Starting phenix.real_space_refine on Sun Mar 17 18:41:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/03_2024/6oeg_20020_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/03_2024/6oeg_20020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/03_2024/6oeg_20020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/03_2024/6oeg_20020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/03_2024/6oeg_20020_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/03_2024/6oeg_20020_neut.pdb" } resolution = 3.8 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= 0.004 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 70 5.16 5 C 11872 2.51 5 N 3206 2.21 5 O 3416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N ARG 410": "NH1" <-> "NH2" Residue "N ARG 465": "NH1" <-> "NH2" Residue "N ARG 468": "NH1" <-> "NH2" Residue "O ARG 410": "NH1" <-> "NH2" Residue "O ARG 465": "NH1" <-> "NH2" Residue "O ARG 468": "NH1" <-> "NH2" Residue "P ARG 410": "NH1" <-> "NH2" Residue "P ARG 465": "NH1" <-> "NH2" Residue "P ARG 468": "NH1" <-> "NH2" Residue "Q ARG 410": "NH1" <-> "NH2" Residue "Q ARG 465": "NH1" <-> "NH2" Residue "Q ARG 468": "NH1" <-> "NH2" Residue "R ARG 410": "NH1" <-> "NH2" Residue "R ARG 465": "NH1" <-> "NH2" Residue "R ARG 468": "NH1" <-> "NH2" Residue "S ARG 410": "NH1" <-> "NH2" Residue "S ARG 465": "NH1" <-> "NH2" Residue "S ARG 468": "NH1" <-> "NH2" Residue "T ARG 410": "NH1" <-> "NH2" Residue "T ARG 465": "NH1" <-> "NH2" Residue "T ARG 468": "NH1" <-> "NH2" Residue "U ARG 410": "NH1" <-> "NH2" Residue "U ARG 465": "NH1" <-> "NH2" Residue "U ARG 468": "NH1" <-> "NH2" Residue "V ARG 410": "NH1" <-> "NH2" Residue "V ARG 465": "NH1" <-> "NH2" Residue "V ARG 468": "NH1" <-> "NH2" Residue "W ARG 410": "NH1" <-> "NH2" Residue "W ARG 465": "NH1" <-> "NH2" Residue "W ARG 468": "NH1" <-> "NH2" Residue "X ARG 410": "NH1" <-> "NH2" Residue "X ARG 465": "NH1" <-> "NH2" Residue "X ARG 468": "NH1" <-> "NH2" Residue "Y ARG 410": "NH1" <-> "NH2" Residue "Y ARG 465": "NH1" <-> "NH2" Residue "Y ARG 468": "NH1" <-> "NH2" Residue "Z ARG 410": "NH1" <-> "NH2" Residue "Z ARG 465": "NH1" <-> "NH2" Residue "Z ARG 468": "NH1" <-> "NH2" Residue "a ARG 410": "NH1" <-> "NH2" Residue "a ARG 465": "NH1" <-> "NH2" Residue "a ARG 468": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18564 Number of models: 1 Model: "" Number of chains: 14 Chain: "N" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "O" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "P" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "Q" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "R" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "S" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "T" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "U" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "V" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "W" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "X" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "Y" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "Z" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Chain: "a" Number of atoms: 1326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1326 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 8, 'TRANS': 153} Time building chain proxies: 9.70, per 1000 atoms: 0.52 Number of scatterers: 18564 At special positions: 0 Unit cell: (188.6, 188.6, 123, 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 70 16.00 O 3416 8.00 N 3206 7.00 C 11872 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 3.6 seconds 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4340 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 28 sheets defined 27.2% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'N' and resid 351 through 356 Processing helix chain 'N' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE N 363 " --> pdb=" O ASN N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY N 463 " --> pdb=" O THR N 460 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'O' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE O 363 " --> pdb=" O ASN O 359 " (cutoff:3.500A) Processing helix chain 'O' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY O 463 " --> pdb=" O THR O 460 " (cutoff:3.500A) Processing helix chain 'P' and resid 351 through 356 Processing helix chain 'P' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE P 363 " --> pdb=" O ASN P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY P 463 " --> pdb=" O THR P 460 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'Q' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE Q 363 " --> pdb=" O ASN Q 359 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Q 463 " --> pdb=" O THR Q 460 " (cutoff:3.500A) Processing helix chain 'R' and resid 351 through 356 Processing helix chain 'R' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE R 363 " --> pdb=" O ASN R 359 " (cutoff:3.500A) Processing helix chain 'R' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY R 463 " --> pdb=" O THR R 460 " (cutoff:3.500A) Processing helix chain 'S' and resid 351 through 356 Processing helix chain 'S' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE S 363 " --> pdb=" O ASN S 359 " (cutoff:3.500A) Processing helix chain 'S' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY S 463 " --> pdb=" O THR S 460 " (cutoff:3.500A) Processing helix chain 'T' and resid 351 through 356 Processing helix chain 'T' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE T 363 " --> pdb=" O ASN T 359 " (cutoff:3.500A) Processing helix chain 'T' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY T 463 " --> pdb=" O THR T 460 " (cutoff:3.500A) Processing helix chain 'U' and resid 351 through 356 Processing helix chain 'U' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE U 363 " --> pdb=" O ASN U 359 " (cutoff:3.500A) Processing helix chain 'U' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY U 463 " --> pdb=" O THR U 460 " (cutoff:3.500A) Processing helix chain 'V' and resid 351 through 356 Processing helix chain 'V' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE V 363 " --> pdb=" O ASN V 359 " (cutoff:3.500A) Processing helix chain 'V' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY V 463 " --> pdb=" O THR V 460 " (cutoff:3.500A) Processing helix chain 'W' and resid 351 through 356 Processing helix chain 'W' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE W 363 " --> pdb=" O ASN W 359 " (cutoff:3.500A) Processing helix chain 'W' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY W 463 " --> pdb=" O THR W 460 " (cutoff:3.500A) Processing helix chain 'X' and resid 351 through 356 Processing helix chain 'X' and resid 359 through 391 removed outlier: 3.870A pdb=" N ILE X 363 " --> pdb=" O ASN X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY X 463 " --> pdb=" O THR X 460 " (cutoff:3.500A) Processing helix chain 'Y' and resid 351 through 356 Processing helix chain 'Y' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE Y 363 " --> pdb=" O ASN Y 359 " (cutoff:3.500A) Processing helix chain 'Y' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Y 463 " --> pdb=" O THR Y 460 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 356 Processing helix chain 'Z' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE Z 363 " --> pdb=" O ASN Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 464 removed outlier: 3.503A pdb=" N GLY Z 463 " --> pdb=" O THR Z 460 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 356 Processing helix chain 'a' and resid 359 through 391 removed outlier: 3.869A pdb=" N ILE a 363 " --> pdb=" O ASN a 359 " (cutoff:3.500A) Processing helix chain 'a' and resid 460 through 464 removed outlier: 3.504A pdb=" N GLY a 463 " --> pdb=" O THR a 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS N 475 " --> pdb=" O VAL N 442 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 420 through 421 Processing sheet with id=AA3, first strand: chain 'O' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS