cc_final: 0.8834 (m-10) REVERT: I 17 SER cc_start: 0.8764 (p) cc_final: 0.8560 (p) REVERT: L 44 LYS cc_start: 0.8570 (tptt) cc_final: 0.7994 (ttmt) REVERT: T 404 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5691 (pttp) REVERT: V 44 LYS cc_start: 0.8573 (tptt) cc_final: 0.7959 (ttpt) REVERT: W 24 TYR cc_start: 0.9145 (m-10) cc_final: 0.8840 (m-80) outliers start: 32 outliers final: 25 residues processed: 340 average time/residue: 0.2423 time to fit residues: 123.9956 Evaluate side-chains 340 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 312 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR 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 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 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 274 ASN Chi-restraints excluded: chain F residue 396 THR Chi-restraints excluded: chain H residue 46 THR 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 106 SER Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain T residue 396 THR Chi-restraints excluded: chain T residue 404 LYS Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain X residue 13 SER 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 12 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 57 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.118396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.089489 restraints weight = 20326.222| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.60 r_work: 0.2960 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1403 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= 0.125 Angle : 0.422 8.935 20430 Z= 0.228 Chirality : 0.034 0.143 2365 Planarity : 0.003 0.032 2550 Dihedral : 3.899 33.400 2053 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.28 % Allowed : 15.77 % Favored : 81.95 % 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: 4.84 (0.18), residues: 1900 helix: 3.78 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.25 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Q 26 PHE 0.013 0.001 PHE Z 43 TYR 0.017 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 Details of bonding type rmsd hydrogen bonds : bond 0.05585 ( 1331) hydrogen bonds : angle 3.27376 ( 3903) covalent geometry : bond 0.00237 (15095) covalent geometry : angle 0.42168 (20430) *********************** 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 to be fit. rotamer outliers: 35 poor density : 318 time to evaluate : 1.731 Fit side-chains REVERT: R 404 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.5701 (pttp) REVERT: P 44 LYS cc_start: 0.8533 (tptt) cc_final: 0.7859 (ttpt) REVERT: Q 24 TYR cc_start: 0.9149 (m-10) cc_final: 0.8833 (m-80) REVERT: B 44 LYS cc_start: 0.8545 (tptt) cc_final: 0.7882 (ttmt) REVERT: C 24 TYR cc_start: 0.9116 (m-10) cc_final: 0.8745 (m-80) REVERT: E 109 ASP cc_start: 0.8854 (t0) cc_final: 0.8601 (t0) REVERT: G 44 LYS cc_start: 0.8410 (tptt) cc_final: 0.7801 (ttmt) REVERT: H 24 TYR cc_start: 0.9189 (m-10) cc_final: 0.8837 (m-10) REVERT: L 44 LYS cc_start: 0.8552 (tptt) cc_final: 0.7965 (ttmt) REVERT: T 404 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5736 (pttp) REVERT: V 44 LYS cc_start: 0.8599 (tptt) cc_final: 0.7980 (ttpt) REVERT: W 24 TYR cc_start: 0.9167 (m-10) cc_final: 0.8805 (m-80) outliers start: 35 outliers final: 29 residues processed: 341 average time/residue: 0.2403 time to fit residues: 123.5211 Evaluate side-chains 342 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 311 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR 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 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 316 THR Chi-restraints excluded: chain A residue 396 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 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 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 T residue 396 THR Chi-restraints excluded: chain T residue 404 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 39 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** Z 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.116352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.087420 