O 475 " --> pdb=" O VAL O 442 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 420 through 421 Processing sheet with id=AA5, first strand: chain 'P' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS P 475 " --> pdb=" O VAL P 442 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 420 through 421 Processing sheet with id=AA7, first strand: chain 'Q' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS Q 475 " --> pdb=" O VAL Q 442 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 420 through 421 Processing sheet with id=AA9, first strand: chain 'R' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS R 475 " --> pdb=" O VAL R 442 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 420 through 421 Processing sheet with id=AB2, first strand: chain 'S' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS S 475 " --> pdb=" O VAL S 442 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 420 through 421 Processing sheet with id=AB4, first strand: chain 'T' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS T 475 " --> pdb=" O VAL T 442 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'T' and resid 420 through 421 Processing sheet with id=AB6, first strand: chain 'U' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS U 475 " --> pdb=" O VAL U 442 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 420 through 421 Processing sheet with id=AB8, first strand: chain 'V' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS V 475 " --> pdb=" O VAL V 442 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'V' and resid 420 through 421 Processing sheet with id=AC1, first strand: chain 'W' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS W 475 " --> pdb=" O VAL W 442 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 420 through 421 Processing sheet with id=AC3, first strand: chain 'X' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS X 475 " --> pdb=" O VAL X 442 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 420 through 421 Processing sheet with id=AC5, first strand: chain 'Y' and resid 403 through 407 removed outlier: 5.188A pdb=" N LYS Y 475 " --> pdb=" O VAL Y 442 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Y' and resid 420 through 421 Processing sheet with id=AC7, first strand: chain 'Z' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS Z 475 " --> pdb=" O VAL Z 442 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 420 through 421 Processing sheet with id=AC9, first strand: chain 'a' and resid 403 through 407 removed outlier: 5.189A pdb=" N LYS a 475 " --> pdb=" O VAL a 442 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'a' and resid 420 through 421 784 hydrogen bonds defined for protein. 2142 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: 5.20 Time building geometry restraints manager: 7.00 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: 5739 1.34 - 1.45: 3274 1.45 - 1.57: 9775 1.57 - 1.69: 14 1.69 - 1.81: 140 Bond restraints: 18942 Sorted by residual: bond pdb=" CB GLU X 418 " pdb=" CG GLU X 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.30e+00 bond pdb=" CB GLU W 418 " pdb=" CG GLU W 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.25e+00 bond pdb=" CB GLU Y 418 " pdb=" CG GLU Y 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.23e+00 bond pdb=" CB GLU R 418 " pdb=" CG GLU R 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.21e+00 bond pdb=" CB GLU a 418 " pdb=" CG GLU a 418 " ideal model delta sigma weight residual 1.520 1.595 -0.075 3.00e-02 1.11e+03 6.18e+00 ... (remaining 18937 not shown) Histogram of bond angle deviations from ideal: 99.01 - 106.00: 504 106.00 - 112.99: 9705 112.99 - 119.98: 6931 119.98 - 126.98: 8267 126.98 - 133.97: 129 Bond angle restraints: 25536 Sorted by residual: angle pdb=" CB GLU P 418 " pdb=" CG GLU P 418 " pdb=" CD GLU P 418 " ideal model delta sigma weight residual 112.60 123.51 -10.91 1.70e+00 3.46e-01 4.12e+01 angle pdb=" CB GLU Q 418 " pdb=" CG GLU Q 418 " pdb=" CD GLU Q 418 " ideal model delta sigma weight residual 112.60 123.51 -10.91 1.70e+00 3.46e-01 4.12e+01 angle pdb=" CB GLU a 418 " pdb=" CG GLU a 418 " pdb=" CD GLU a 418 " ideal model delta sigma weight residual 112.60 123.50 -10.90 1.70e+00 3.46e-01 4.11e+01 angle pdb=" CB GLU S 418 " pdb=" CG GLU S 418 " pdb=" CD GLU S 418 " ideal model delta sigma weight residual 112.60 123.49 -10.89 1.70e+00 3.46e-01 4.11e+01 angle pdb=" CB GLU T 418 " pdb=" CG GLU T 418 " pdb=" CD GLU T 418 " ideal model delta sigma weight residual 112.60 123.49 -10.89 1.70e+00 3.46e-01 4.10e+01 ... (remaining 25531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 10766 17.54 - 35.07: 672 35.07 - 52.61: 224 52.61 - 70.15: 28 70.15 - 87.68: 14 Dihedral angle restraints: 11704 sinusoidal: 4970 harmonic: 6734 Sorted by residual: dihedral pdb=" CA ILE V 479 " pdb=" C ILE V 479 " pdb=" N LYS V 480 " pdb=" CA LYS V 480 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE T 479 " pdb=" C ILE T 479 " pdb=" N LYS T 480 " pdb=" CA LYS T 480 " ideal model delta harmonic sigma weight residual 180.00 151.10 28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA ILE R 479 " pdb=" C ILE R 479 " pdb=" N LYS R 480 " pdb=" CA LYS R 480 " ideal model delta harmonic sigma weight residual 180.00 151.12 28.88 0 5.00e+00 4.00e-02 3.34e+01 ... (remaining 11701 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1640 0.050 - 0.100: 827 0.100 - 0.150: 249 0.150 - 0.200: 14 0.200 - 0.250: 14 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CB ILE Q 503 " pdb=" CA ILE Q 503 " pdb=" CG1 ILE Q 503 " pdb=" CG2 ILE Q 503 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE W 503 " pdb=" CA ILE W 503 " pdb=" CG1 ILE W 503 " pdb=" CG2 ILE W 503 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB ILE T 503 " pdb=" CA ILE T 503 " pdb=" CG1 ILE T 503 " pdb=" CG2 ILE T 503 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 2741 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE P 376 " -0.011 2.00e-02 2.50e+03 2.12e-02 4.49e+00 pdb=" C ILE P 376 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE P 376 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU P 377 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE V 376 " 0.011 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C ILE V 376 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE V 376 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU V 377 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE Y 376 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C ILE Y 376 " -0.036 2.00e-02 2.50e+03 pdb=" O ILE Y 376 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU Y 377 " 0.012 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 6587 2.88 - 3.38: 17093 3.38 - 3.89: 29490 3.89 - 4.39: 31340 4.39 - 4.90: 53217 Nonbonded interactions: 137727 Sorted by model distance: nonbonded pdb=" O MET T 355 " pdb=" OG SER T 358 " model vdw 2.370 2.440 nonbonded pdb=" O MET Y 355 " pdb=" OG SER Y 358 " model vdw 2.370 2.440 nonbonded pdb=" O MET S 355 " pdb=" OG SER S 358 " model vdw 2.370 2.440 nonbonded pdb=" O MET U 355 " pdb=" OG SER U 358 " model vdw 2.370 2.440 nonbonded pdb=" O MET a 355 " pdb=" OG SER a 358 " model vdw 2.370 2.440 ... (remaining 137722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 30.340 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 46.070 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.008 0.075 18942 Z= 0.504 Angle : 1.117 12.097 25536 Z= 0.623 Chirality : 0.061 0.250 2744 Planarity : 0.008 0.052 3304 Dihedral : 13.456 87.684 7364 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.56 % Allowed : 4.17 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.12), residues: 2240 helix: -2.82 (0.17), residues: 560 sheet: -2.75 (0.17), residues: 434 loop : -3.81 (0.12), residues: 1246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP U 466 HIS 0.002 0.001 HIS P 389 PHE 0.022 0.004 PHE X 420 TYR 0.018 0.003 TYR R 467 ARG 0.005 0.001 ARG N 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 841 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8631 (tp40) cc_final: 0.8379 (tp40) REVERT: N 379 GLN cc_start: 0.8787 (tt0) cc_final: 0.8450 (tm-30) REVERT: N 384 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: N 404 TYR cc_start: 0.8339 (m-10) cc_final: 0.4589 (t80) REVERT: N 405 GLN cc_start: 0.8704 (pt0) cc_final: 0.8190 (pt0) REVERT: N 415 MET cc_start: 0.8081 (ttm) cc_final: 0.7830 (ttm) REVERT: N 449 SER cc_start: 0.8969 (t) cc_final: 0.8694 (p) REVERT: N 450 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6226 (ptp) REVERT: O 379 GLN cc_start: 0.8903 (tt0) cc_final: 0.8442 (tm-30) REVERT: O 404 TYR cc_start: 0.8148 (m-10) cc_final: 0.5684 (t80) REVERT: O 405 GLN cc_start: 0.8791 (pt0) cc_final: 0.8442 (pt0) REVERT: O 415 MET cc_start: 0.7742 (ttm) cc_final: 0.7415 (ttm) REVERT: O 450 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.6721 (ptp) REVERT: P 364 ASN cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (t0) REVERT: P 367 LYS cc_start: 0.8501 (ptmt) cc_final: 0.8267 (pttm) REVERT: P 379 GLN cc_start: 0.8753 (tt0) cc_final: 0.7994 (tm-30) REVERT: P 387 TYR cc_start: 0.8924 (t80) cc_final: 0.8713 (t80) REVERT: P 404 TYR cc_start: 0.8104 (m-10) cc_final: 0.5385 (t80) REVERT: P 415 MET cc_start: 0.7759 (ttm) cc_final: 0.7540 (ttm) REVERT: P 450 MET cc_start: 0.7349 (OUTLIER) cc_final: 0.6715 (ttt) REVERT: P 456 ASP cc_start: 0.8783 (t0) cc_final: 0.8511 (t0) REVERT: P 464 LEU cc_start: 0.9307 (mp) cc_final: 0.9013 (mm) REVERT: Q 383 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7566 (mt) REVERT: Q 404 TYR cc_start: 0.8737 (m-10) cc_final: 0.5699 (t80) REVERT: Q 421 ASP cc_start: 0.8568 (p0) cc_final: 0.8155 (p0) REVERT: Q 427 TYR cc_start: 0.8761 (m-80) cc_final: 0.8455 (m-80) REVERT: Q 452 ASP cc_start: 0.7911 (p0) cc_final: 0.7663 (p0) REVERT: R 481 ASP cc_start: 0.7718 (p0) cc_final: 0.7492 (p0) REVERT: S 383 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7176 (mt) REVERT: S 384 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: S 404 TYR cc_start: 0.8072 (m-10) cc_final: 0.5835 (t80) REVERT: S 422 ASP cc_start: 0.8663 (p0) cc_final: 0.8398 (p0) REVERT: S 450 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.7053 (ptp) REVERT: S 452 ASP cc_start: 0.8033 (p0) cc_final: 0.7795 (p0) REVERT: S 478 LEU cc_start: 0.9318 (mp) cc_final: 0.9082 (mp) REVERT: T 364 ASN cc_start: 0.8299 (OUTLIER) cc_final: 0.7924 (t0) REVERT: T 379 GLN cc_start: 0.8477 (tt0) cc_final: 0.7663 (tm-30) REVERT: T 404 TYR cc_start: 0.7904 (m-10) cc_final: 0.5477 (t80) REVERT: T 405 GLN cc_start: 0.8588 (pt0) cc_final: 0.8064 (pt0) REVERT: T 456 ASP cc_start: 0.8828 (t0) cc_final: 0.8407 (t0) REVERT: U 367 LYS cc_start: 0.8713 (ptmt) cc_final: 0.8473 (pttm) REVERT: U 379 GLN cc_start: 0.9016 (tt0) cc_final: 0.8175 (tm-30) REVERT: U 404 TYR cc_start: 0.8317 (m-10) cc_final: 0.4864 (t80) REVERT: U 414 ILE cc_start: 0.9539 (tp) cc_final: 0.9337 (tt) REVERT: U 415 MET cc_start: 0.8070 (ttm) cc_final: 0.7854 (ttm) REVERT: U 434 THR cc_start: 0.8577 (t) cc_final: 0.8370 (t) REVERT: U 449 SER cc_start: 0.9326 (t) cc_final: 0.9046 (m) REVERT: U 450 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.6711 (ptp) REVERT: V 366 GLU cc_start: 0.8517 (pp20) cc_final: 0.8298 (tm-30) REVERT: V 408 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5901 (mm-30) REVERT: V 411 SER cc_start: 0.9173 (m) cc_final: 0.8943 (m) REVERT: V 450 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.6105 (ptp) REVERT: W 379 GLN cc_start: 0.8973 (tt0) cc_final: 0.8207 (tm-30) REVERT: W 417 SER cc_start: 0.9016 (t) cc_final: 0.8815 (t) REVERT: W 450 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6810 (ptp) REVERT: X 384 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7054 (tm-30) REVERT: X 404 TYR cc_start: 0.8106 (m-10) cc_final: 0.5678 (t80) REVERT: X 414 ILE cc_start: 0.9140 (tp) cc_final: 0.8921 (tp) REVERT: X 421 ASP cc_start: 0.8751 (p0) cc_final: 0.8300 (p0) REVERT: X 427 TYR cc_start: 0.8788 (m-80) cc_final: 0.8500 (m-80) REVERT: X 450 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.5807 (ptp) REVERT: X 501 TYR cc_start: 0.7631 (t80) cc_final: 0.7379 (t80) REVERT: Y 364 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.8192 (t0) REVERT: Y 372 LYS cc_start: 0.9185 (pptt) cc_final: 0.8913 (mmmt) REVERT: Y 377 LEU cc_start: 0.8759 (tp) cc_final: 0.8549 (tp) REVERT: Y 379 GLN cc_start: 0.8839 (tt0) cc_final: 0.8475 (tm-30) REVERT: Y 384 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7737 (tm-30) REVERT: Y 387 TYR cc_start: 0.8999 (t80) cc_final: 0.8746 (t80) REVERT: Y 404 TYR cc_start: 0.8002 (m-10) cc_final: 0.5194 (t80) REVERT: Y 415 MET cc_start: 0.7784 (ttm) cc_final: 0.7512 (ttm) REVERT: Y 421 ASP cc_start: 0.8712 (p0) cc_final: 0.8351 (p0) REVERT: Y 456 ASP cc_start: 0.8886 (t0) cc_final: 0.8683 (t0) REVERT: Z 367 LYS cc_start: 0.8653 (ptmt) cc_final: 0.8203 (pttm) REVERT: Z 372 LYS cc_start: 0.8987 (pptt) cc_final: 0.8621 (mtpt) REVERT: Z 379 GLN cc_start: 0.8790 (tt0) cc_final: 0.8401 (tm-30) REVERT: Z 404 TYR cc_start: 0.8258 (m-10) cc_final: 0.5767 (t80) REVERT: Z 405 GLN cc_start: 0.8755 (pt0) cc_final: 0.8456 (pt0) REVERT: Z 415 MET cc_start: 0.7918 (ttm) cc_final: 0.7684 (ttm) REVERT: Z 432 ASN cc_start: 0.9259 (p0) cc_final: 0.9020 (p0) REVERT: Z 450 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.6712 (ptp) REVERT: Z 456 ASP cc_start: 0.8909 (t0) cc_final: 0.8624 (t0) REVERT: a 371 GLU cc_start: 0.8587 (tp30) cc_final: 0.8357 (tp30) REVERT: a 381 LYS cc_start: 0.8701 (tppt) cc_final: 0.8438 (ttmm) REVERT: a 421 ASP cc_start: 0.8677 (p0) cc_final: 0.8359 (p0) REVERT: a 432 ASN cc_start: 0.9075 (p0) cc_final: 0.8872 (p0) REVERT: a 449 SER cc_start: 0.9223 (t) cc_final: 0.8662 (m) REVERT: a 450 MET cc_start: 0.7482 (OUTLIER) cc_final: 0.6481 (ptp) outliers start: 112 outliers final: 30 residues processed: 856 average time/residue: 0.3083 time to fit residues: 383.9193 Evaluate side-chains 684 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 635 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 383 LEU Chi-restraints excluded: chain N residue 384 GLU Chi-restraints excluded: chain N residue 450 MET Chi-restraints excluded: chain N residue 509 LEU Chi-restraints excluded: chain O residue 383 LEU Chi-restraints excluded: chain O residue 384 GLU Chi-restraints excluded: chain O residue 450 MET Chi-restraints excluded: chain O residue 509 LEU Chi-restraints excluded: chain P residue 364 ASN Chi-restraints excluded: chain P residue 384 GLU Chi-restraints excluded: chain P residue 418 GLU Chi-restraints excluded: chain P residue 450 MET Chi-restraints excluded: chain P residue 509 LEU Chi-restraints excluded: chain Q residue 383 LEU Chi-restraints excluded: chain Q residue 384 GLU Chi-restraints excluded: chain Q residue 509 LEU Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain S residue 383 LEU Chi-restraints excluded: chain S residue 384 GLU Chi-restraints excluded: chain S residue 450 MET Chi-restraints excluded: chain S residue 509 LEU Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 383 LEU Chi-restraints excluded: chain T residue 384 GLU Chi-restraints excluded: chain T residue 509 LEU Chi-restraints excluded: chain U residue 383 LEU Chi-restraints excluded: chain U residue 450 MET Chi-restraints excluded: chain U residue 509 LEU Chi-restraints excluded: chain V residue 418 GLU Chi-restraints excluded: chain V residue 450 MET Chi-restraints excluded: chain V residue 509 LEU Chi-restraints excluded: chain W residue 383 LEU Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 450 MET Chi-restraints excluded: chain W residue 509 LEU Chi-restraints excluded: chain X residue 384 GLU Chi-restraints excluded: chain X residue 418 GLU Chi-restraints excluded: chain X residue 450 MET Chi-restraints excluded: chain X residue 509 LEU Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 384 GLU Chi-restraints excluded: chain Y residue 418 GLU Chi-restraints excluded: chain Y residue 509 LEU Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 