restraints weight = 20494.862| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.60 r_work: 0.2928 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15095 Z= 0.143 Angle : 0.437 9.189 20430 Z= 0.237 Chirality : 0.034 0.149 2365 Planarity : 0.003 0.034 2550 Dihedral : 3.888 33.573 2053 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.35 % Allowed : 15.83 % 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: 4.71 (0.18), residues: 1900 helix: 3.69 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.20 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP J 110 PHE 0.014 0.001 PHE K 377 TYR 0.015 0.001 TYR M 24 ARG 0.001 0.000 ARG K 378 Details of bonding type rmsd hydrogen bonds : bond 0.05885 ( 1331) hydrogen bonds : angle 3.32809 ( 3903) covalent geometry : bond 0.00302 (15095) covalent geometry : angle 0.43686 (20430) *********************** 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 358 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 322 time to evaluate : 1.545 Fit side-chains REVERT: R 404 LYS cc_start: 0.6183 (OUTLIER) cc_final: 0.5658 (pttp) REVERT: P 44 LYS cc_start: 0.8558 (tptt) cc_final: 0.7889 (ttpt) REVERT: Q 24 TYR cc_start: 0.9163 (m-10) cc_final: 0.8840 (m-80) REVERT: B 44 LYS cc_start: 0.8541 (tptt) cc_final: 0.7899 (ttmt) REVERT: C 24 TYR cc_start: 0.9124 (m-10) cc_final: 0.8765 (m-80) REVERT: E 109 ASP cc_start: 0.8894 (t0) cc_final: 0.8667 (t0) REVERT: G 44 LYS cc_start: 0.8440 (tptt) cc_final: 0.7866 (ttpt) REVERT: H 24 TYR cc_start: 0.9190 (m-10) cc_final: 0.8830 (m-10) REVERT: L 44 LYS cc_start: 0.8568 (tptt) cc_final: 0.7969 (ttmt) REVERT: M 24 TYR cc_start: 0.9099 (m-80) cc_final: 0.8839 (m-80) REVERT: T 404 LYS cc_start: 0.6392 (OUTLIER) cc_final: 0.5900 (pttp) REVERT: V 44 LYS cc_start: 0.8579 (tptt) cc_final: 0.7955 (ttpt) REVERT: W 24 TYR cc_start: 0.9175 (m-10) cc_final: 0.8812 (m-80) outliers start: 36 outliers final: 31 residues processed: 345 average time/residue: 0.2386 time to fit residues: 123.2162 Evaluate side-chains 351 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 318 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR 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 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 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 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 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 T residue 396 THR Chi-restraints excluded: chain T residue 404 LYS 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 142 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 108 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 O 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089265 restraints weight = 20335.112| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.60 r_work: 0.2958 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 15095 Z= 0.127 Angle : 0.436 9.652 20430 Z= 0.234 Chirality : 0.034 0.160 2365 Planarity : 0.003 0.032 2550 Dihedral : 3.828 33.031 2053 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.08 % Allowed : 16.61 % Favored : 81.30 % 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: 4.81 (0.18), residues: 1900 helix: 3.77 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.18 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP Q 26 PHE 0.013 0.001 PHE Z 43 TYR 0.014 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 Details of bonding type rmsd hydrogen bonds : bond 0.05617 ( 1331) hydrogen bonds : angle 3.29351 ( 3903) covalent geometry : bond 0.00242 (15095) covalent geometry : angle 0.43565 (20430) *********************** 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 to be fit. rotamer outliers: 32 poor density : 318 time to evaluate : 1.586 Fit side-chains REVERT: R 404 LYS cc_start: 0.6182 (OUTLIER) cc_final: 0.5769 (pttp) REVERT: P 44 LYS cc_start: 0.8559 (tptt) cc_final: 0.7897 (ttpt) REVERT: Q 24 TYR cc_start: 0.9167 (m-10) cc_final: 0.8852 (m-80) REVERT: B 44 LYS cc_start: 0.8530 (tptt) cc_final: 0.7927 (ttmt) REVERT: C 24 TYR cc_start: 0.9118 (m-10) cc_final: 0.8767 (m-80) REVERT: D 20 GLU cc_start: 0.8321 (pt0) cc_final: 0.8088 (pm20) REVERT: E 109 ASP cc_start: 0.8880 (t0) cc_final: 0.8664 (t0) REVERT: G 44 LYS cc_start: 0.8424 (tptt) cc_final: 0.7873 (ttpt) REVERT: H 24 TYR cc_start: 0.9191 (m-10) cc_final: 0.8834 (m-10) REVERT: L 44 LYS cc_start: 0.8572 (tptt) cc_final: 0.8001 (ttmt) REVERT: M 24 TYR cc_start: 0.9107 (m-80) cc_final: 0.8836 (m-80) REVERT: T 404 LYS cc_start: 0.6425 (OUTLIER) cc_final: 0.5944 (pttp) REVERT: V 44 LYS cc_start: 0.8586 (tptt) cc_final: 0.8009 (ttpt) REVERT: W 24 TYR cc_start: 0.9175 (m-10) cc_final: 0.8816 (m-80) outliers start: 32 outliers final: 28 residues processed: 337 average time/residue: 0.2423 time to fit residues: 123.1262 Evaluate side-chains 344 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 404 LYS 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 A residue 316 THR Chi-restraints excluded: chain A residue 396 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 274 ASN Chi-restraints excluded: chain F residue 316 THR Chi-restraints excluded: chain G residue 36 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 T residue 404 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 130 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087721 restraints weight = 20291.604| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.59 r_work: 0.2931 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 15095 Z= 0.142 Angle : 0.442 9.638 20430 Z= 0.241 Chirality : 0.035 0.167 2365 Planarity : 0.003 0.033 2550 Dihedral : 3.829 32.987 2053 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.08 % Allowed : 17.33 % Favored : 80.59 % 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: 4.72 (0.18), residues: 1900 helix: 3.70 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.17 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP J 110 PHE 0.014 0.001 PHE K 377 TYR 0.014 0.001 TYR M 24 ARG 0.001 0.000 ARG K 378 Details of bonding type rmsd hydrogen bonds : bond 0.05831 ( 1331) hydrogen bonds : angle 3.33602 ( 3903) covalent geometry : bond 0.00302 (15095) covalent geometry : angle 0.44189 (20430) *********************** 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 346 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 314 time to evaluate : 1.738 Fit side-chains REVERT: R 404 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5712 (pttp) REVERT: P 44 LYS cc_start: 0.8533 (tptt) cc_final: 0.7870 (ttpt) REVERT: Q 24 TYR cc_start: 0.9165 (m-10) cc_final: 0.8847 (m-80) REVERT: B 44 LYS cc_start: 0.8543 (tptt) cc_final: 0.7934 (ttmt) REVERT: C 24 TYR cc_start: 0.9106 (m-10) cc_final: 0.8738 (m-80) REVERT: E 109 ASP cc_start: 0.8908 (t0) cc_final: 0.8693 (t0) REVERT: G 28 MET cc_start: 0.9158 (ttp) cc_final: 0.8930 (ttp) REVERT: G 44 LYS cc_start: 0.8439 (tptt) cc_final: 0.7891 (ttpt) REVERT: H 24 TYR cc_start: 0.9205 (m-10) cc_final: 0.8839 (m-10) REVERT: L 44 LYS cc_start: 0.8545 (tptt) cc_final: 0.7968 (ttmt) REVERT: M 24 TYR cc_start: 0.9112 (m-80) cc_final: 0.8840 (m-80) REVERT: T 404 LYS cc_start: 0.6409 (OUTLIER) cc_final: 0.6026 (pttp) REVERT: V 44 LYS cc_start: 0.8565 (tptt) cc_final: 0.7991 (ttpt) REVERT: W 24 TYR cc_start: 0.9174 (m-10) cc_final: 0.8809 (m-80) outliers start: 32 outliers final: 30 residues processed: 333 average time/residue: 0.2512 time to fit residues: 124.8676 Evaluate side-chains 342 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 310 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 404 LYS 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 A residue 316 THR Chi-restraints excluded: chain A residue 396 THR 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 G residue 36 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 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 T residue 404 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 115 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 44 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 153 optimal weight: 0.7980 chunk 11 optimal weight: 0.0030 chunk 113 optimal weight: 0.5980 chunk 101 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.4228 