450 MET Chi-restraints excluded: chain Z residue 509 LEU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 450 MET Chi-restraints excluded: chain a residue 509 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 175 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 203 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 505 ASN O 505 ASN P 373 GLN P 505 ASN Q 500 ASN Q 505 ASN R 364 ASN R 500 ASN R 505 ASN S 505 ASN T 373 GLN T 461 ASN T 505 ASN U 505 ASN V 505 ASN W 505 ASN X 505 ASN Y 373 GLN Y 505 ASN Z 505 ASN a 373 GLN a 505 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18942 Z= 0.200 Angle : 0.642 7.780 25536 Z= 0.340 Chirality : 0.046 0.143 2744 Planarity : 0.006 0.045 3304 Dihedral : 7.693 49.430 2614 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 4.22 % Allowed : 13.34 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.14), residues: 2240 helix: -1.26 (0.19), residues: 574 sheet: -2.49 (0.18), residues: 462 loop : -3.29 (0.14), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP Q 466 HIS 0.003 0.001 HIS R 389 PHE 0.026 0.002 PHE R 420 TYR 0.014 0.001 TYR T 467 ARG 0.007 0.001 ARG a 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 799 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 714 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 373 GLN cc_start: 0.8633 (tp40) cc_final: 0.8391 (tp40) REVERT: N 379 GLN cc_start: 0.9014 (tt0) cc_final: 0.8497 (tm-30) REVERT: N 404 TYR cc_start: 0.7979 (m-10) cc_final: 0.5064 (t80) REVERT: N 405 GLN cc_start: 0.8605 (pt0) cc_final: 0.8103 (pt0) REVERT: N 415 MET cc_start: 0.8056 (ttm) cc_final: 0.7608 (ttm) REVERT: N 449 SER cc_start: 0.9180 (t) cc_final: 0.8904 (t) REVERT: N 450 MET cc_start: 0.7580 (ttp) cc_final: 0.6201 (ptp) REVERT: O 379 GLN cc_start: 0.8886 (tt0) cc_final: 0.8319 (tm-30) REVERT: O 386 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8592 (tm-30) REVERT: O 404 TYR cc_start: 0.8038 (m-10) cc_final: 0.5517 (t80) REVERT: O 418 GLU cc_start: 0.5987 (mp0) cc_final: 0.5706 (mp0) REVERT: O 422 ASP cc_start: 0.8653 (p0) cc_final: 0.8432 (p0) REVERT: O 450 MET cc_start: 0.7716 (ttp) cc_final: 0.6735 (ptp) REVERT: P 372 LYS cc_start: 0.8861 (pptt) cc_final: 0.8401 (mtpt) REVERT: P 379 GLN cc_start: 0.8813 (tt0) cc_final: 0.7867 (tm-30) REVERT: P 384 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7986 (pp20) REVERT: P 386 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8253 (tm-30) REVERT: P 387 TYR cc_start: 0.9082 (t80) cc_final: 0.8862 (t80) REVERT: P 404 TYR cc_start: 0.8101 (m-10) cc_final: 0.5413 (t80) REVERT: P 415 MET cc_start: 0.7666 (ttm) cc_final: 0.7308 (ttm) REVERT: P 422 ASP cc_start: 0.9080 (p0) cc_final: 0.8797 (p0) REVERT: P 464 LEU cc_start: 0.9371 (mp) cc_final: 0.8993 (mm) REVERT: Q 404 TYR cc_start: 0.8739 (m-10) cc_final: 0.5640 (t80) REVERT: Q 405 GLN cc_start: 0.8268 (pt0) cc_final: 0.7959 (pt0) REVERT: Q 415 MET cc_start: 0.7712 (ttm) cc_final: 0.7332 (ttm) REVERT: Q 421 ASP cc_start: 0.8575 (p0) cc_final: 0.7963 (p0) REVERT: Q 422 ASP cc_start: 0.8987 (p0) cc_final: 0.8699 (p0) REVERT: Q 427 TYR cc_start: 0.8854 (m-80) cc_final: 0.8488 (m-80) REVERT: Q 448 LEU cc_start: 0.8835 (mt) cc_final: 0.8634 (mt) REVERT: Q 450 MET cc_start: 0.8764 (ppp) cc_final: 0.7462 (ttt) REVERT: Q 452 ASP cc_start: 0.8112 (p0) cc_final: 0.7880 (p0) REVERT: Q 459 MET cc_start: 0.7861 (mtp) cc_final: 0.7448 (mtp) REVERT: R 386 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7598 (pp30) REVERT: R 389 HIS cc_start: 0.7069 (t-90) cc_final: 0.6740 (t70) REVERT: R 421 ASP cc_start: 0.8255 (p0) cc_final: 0.8029 (p0) REVERT: R 452 ASP cc_start: 0.7268 (p0) cc_final: 0.7054 (p0) REVERT: S 364 ASN cc_start: 0.8042 (t0) cc_final: 0.7599 (t0) REVERT: S 383 LEU cc_start: 0.7436 (tm) cc_final: 0.7188 (mt) REVERT: S 404 TYR cc_start: 0.7946 (m-10) cc_final: 0.5924 (t80) REVERT: S 422 ASP cc_start: 0.8863 (p0) cc_final: 0.8514 (p0) REVERT: S 452 ASP cc_start: 0.8098 (p0) cc_final: 0.7785 (p0) REVERT: T 364 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8152 (t0) REVERT: T 379 GLN cc_start: 0.8468 (tt0) cc_final: 0.7511 (tm-30) REVERT: T 404 TYR cc_start: 0.7934 (m-10) cc_final: 0.5855 (t80) REVERT: T 405 GLN cc_start: 0.8679 (pt0) cc_final: 0.8156 (pt0) REVERT: T 456 ASP cc_start: 0.8760 (t0) cc_final: 0.8460 (t0) REVERT: U 367 LYS cc_start: 0.8743 (ptmt) cc_final: 0.8479 (pttm) REVERT: U 379 GLN cc_start: 0.9055 (tt0) cc_final: 0.8200 (tm-30) REVERT: U 404 TYR cc_start: 0.7957 (m-10) cc_final: 0.5267 (t80) REVERT: U 415 MET cc_start: 0.8025 (ttm) cc_final: 0.7617 (ttm) REVERT: U 427 TYR cc_start: 0.8985 (m-80) cc_final: 0.8668 (m-80) REVERT: U 450 MET cc_start: 0.7554 (ttp) cc_final: 0.6531 (ptp) REVERT: U 456 ASP cc_start: 0.8903 (t0) cc_final: 0.8620 (t0) REVERT: V 384 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7170 (tm-30) REVERT: V 417 SER cc_start: 0.9106 (t) cc_final: 0.8716 (t) REVERT: V 450 MET cc_start: 0.6922 (ttp) cc_final: 0.5631 (ptp) REVERT: V 452 ASP cc_start: 0.8100 (p0) cc_final: 0.7712 (m-30) REVERT: W 379 GLN cc_start: 0.8863 (tt0) cc_final: 0.8195 (tm-30) REVERT: W 386 GLN cc_start: 0.9143 (tm-30) cc_final: 0.8645 (tm-30) REVERT: W 402 ASN cc_start: 0.8506 (t0) cc_final: 0.7885 (t0) REVERT: W 450 MET cc_start: 0.7449 (ttp) cc_final: 0.6787 (ptp) REVERT: X 355 MET cc_start: 0.8269 (mmp) cc_final: 0.7154 (tpt) REVERT: X 360 GLU cc_start: 0.8134 (pp20) cc_final: 0.7636 (pp20) REVERT: X 384 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7011 (tm-30) REVERT: X 386 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8948 (tm-30) REVERT: X 404 TYR cc_start: 0.7957 (m-10) cc_final: 0.6064 (t80) REVERT: X 414 ILE cc_start: 0.9217 (tp) cc_final: 0.8946 (tp) REVERT: X 418 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6739 (mp0) REVERT: X 421 ASP cc_start: 0.8523 (p0) cc_final: 0.8073 (p0) REVERT: X 427 TYR cc_start: 0.8701 (m-80) cc_final: 0.8451 (m-80) REVERT: X 436 GLN cc_start: 0.9239 (tp40) cc_final: 0.9030 (tp40) REVERT: X 450 MET cc_start: 0.7709 (ttp) cc_final: 0.5966 (ptp) REVERT: X 459 MET cc_start: 0.8532 (mtp) cc_final: 0.8195 (ttm) REVERT: Y 367 LYS cc_start: 0.8533 (ptmt) cc_final: 0.8299 (pttm) REVERT: Y 372 LYS cc_start: 0.9107 (pptt) cc_final: 0.8902 (mmmt) REVERT: Y 379 GLN cc_start: 0.8934 (tt0) cc_final: 0.8425 (tm-30) REVERT: Y 404 TYR cc_start: 0.7903 (m-10) cc_final: 0.5091 (t80) REVERT: Y 415 MET cc_start: 0.7790 (ttm) cc_final: 0.7405 (ttm) REVERT: Y 418 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6356 (mm-30) REVERT: Y 421 ASP cc_start: 0.8638 (p0) cc_final: 0.8394 (p0) REVERT: Y 456 ASP cc_start: 0.8718 (t0) cc_final: 0.8483 (t0) REVERT: Z 367 LYS cc_start: 0.8798 (ptmt) cc_final: 0.8215 (pttm) REVERT: Z 372 LYS cc_start: 0.9064 (pptt) cc_final: 0.8770 (pttm) REVERT: Z 379 GLN cc_start: 0.8848 (tt0) cc_final: 0.8466 (tm-30) REVERT: Z 404 TYR cc_start: 0.8268 (m-10) cc_final: 0.5867 (t80) REVERT: Z 405 GLN cc_start: 0.8593 (pt0) cc_final: 0.8237 (pt0) REVERT: Z 450 MET cc_start: 0.7687 (ttp) cc_final: 0.6870 (ptp) REVERT: Z 456 ASP cc_start: 0.8634 (t0) cc_final: 0.8332 (t0) REVERT: a 355 MET cc_start: 0.8217 (mmp) cc_final: 0.7886 (tpt) REVERT: a 371 GLU cc_start: 0.8646 (tp30) cc_final: 0.8405 (tp30) REVERT: a 417 SER cc_start: 0.8643 (t) cc_final: 0.8196 (t) REVERT: a 432 ASN cc_start: 0.9143 (p0) cc_final: 0.8939 (p0) REVERT: a 449 SER cc_start: 0.9235 (t) cc_final: 0.8721 (m) REVERT: a 450 MET cc_start: 0.6950 (ttp) cc_final: 0.6465 (ptp) outliers start: 85 outliers final: 56 residues processed: 740 average time/residue: 0.2876 time to fit residues: 317.9989 Evaluate side-chains 702 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 644 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 354 VAL Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 424 THR Chi-restraints excluded: chain O residue 364 ASN Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain P residue 354 VAL Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 386 GLN Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 464 LEU Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 509 LEU Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain S residue 354 VAL Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain T residue 354 VAL Chi-restraints excluded: chain T residue 358 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 354 VAL Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 358 SER Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 424 THR Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain W residue 364 ASN Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain X residue 364 ASN Chi-restraints excluded: chain X residue 424 THR Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 484 LEU Chi-restraints excluded: chain Y residue 354 VAL Chi-restraints excluded: chain Y residue 358 SER Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 449 SER Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Z residue 354 VAL Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 388 VAL Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain a residue 354 VAL Chi-restraints excluded: chain a residue 364 ASN Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 169 optimal weight: 0.7980 chunk 138 optimal weight: 0.0050 chunk 56 optimal weight: 0.2980 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 202 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 500 ASN O 432 ASN P 461 ASN R 389 HIS T 364 ASN U 500 ASN V 443 GLN V 470 ASN W 500 ASN X 373 GLN Y 461 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18942 Z= 0.166 Angle : 0.652 8.706 25536 Z= 0.328 Chirality : 0.046 0.177 2744 Planarity : 0.005 0.040 3304 Dihedral : 5.414 45.612 2496 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 3.92 % Allowed : 16.37 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.15), residues: 2240 helix: -0.01 (0.20), residues: 574 sheet: -1.85 (0.19), residues: 462 loop : -3.22 (0.14), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 466 HIS 0.005 0.001 HIS T 389 PHE 0.030 0.001 PHE R 420 TYR 0.019 0.001 TYR X 506 ARG 0.006 0.001 ARG X 468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 694 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9056 (tt0) cc_final: 0.8486 (tm-30) REVERT: N 404 TYR cc_start: 0.8024 (m-10) cc_final: 0.5055 (t80) REVERT: N 405 GLN cc_start: 0.8539 (pt0) cc_final: 0.8184 (pt0) REVERT: N 415 MET cc_start: 0.8071 (ttm) cc_final: 0.7531 (ttm) REVERT: N 418 GLU cc_start: 0.6854 (mp0) cc_final: 0.6609 (mp0) REVERT: N 450 MET cc_start: 0.7536 (ttp) cc_final: 0.6195 (ptp) REVERT: O 373 GLN cc_start: 0.8723 (tp-100) cc_final: 0.8409 (tp-100) REVERT: O 379 GLN cc_start: 0.8799 (tt0) cc_final: 0.8322 (tm-30) REVERT: O 386 GLN cc_start: 0.9274 (tm-30) cc_final: 0.8618 (tm-30) REVERT: O 404 TYR cc_start: 0.8019 (m-10) cc_final: 0.5443 (t80) REVERT: O 415 MET cc_start: 0.7581 (ttm) cc_final: 0.7379 (ttm) REVERT: O 418 GLU cc_start: 0.6179 (mp0) cc_final: 0.5865 (mp0) REVERT: O 450 MET cc_start: 0.7696 (ttp) cc_final: 0.6710 (ptp) REVERT: O 509 LEU cc_start: 0.6733 (mm) cc_final: 0.6423 (mm) REVERT: P 364 ASN cc_start: 0.8566 (m-40) cc_final: 0.7612 (t0) REVERT: P 379 GLN cc_start: 0.8689 (tt0) cc_final: 0.7918 (tm-30) REVERT: P 384 GLU cc_start: 0.8274 (tm-30) cc_final: 0.8001 (pp20) REVERT: P 387 TYR cc_start: 0.9077 (t80) cc_final: 0.8777 (t80) REVERT: P 404 TYR cc_start: 0.8091 (m-10) cc_final: 0.5362 (t80) REVERT: P 415 MET cc_start: 0.7788 (ttm) cc_final: 0.7361 (ttm) REVERT: P 422 ASP cc_start: 0.9125 (p0) cc_final: 0.8629 (p0) REVERT: P 464 LEU cc_start: 0.9331 (mp) cc_final: 0.8948 (mt) REVERT: Q 403 TYR cc_start: 0.9084 (m-10) cc_final: 0.7932 (m-10) REVERT: Q 404 TYR cc_start: 0.8778 (m-10) cc_final: 0.5638 (t80) REVERT: Q 405 GLN cc_start: 0.8242 (pt0) cc_final: 0.7993 (pt0) REVERT: Q 415 MET cc_start: 0.7672 (ttm) cc_final: 0.7414 (ttm) REVERT: Q 421 ASP cc_start: 0.8603 (p0) cc_final: 0.7809 (p0) REVERT: Q 427 TYR cc_start: 0.8882 (m-80) cc_final: 0.8503 (m-80) REVERT: Q 448 LEU cc_start: 0.8963 (mt) cc_final: 0.8747 (mt) REVERT: Q 459 MET cc_start: 0.7962 (mtp) cc_final: 0.7619 (mtp) REVERT: R 386 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8072 (pp30) REVERT: R 389 HIS cc_start: 0.7549 (t70) cc_final: 0.7055 (t70) REVERT: R 415 MET cc_start: 0.8108 (ttm) cc_final: 0.7855 (ttm) REVERT: R 452 ASP cc_start: 0.7444 (p0) cc_final: 0.7207 (p0) REVERT: S 364 ASN cc_start: 0.7870 (t0) cc_final: 0.7493 (t0) REVERT: S 384 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8368 (tm-30) REVERT: S 404 TYR cc_start: 0.8012 (m-10) cc_final: 0.5885 (t80) REVERT: S 417 SER cc_start: 0.8450 (t) cc_final: 0.8205 (t) REVERT: S 422 ASP cc_start: 0.8923 (p0) cc_final: 0.8253 (p0) REVERT: S 436 GLN cc_start: 0.9356 (tp40) cc_final: 0.6410 (pm20) REVERT: S 452 ASP cc_start: 0.8071 (p0) cc_final: 0.7751 (p0) REVERT: T 364 ASN cc_start: 0.8244 (t0) cc_final: 0.8040 (t0) REVERT: T 379 GLN cc_start: 0.8389 (tt0) cc_final: 0.7347 (pp30) REVERT: T 384 GLU cc_start: 0.8483 (tm-30) cc_final: 0.8184 (tm-30) REVERT: T 404 TYR cc_start: 0.7937 (m-10) cc_final: 0.5650 (t80) REVERT: T 405 GLN cc_start: 0.8543 (pt0) cc_final: 0.8102 (pt0) REVERT: T 456 ASP cc_start: 0.8685 (t0) cc_final: 0.8410 (t0) REVERT: U 367 LYS cc_start: 0.8886 (ptmt) cc_final: 0.8393 (pttm) REVERT: U 379 GLN cc_start: 0.9090 (tt0) cc_final: 0.8150 (tm-30) REVERT: U 384 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8033 (pp20) REVERT: U 404 TYR cc_start: 0.7965 (m-10) cc_final: 0.5075 (t80) REVERT: U 415 MET cc_start: 0.8079 (ttm) cc_final: 0.7658 (ttm) REVERT: U 450 MET cc_start: 0.7305 (ttp) cc_final: 0.6642 (ptp) REVERT: U 456 ASP cc_start: 0.8845 (t0) cc_final: 0.8618 (t0) REVERT: V 356 MET cc_start: 0.7803 (mmp) cc_final: 0.7021 (ptt) REVERT: V 384 GLU cc_start: 0.7585 (tm-30) cc_final: 0.6999 (tm-30) REVERT: V 386 GLN cc_start: 0.9191 (tm-30) cc_final: 0.8929 (tm-30) REVERT: V 387 TYR cc_start: 0.9380 (t80) cc_final: 0.9172 (t80) REVERT: V 417 SER cc_start: 0.8590 (t) cc_final: 0.8303 (t) REVERT: V 450 MET cc_start: 0.6778 (ttp) cc_final: 0.5364 (ptp) REVERT: W 377 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8512 (pp) REVERT: W 379 GLN cc_start: 0.8958 (tt0) cc_final: 0.8170 (tm-30) REVERT: W 384 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7882 (tm-30) REVERT: W 386 GLN cc_start: 0.9179 (tm-30) cc_final: 0.8511 (tm-30) REVERT: W 410 ARG cc_start: 0.8444 (ptp-110) cc_final: 0.8111 (ptp90) REVERT: W 450 MET cc_start: 0.6925 (ttp) cc_final: 0.6606 (ptp) REVERT: W 485 VAL cc_start: 0.9223 (OUTLIER) cc_final: 0.8999 (p) REVERT: X 355 MET cc_start: 0.8211 (mmp) cc_final: 0.8009 (mmm) REVERT: X 361 GLN cc_start: 0.8689 (tt0) cc_final: 0.7853 (tm-30) REVERT: X 384 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7191 (tm-30) REVERT: X 386 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8915 (tm-30) REVERT: X 404 TYR cc_start: 0.7755 (m-10) cc_final: 0.5712 (t80) REVERT: X 417 SER cc_start: 0.8802 (t) cc_final: 0.8406 (t) REVERT: X 418 GLU cc_start: 0.6772 (mm-30) cc_final: 0.6515 (mm-30) REVERT: X 421 ASP cc_start: 0.8451 (p0) cc_final: 0.7853 (p0) REVERT: X 427 TYR cc_start: 0.8720 (m-80) cc_final: 0.8481 (m-80) REVERT: X 450 MET cc_start: 0.7722 (ttp) cc_final: 0.5992 (ptp) REVERT: Y 367 LYS cc_start: 0.8531 (ptmt) cc_final: 0.8140 (pttt) REVERT: Y 372 LYS cc_start: 0.9112 (pptt) cc_final: 0.8898 (mmmt) REVERT: Y 379 GLN cc_start: 0.8991 (tt0) cc_final: 0.8384 (tm-30) REVERT: Y 384 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7484 (tm-30) REVERT: Y 386 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: Y 404 TYR cc_start: 0.7783 (m-10) cc_final: 0.5031 (t80) REVERT: Y 421 ASP cc_start: 0.8619 (p0) cc_final: 0.8363 (p0) REVERT: Y 422 ASP cc_start: 0.8833 (p0) cc_final: 0.8583 (p0) REVERT: Y 441 VAL cc_start: 0.9559 (t) cc_final: 0.9194 (p) REVERT: Z 367 LYS cc_start: 0.8819 (ptmt) cc_final: 0.8463 (pttm) REVERT: Z 372 LYS cc_start: 0.9041 (pptt) cc_final: 0.8730 (pttm) REVERT: Z 379 GLN cc_start: 0.8916 (tt0) cc_final: 0.8423 (pp30) REVERT: Z 384 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8174 (tm-30) REVERT: Z 404 TYR cc_start: 0.8145 (m-10) cc_final: 0.5451 (t80) REVERT: Z 450 MET cc_start: 0.7502 (ttp) cc_final: 0.6706 (ptp) REVERT: a 355 MET cc_start: 0.8155 (mmp) cc_final: 0.7857 (tpt) REVERT: a 383 LEU cc_start: 0.9029 (tm) cc_final: 0.8682 (tt) REVERT: a 418 GLU cc_start: 0.7174 (mp0) cc_final: 0.6893 (mp0) REVERT: a 449 SER cc_start: 0.9173 (t) cc_final: 0.8661 (m) REVERT: a 450 MET cc_start: 0.6832 (ttp) cc_final: 0.6336 (ptp) REVERT: a 452 ASP cc_start: 0.8340 (p0) cc_final: 0.6610 (m-30) outliers start: 79 outliers final: 50 residues processed: 720 average time/residue: 0.2856 time to fit residues: 307.3458 Evaluate side-chains 699 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 646 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 464 LEU Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain R residue 441 VAL Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain T residue 424 THR Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 358 SER Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 424 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 449 SER Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 364 ASN Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 421 ASP Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 497 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 204 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 106 optimal weight: 0.0020 chunk 193 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 overall best weight: 0.8790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN O 361 GLN S 470 ASN V 470 ASN ** W 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN X 413 HIS Y 373 GLN a 500 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18942 Z= 0.190 Angle : 0.638 9.601 25536 Z= 0.323 Chirality : 0.045 0.155 2744 Planarity : 0.005 0.035 3304 Dihedral : 5.118 18.822 2492 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 4.61 % Allowed : 18.25 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.16), residues: 2240 helix: 0.64 (0.21), residues: 574 sheet: -1.37 (0.19), residues: 462 loop : -3.11 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP V 466 HIS 0.004 0.001 HIS T 389 PHE 0.032 0.001 PHE R 420 TYR 0.014 0.001 TYR N 506 ARG 0.008 0.001 ARG V 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 674 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 371 GLU cc_start: 0.8718 (tp30) cc_final: 0.8419 (tp30) REVERT: N 379 GLN cc_start: 0.9081 (tt0) cc_final: 0.8468 (tm-30) REVERT: N 404 TYR cc_start: 0.8010 (m-10) cc_final: 0.4871 (t80) REVERT: N 405 GLN cc_start: 0.8517 (pt0) cc_final: 0.8168 (pt0) REVERT: N 415 MET cc_start: 0.8032 (ttm) cc_final: 0.7455 (ttm) REVERT: N 418 GLU cc_start: 0.6476 (mp0) cc_final: 0.6252 (mp0) REVERT: N 450 MET cc_start: 0.7532 (ttp) cc_final: 0.6123 (ptp) REVERT: O 373 GLN cc_start: 0.8690 (tp-100) cc_final: 0.8421 (tp-100) REVERT: O 379 GLN cc_start: 0.8857 (tt0) cc_final: 0.8303 (tm-30) REVERT: O 384 GLU cc_start: 0.8219 (tm-30) cc_final: 0.7947 (tm-30) REVERT: O 386 GLN cc_start: 0.9299 (tm-30) cc_final: 0.8508 (tm-30) REVERT: O 404 TYR cc_start: 0.8077 (m-10) cc_final: 0.5417 (t80) REVERT: O 415 MET cc_start: 0.7713 (ttm) cc_final: 0.7494 (ttm) REVERT: O 418 GLU cc_start: 0.6211 (mp0) cc_final: 0.5978 (mp0) REVERT: O 422 ASP cc_start: 0.8732 (p0) cc_final: 0.8449 (p0) REVERT: O 450 MET cc_start: 0.7768 (ttp) cc_final: 0.6634 (ptp) REVERT: O 509 LEU cc_start: 0.6781 (mm) cc_final: 0.6468 (mm) REVERT: P 358 SER cc_start: 0.8365 (OUTLIER) cc_final: 0.7945 (t) REVERT: P 364 ASN cc_start: 0.8616 (m-40) cc_final: 0.7622 (t0) REVERT: P 379 GLN cc_start: 0.8794 (tt0) cc_final: 0.7942 (tm-30) REVERT: P 384 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7774 (tm-30) REVERT: P 387 TYR cc_start: 0.9205 (t80) cc_final: 0.8803 (t80) REVERT: P 404 TYR cc_start: 0.8065 (m-10) cc_final: 0.5218 (t80) REVERT: P 415 MET cc_start: 0.7782 (ttm) cc_final: 0.7523 (ttm) REVERT: P 422 ASP cc_start: 0.9173 (p0) cc_final: 0.8585 (p0) REVERT: P 464 LEU cc_start: 0.9304 (mp) cc_final: 0.8895 (mt) REVERT: Q 405 GLN cc_start: 0.8094 (pt0) cc_final: 0.7865 (pt0) REVERT: Q 415 MET cc_start: 0.7768 (ttm) cc_final: 0.7491 (ttm) REVERT: Q 421 ASP cc_start: 0.8507 (p0) cc_final: 0.8001 (p0) REVERT: Q 427 TYR cc_start: 0.8907 (m-80) cc_final: 0.8536 (m-80) REVERT: Q 459 MET cc_start: 0.8071 (mtp) cc_final: 0.7656 (mtp) REVERT: R 386 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8322 (pp30) REVERT: R 418 GLU cc_start: 0.5587 (mp0) cc_final: 0.5370 (mp0) REVERT: R 452 ASP cc_start: 0.7737 (p0) cc_final: 0.7468 (p0) REVERT: R 497 LEU cc_start: 0.7631 (mp) cc_final: 0.7345 (mt) REVERT: S 364 ASN cc_start: 0.7974 (t0) cc_final: 0.7662 (t0) REVERT: S 384 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8380 (tm-30) REVERT: S 404 TYR cc_start: 0.8095 (m-10) cc_final: 0.5849 (t80) REVERT: S 417 SER cc_start: 0.8393 (t) cc_final: 0.8126 (t) REVERT: S 418 GLU cc_start: 0.6979 (mp0) cc_final: 0.6577 (mm-30) REVERT: S 422 ASP cc_start: 0.8980 (p0) cc_final: 0.8472 (p0) REVERT: S 436 GLN cc_start: 0.9399 (tp40) cc_final: 0.6343 (pm20) REVERT: S 452 ASP cc_start: 0.8101 (p0) cc_final: 0.7797 (p0) REVERT: T 364 ASN cc_start: 0.8296 (t0) cc_final: 0.8089 (t0) REVERT: T 379 GLN cc_start: 0.8332 (tt0) cc_final: 0.7467 (pp30) REVERT: T 404 TYR cc_start: 0.8072 (m-10) cc_final: 0.5614 (t80) REVERT: T 405 GLN cc_start: 0.8891 (pt0) cc_final: 0.8248 (pt0) REVERT: T 417 SER cc_start: 0.8259 (t) cc_final: 0.7900 (t) REVERT: T 418 GLU cc_start: 0.7009 (mp0) cc_final: 0.6773 (mp0) REVERT: T 456 ASP cc_start: 0.8675 (t0) cc_final: 0.8444 (t0) REVERT: U 367 LYS cc_start: 0.8830 (ptmt) cc_final: 0.8526 (pttm) REVERT: U 379 GLN cc_start: 0.9118 (tt0) cc_final: 0.8163 (tm-30) REVERT: U 404 TYR cc_start: 0.8041 (m-10) cc_final: 0.5033 (t80) REVERT: U 415 MET cc_start: 0.7985 (ttm) cc_final: 0.7590 (ttm) REVERT: U 418 GLU cc_start: 0.6924 (mp0) cc_final: 0.6653 (mp0) REVERT: U 421 ASP cc_start: 0.8404 (p0) cc_final: 0.8075 (p0) REVERT: U 450 MET cc_start: 0.7229 (ttp) cc_final: 0.6561 (ptp) REVERT: U 456 ASP cc_start: 0.8836 (t0) cc_final: 0.8634 (t0) REVERT: V 384 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7139 (tm-30) REVERT: V 386 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8930 (tm-30) REVERT: V 450 MET cc_start: 0.6856 (ttp) cc_final: 0.5344 (ptp) REVERT: V 503 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7251 (mp) REVERT: W 377 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8470 (pp) REVERT: W 379 GLN cc_start: 0.9020 (tt0) cc_final: 0.8167 (tm-30) REVERT: W 386 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8634 (tm-30) REVERT: W 450 MET cc_start: 0.7407 (ttp) cc_final: 0.6300 (ptp) REVERT: X 361 GLN cc_start: 0.8812 (tt0) cc_final: 0.7933 (tm-30) REVERT: X 384 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7048 (tm-30) REVERT: X 386 GLN cc_start: 0.9278 (tm-30) cc_final: 0.8952 (tm-30) REVERT: X 404 TYR cc_start: 0.7998 (m-10) cc_final: 0.5787 (t80) REVERT: X 417 SER cc_start: 0.8770 (t) cc_final: 0.8304 (t) REVERT: X 418 GLU cc_start: 0.6443 (mm-30) cc_final: 0.6135 (mm-30) REVERT: X 421 ASP cc_start: 0.8486 (p0) cc_final: 0.7915 (p0) REVERT: X 427 TYR cc_start: 0.8727 (m-80) cc_final: 0.8443 (m-80) REVERT: X 450 MET cc_start: 0.7887 (ttp) cc_final: 0.6040 (ptp) REVERT: X 503 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7225 (mp) REVERT: Y 367 LYS cc_start: 0.8632 (ptmt) cc_final: 0.8413 (pttm) REVERT: Y 372 LYS cc_start: 0.9144 (pptt) cc_final: 0.8826 (pttm) REVERT: Y 379 GLN cc_start: 0.8724 (tt0) cc_final: 0.8138 (tm-30) REVERT: Y 386 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8588 (tt0) REVERT: Y 404 TYR cc_start: 0.7923 (m-10) cc_final: 0.5951 (t80) REVERT: Y 421 ASP cc_start: 0.8569 (p0) cc_final: 0.8304 (p0) REVERT: Y 422 ASP cc_start: 0.8845 (p0) cc_final: 0.8594 (p0) REVERT: Y 485 VAL cc_start: 0.9265 (OUTLIER) cc_final: 0.9018 (p) REVERT: Z 367 LYS cc_start: 0.8942 (ptmt) cc_final: 0.8289 (pttm) REVERT: Z 372 LYS cc_start: 0.9051 (pptt) cc_final: 0.8760 (pttm) REVERT: Z 379 GLN cc_start: 0.8917 (tt0) cc_final: 0.8459 (pp30) REVERT: Z 386 GLN cc_start: 0.8948 (tp40) cc_final: 0.8684 (tm-30) REVERT: Z 404 TYR cc_start: 0.8143 (m-10) cc_final: 0.5425 (t80) REVERT: Z 450 MET cc_start: 0.7644 (ttp) cc_final: 0.6774 (ptp) REVERT: a 355 MET cc_start: 0.8190 (mmp) cc_final: 0.7872 (tpt) REVERT: a 371 GLU cc_start: 0.8658 (tp30) cc_final: 0.8447 (tp30) REVERT: a 375 ILE cc_start: 0.8851 (mm) cc_final: 0.8572 (mm) REVERT: a 383 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8693 (tt) REVERT: a 418 GLU cc_start: 0.6832 (mp0) cc_final: 0.6413 (mp0) REVERT: a 450 MET cc_start: 0.6816 (ttp) cc_final: 0.6364 (ptp) REVERT: a 456 ASP cc_start: 0.8811 (t0) cc_final: 0.8412 (t0) REVERT: a 503 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7326 (mp) outliers start: 93 outliers final: 70 residues processed: 716 average time/residue: 0.2827 time to fit residues: 303.0333 Evaluate side-chains 722 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 644 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 424 THR Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 449 SER Chi-restraints excluded: chain O residue 460 THR Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 424 THR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain R residue 383 LEU Chi-restraints excluded: chain R residue 441 VAL Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 439 ILE Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 424 THR Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain V residue 503 ILE Chi-restraints excluded: chain W residue 364 ASN Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 364 ASN Chi-restraints excluded: chain X residue 424 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain X residue 503 ILE Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 415 MET Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 415 MET Chi-restraints excluded: chain Z residue 421 ASP Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 449 SER Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 89 optimal weight: 0.0020 chunk 184 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 54 optimal weight: 0.0470 overall best weight: 0.4486 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 361 GLN R 389 HIS R 443 GLN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 413 HIS X 373 GLN Y 373 GLN Y 413 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18942 Z= 0.168 Angle : 0.642 9.954 25536 Z= 0.322 Chirality : 0.045 0.147 2744 Planarity : 0.004 0.035 3304 Dihedral : 4.864 19.073 2492 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 5.01 % Allowed : 19.64 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.16), residues: 2240 helix: 1.05 (0.21), residues: 574 sheet: -0.99 (0.20), residues: 462 loop : -3.03 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.003 0.000 HIS T 389 PHE 0.031 0.001 PHE R 420 TYR 0.017 0.001 TYR T 506 ARG 0.008 0.001 ARG V 369 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 789 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 688 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9084 (tt0) cc_final: 0.8469 (tm-30) REVERT: N 404 TYR cc_start: 0.8001 (m-10) cc_final: 0.4849 (t80) REVERT: N 405 GLN cc_start: 0.8434 (pt0) cc_final: 0.8043 (pt0) REVERT: N 414 ILE cc_start: 0.9528 (tp) cc_final: 0.9270 (tt) REVERT: N 415 MET cc_start: 0.8086 (ttm) cc_final: 0.7453 (ttm) REVERT: N 418 GLU cc_start: 0.6544 (mp0) cc_final: 0.6305 (mp0) REVERT: N 450 MET cc_start: 0.7367 (ttp) cc_final: 0.6272 (ptp) REVERT: N 503 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.7286 (mp) REVERT: O 373 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8484 (tp-100) REVERT: O 379 GLN cc_start: 0.8765 (tt0) cc_final: 0.8317 (tm-30) REVERT: O 386 GLN cc_start: 0.9320 (tm-30) cc_final: 0.8538 (tm-30) REVERT: O 404 TYR cc_start: 0.8056 (m-10) cc_final: 0.5909 (t80) REVERT: O 415 MET cc_start: 0.7804 (ttm) cc_final: 0.7585 (ttm) REVERT: O 422 ASP cc_start: 0.8777 (p0) cc_final: 0.8424 (p0) REVERT: O 450 MET cc_start: 0.7704 (ttp) cc_final: 0.6589 (ptp) REVERT: O 509 LEU cc_start: 0.6873 (mm) cc_final: 0.6651 (mm) REVERT: P 358 SER cc_start: 0.8438 (OUTLIER) cc_final: 0.7967 (t) REVERT: P 364 ASN cc_start: 0.8570 (m-40) cc_final: 0.7547 (t0) REVERT: P 379 GLN cc_start: 0.8784 (tt0) cc_final: 0.7860 (tm-30) REVERT: P 384 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7949 (pp20) REVERT: P 387 TYR cc_start: 0.9170 (t80) cc_final: 0.8692 (t80) REVERT: P 404 TYR cc_start: 0.7999 (m-10) cc_final: 0.5927 (t80) REVERT: P 415 MET cc_start: 0.7774 (ttm) cc_final: 0.7480 (ttm) REVERT: P 418 GLU cc_start: 0.6185 (mp0) cc_final: 0.5973 (mp0) REVERT: P 422 ASP cc_start: 0.9119 (p0) cc_final: 0.8574 (p0) REVERT: P 464 LEU cc_start: 0.9299 (mp) cc_final: 0.8883 (mt) REVERT: P 485 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9039 (p) REVERT: P 497 LEU cc_start: 0.7599 (mt) cc_final: 0.7362 (mt) REVERT: P 503 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7348 (mp) REVERT: Q 403 TYR cc_start: 0.9084 (m-10) cc_final: 0.8481 (m-10) REVERT: Q 415 MET cc_start: 0.7868 (ttm) cc_final: 0.7515 (ttm) REVERT: Q 421 ASP cc_start: 0.8485 (p0) cc_final: 0.7979 (p0) REVERT: Q 427 TYR cc_start: 0.8902 (m-80) cc_final: 0.8533 (m-80) REVERT: Q 459 MET cc_start: 0.8037 (mtp) cc_final: 0.7584 (mtp) REVERT: Q 503 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8111 (mp) REVERT: R 386 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8340 (pp30) REVERT: R 404 TYR cc_start: 0.8399 (m-80) cc_final: 0.8117 (m-80) REVERT: R 443 GLN cc_start: 0.8184 (tp-100) cc_final: 0.7865 (mm-40) REVERT: R 452 ASP cc_start: 0.7949 (p0) cc_final: 0.7716 (p0) REVERT: R 497 LEU cc_start: 0.7551 (mp) cc_final: 0.7220 (mt) REVERT: S 364 ASN cc_start: 0.8086 (t0) cc_final: 0.7801 (t0) REVERT: S 417 SER cc_start: 0.8408 (t) cc_final: 0.8041 (t) REVERT: S 418 GLU cc_start: 0.6910 (mp0) cc_final: 0.6492 (mm-30) REVERT: S 422 ASP cc_start: 0.8947 (p0) cc_final: 0.8518 (p0) REVERT: S 436 GLN cc_start: 0.9409 (tp40) cc_final: 0.6429 (pm20) REVERT: S 452 ASP cc_start: 0.8037 (p0) cc_final: 0.7721 (p0) REVERT: T 367 LYS cc_start: 0.8603 (ptmt) cc_final: 0.8099 (pttm) REVERT: T 379 GLN cc_start: 0.8413 (tt0) cc_final: 0.7538 (pp30) REVERT: T 404 TYR cc_start: 0.8094 (m-10) cc_final: 0.5603 (t80) REVERT: T 405 GLN cc_start: 0.8829 (pt0) cc_final: 0.8188 (pt0) REVERT: T 418 GLU cc_start: 0.6983 (mp0) cc_final: 0.6748 (mp0) REVERT: T 432 ASN cc_start: 0.8626 (p0) cc_final: 0.8264 (p0) REVERT: T 456 ASP cc_start: 0.8584 (t0) cc_final: 0.8307 (t0) REVERT: U 365 LYS cc_start: 0.8598 (ptpp) cc_final: 0.8293 (ptpt) REVERT: U 367 LYS cc_start: 0.8828 (ptmt) cc_final: 0.8573 (pttm) REVERT: U 379 GLN cc_start: 0.9054 (tt0) cc_final: 0.8112 (tm-30) REVERT: U 404 TYR cc_start: 0.8033 (m-10) cc_final: 0.5016 (t80) REVERT: U 415 MET cc_start: 0.8092 (ttm) cc_final: 0.7842 (ttm) REVERT: U 418 GLU cc_start: 0.6993 (mp0) cc_final: 0.6566 (mp0) REVERT: U 421 ASP cc_start: 0.8448 (p0) cc_final: 0.7964 (p0) REVERT: U 450 MET cc_start: 0.7296 (ttp) cc_final: 0.6700 (ptp) REVERT: U 503 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.7460 (mp) REVERT: V 355 MET cc_start: 0.8054 (mmp) cc_final: 0.7346 (tpt) REVERT: V 361 GLN cc_start: 0.7929 (pp30) cc_final: 0.7637 (tm-30) REVERT: V 377 LEU cc_start: 0.8594 (tp) cc_final: 0.8052 (pp) REVERT: V 384 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7137 (tm-30) REVERT: V 386 GLN cc_start: 0.9264 (tm-30) cc_final: 0.8997 (tm-30) REVERT: V 450 MET cc_start: 0.6813 (ttp) cc_final: 0.5308 (ptp) REVERT: W 371 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8419 (mm-30) REVERT: W 377 LEU cc_start: 0.8957 (tt) cc_final: 0.8505 (pp) REVERT: W 379 GLN cc_start: 0.8998 (tt0) cc_final: 0.8228 (tm-30) REVERT: W 450 MET cc_start: 0.6953 (ttp) cc_final: 0.6190 (ptp) REVERT: W 485 