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091887 restraints weight = 20069.355| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.59 r_work: 0.3000 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 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 0.062 15095 Z= 0.119 Angle : 0.439 10.074 20430 Z= 0.234 Chirality : 0.034 0.168 2365 Planarity : 0.003 0.030 2550 Dihedral : 3.725 31.062 2053 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.50 % Allowed : 18.05 % Favored : 80.46 % 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: 4.90 (0.18), residues: 1900 helix: 3.84 (0.12), residues: 1545 sheet: None (None), residues: 0 loop : 0.13 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP M 26 PHE 0.010 0.001 PHE Z 43 TYR 0.014 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 Details of bonding type rmsd hydrogen bonds : bond 0.05227 ( 1331) hydrogen bonds : angle 3.24025 ( 3903) covalent geometry : bond 0.00210 (15095) covalent geometry : angle 0.43886 (20430) ********************** 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 353 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 330 time to evaluate : 1.703 Fit side-chains REVERT: R 404 LYS cc_start: 0.6118 (OUTLIER) cc_final: 0.5631 (pttp) REVERT: P 44 LYS cc_start: 0.8490 (tptt) cc_final: 0.7836 (ttpt) REVERT: Q 24 TYR cc_start: 0.9144 (m-10) cc_final: 0.8839 (m-80) REVERT: B 44 LYS cc_start: 0.8562 (tptt) cc_final: 0.7981 (ttmt) REVERT: C 24 TYR cc_start: 0.9072 (m-10) cc_final: 0.8720 (m-80) REVERT: E 109 ASP cc_start: 0.8875 (t0) cc_final: 0.8663 (t0) REVERT: G 28 MET cc_start: 0.9151 (ttp) cc_final: 0.8918 (ttp) REVERT: G 44 LYS cc_start: 0.8349 (tptt) cc_final: 0.7804 (ttpt) REVERT: H 24 TYR cc_start: 0.9155 (m-10) cc_final: 0.8800 (m-10) REVERT: L 44 LYS cc_start: 0.8498 (tptt) cc_final: 0.7931 (ttmt) REVERT: M 24 TYR cc_start: 0.9094 (m-80) cc_final: 0.8828 (m-80) REVERT: T 404 LYS cc_start: 0.6457 (OUTLIER) cc_final: 0.6070 (pttp) REVERT: V 44 LYS cc_start: 0.8536 (tptt) cc_final: 0.7950 (ttpt) REVERT: W 24 TYR cc_start: 0.9138 (m-10) cc_final: 0.8784 (m-80) outliers start: 23 outliers final: 20 residues processed: 341 average time/residue: 0.2400 time to fit residues: 122.7460 Evaluate side-chains 341 residues out of total 1535 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 319 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 404 LYS 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 C residue 46 THR 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 K residue 274 ASN Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain M residue 46 THR Chi-restraints excluded: chain T residue 316 THR Chi-restraints excluded: chain T residue 396 THR Chi-restraints excluded: chain T residue 404 LYS Chi-restraints excluded: chain V residue 37 ILE Chi-restraints excluded: chain W residue 46 THR Chi-restraints excluded: chain Y residue 76 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 71 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 99 optimal weight: 0.0060 chunk 33 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 350 GLN Y 74 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.120419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091465 restraints weight = 20224.242| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.60 r_work: 0.2993 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 15095 Z= 0.124 Angle : 0.455 11.927 20430 Z= 0.241 Chirality : 0.034 0.164 2365 Planarity : 0.003 0.031 2550 Dihedral : 3.647 28.890 2053 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.56 % Allowed : 18.37 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.91 (0.18), residues: 1900 helix: 3.84 (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 0.014 0.001 TYR M 24 ARG 0.001 0.000 ARG T 402 Details of bonding type rmsd hydrogen bonds : bond 0.05277 ( 1331) hydrogen bonds : angle 3.24910 ( 3903) covalent geometry : bond 0.00242 (15095) covalent geometry : angle 0.45547 (20430) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6752.63 seconds wall clock time: 117 minutes 50.57 seconds (7070.57 seconds total)