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8954 (p) REVERT: X 355 MET cc_start: 0.8260 (mmp) cc_final: 0.7931 (mmm) REVERT: X 361 GLN cc_start: 0.8847 (tt0) cc_final: 0.7935 (tm-30) REVERT: X 384 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7564 (tm-30) REVERT: X 386 GLN cc_start: 0.9244 (tm-30) cc_final: 0.8871 (tm-30) REVERT: X 404 TYR cc_start: 0.7342 (m-10) cc_final: 0.5303 (t80) REVERT: X 417 SER cc_start: 0.8725 (t) cc_final: 0.8267 (t) REVERT: X 418 GLU cc_start: 0.6454 (mm-30) cc_final: 0.6151 (mm-30) REVERT: X 421 ASP cc_start: 0.8537 (p0) cc_final: 0.8052 (p0) REVERT: X 427 TYR cc_start: 0.8671 (m-80) cc_final: 0.8470 (m-80) REVERT: X 450 MET cc_start: 0.7860 (ttp) cc_final: 0.6179 (ptp) REVERT: X 456 ASP cc_start: 0.9039 (t0) cc_final: 0.8700 (t0) REVERT: Y 372 LYS cc_start: 0.9079 (pptt) cc_final: 0.8836 (pttm) REVERT: Y 379 GLN cc_start: 0.8669 (tt0) cc_final: 0.8016 (tm-30) REVERT: Y 386 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: Y 404 TYR cc_start: 0.7429 (m-10) cc_final: 0.6014 (t80) REVERT: Y 421 ASP cc_start: 0.8530 (p0) cc_final: 0.8284 (p0) REVERT: Y 422 ASP cc_start: 0.8851 (p0) cc_final: 0.8552 (p0) REVERT: Y 485 VAL cc_start: 0.9254 (OUTLIER) cc_final: 0.8952 (p) REVERT: Y 503 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7160 (mp) REVERT: Z 358 SER cc_start: 0.7645 (m) cc_final: 0.7228 (p) REVERT: Z 372 LYS cc_start: 0.9054 (pptt) cc_final: 0.8784 (pttm) REVERT: Z 379 GLN cc_start: 0.8931 (tt0) cc_final: 0.8483 (pp30) REVERT: Z 404 TYR cc_start: 0.8100 (m-10) cc_final: 0.6030 (t80) REVERT: Z 450 MET cc_start: 0.7586 (ttp) cc_final: 0.6706 (ptp) REVERT: a 355 MET cc_start: 0.8173 (mmp) cc_final: 0.7874 (tpt) REVERT: a 371 GLU cc_start: 0.8731 (tp30) cc_final: 0.8362 (tp30) REVERT: a 375 ILE cc_start: 0.8851 (mm) cc_final: 0.8553 (mm) REVERT: a 383 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8673 (tt) REVERT: a 418 GLU cc_start: 0.6848 (mp0) cc_final: 0.6432 (mp0) REVERT: a 450 MET cc_start: 0.6669 (ttp) cc_final: 0.6214 (ptp) REVERT: a 459 MET cc_start: 0.8265 (ptm) cc_final: 0.7990 (ptm) REVERT: a 503 ILE cc_start: 0.8197 (OUTLIER) cc_final: 0.7320 (mp) outliers start: 101 outliers final: 67 residues processed: 741 average time/residue: 0.2915 time to fit residues: 322.5564 Evaluate side-chains 734 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 655 time to evaluate : 2.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 449 SER Chi-restraints excluded: chain O residue 484 LEU Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 485 VAL Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain Q residue 503 ILE Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 421 ASP Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 370 GLU Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 364 ASN Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 415 MET Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 179 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN Q 500 ASN R 389 HIS S 470 ASN S 500 ASN T 413 HIS T 461 ASN T 500 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 500 ASN X 373 GLN Y 373 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18942 Z= 0.197 Angle : 0.655 10.312 25536 Z= 0.330 Chirality : 0.045 0.147 2744 Planarity : 0.004 0.031 3304 Dihedral : 4.867 18.854 2492 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 5.31 % Allowed : 20.29 % Favored : 74.40 % 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: -1.90 (0.16), residues: 2240 helix: 1.28 (0.21), residues: 574 sheet: -0.67 (0.20), residues: 462 loop : -2.97 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.003 0.000 HIS T 389 PHE 0.027 0.001 PHE R 420 TYR 0.014 0.001 TYR N 506 ARG 0.008 0.001 ARG X 369 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 665 time to evaluate : 2.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9127 (tt0) cc_final: 0.8465 (tm-30) REVERT: N 404 TYR cc_start: 0.7474 (m-10) cc_final: 0.5218 (t80) REVERT: N 405 GLN cc_start: 0.8414 (pt0) cc_final: 0.8117 (pt0) REVERT: N 415 MET cc_start: 0.7999 (ttm) cc_final: 0.7385 (ttm) REVERT: N 418 GLU cc_start: 0.6622 (mp0) cc_final: 0.6246 (mp0) REVERT: N 450 MET cc_start: 0.7605 (ttp) cc_final: 0.6081 (ptp) REVERT: N 503 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.7365 (mp) REVERT: O 373 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8513 (tp-100) REVERT: O 379 GLN cc_start: 0.8805 (tt0) cc_final: 0.8070 (pp30) REVERT: O 386 GLN cc_start: 0.9289 (tm-30) cc_final: 0.8959 (tm-30) REVERT: O 404 TYR cc_start: 0.7140 (m-10) cc_final: 0.6100 (t80) REVERT: O 422 ASP cc_start: 0.8856 (p0) cc_final: 0.8494 (p0) REVERT: O 450 MET cc_start: 0.7760 (ttp) cc_final: 0.6544 (ptp) REVERT: P 358 SER cc_start: 0.8492 (OUTLIER) cc_final: 0.8112 (t) REVERT: P 364 ASN cc_start: 0.8504 (m-40) cc_final: 0.7467 (t0) REVERT: P 379 GLN cc_start: 0.8751 (tt0) cc_final: 0.7884 (tm-30) REVERT: P 384 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7987 (pp20) REVERT: P 387 TYR cc_start: 0.9176 (t80) cc_final: 0.8692 (t80) REVERT: P 404 TYR cc_start: 0.7495 (m-10) cc_final: 0.5881 (t80) REVERT: P 415 MET cc_start: 0.7731 (ttm) cc_final: 0.7459 (ttm) REVERT: P 422 ASP cc_start: 0.9126 (p0) cc_final: 0.8540 (p0) REVERT: P 464 LEU cc_start: 0.9266 (mp) cc_final: 0.8877 (mt) REVERT: P 485 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8999 (p) REVERT: P 497 LEU cc_start: 0.7968 (mt) cc_final: 0.7630 (mt) REVERT: P 503 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.7345 (mp) REVERT: Q 403 TYR cc_start: 0.9152 (m-10) cc_final: 0.8454 (m-10) REVERT: Q 421 ASP cc_start: 0.8517 (p0) cc_final: 0.7991 (p0) REVERT: Q 427 TYR cc_start: 0.8996 (m-80) cc_final: 0.8686 (m-80) REVERT: Q 459 MET cc_start: 0.8103 (mtp) cc_final: 0.7670 (mtp) REVERT: R 363 ILE cc_start: 0.6228 (mm) cc_final: 0.5684 (tp) REVERT: R 384 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8178 (tm-30) REVERT: R 386 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8527 (pp30) REVERT: R 443 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7931 (mm-40) REVERT: R 497 LEU cc_start: 0.7712 (mp) cc_final: 0.7366 (mt) REVERT: S 364 ASN cc_start: 0.8068 (t0) cc_final: 0.7774 (t0) REVERT: S 372 LYS cc_start: 0.8393 (pptt) cc_final: 0.7887 (mtpt) REVERT: S 417 SER cc_start: 0.8694 (t) cc_final: 0.8157 (t) REVERT: S 418 GLU cc_start: 0.6960 (mp0) cc_final: 0.6517 (mm-30) REVERT: S 422 ASP cc_start: 0.8907 (p0) cc_final: 0.8500 (p0) REVERT: S 436 GLN cc_start: 0.9448 (tp40) cc_final: 0.6425 (pm20) REVERT: S 452 ASP cc_start: 0.8034 (p0) cc_final: 0.7734 (p0) REVERT: T 367 LYS cc_start: 0.8657 (ptmt) cc_final: 0.8028 (pttm) REVERT: T 379 GLN cc_start: 0.8520 (tt0) cc_final: 0.7727 (pp30) REVERT: T 404 TYR cc_start: 0.8118 (m-10) cc_final: 0.5660 (t80) REVERT: T 405 GLN cc_start: 0.8809 (pt0) cc_final: 0.8215 (pt0) REVERT: T 456 ASP cc_start: 0.8591 (t0) cc_final: 0.8319 (t0) REVERT: U 365 LYS cc_start: 0.8592 (ptpp) cc_final: 0.8263 (ptpt) REVERT: U 379 GLN cc_start: 0.9072 (tt0) cc_final: 0.8131 (tm-30) REVERT: U 384 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8223 (pp20) REVERT: U 404 TYR cc_start: 0.8009 (m-10) cc_final: 0.5562 (t80) REVERT: U 415 MET cc_start: 0.8098 (ttm) cc_final: 0.7839 (ttm) REVERT: U 418 GLU cc_start: 0.6130 (mp0) cc_final: 0.5628 (mp0) REVERT: U 421 ASP cc_start: 0.8584 (p0) cc_final: 0.7901 (p0) REVERT: U 422 ASP cc_start: 0.9263 (p0) cc_final: 0.8963 (p0) REVERT: U 450 MET cc_start: 0.7660 (ttp) cc_final: 0.7233 (ptp) REVERT: V 355 MET cc_start: 0.8094 (mmp) cc_final: 0.7433 (tpt) REVERT: V 356 MET cc_start: 0.7743 (mmp) cc_final: 0.7309 (ptt) REVERT: V 361 GLN cc_start: 0.8032 (pp30) cc_final: 0.7738 (tm-30) REVERT: V 384 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7203 (tm-30) REVERT: V 386 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8870 (tm-30) REVERT: V 450 MET cc_start: 0.6914 (ttp) cc_final: 0.5343 (ptp) REVERT: W 377 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8474 (pp) REVERT: W 379 GLN cc_start: 0.9027 (tt0) cc_final: 0.8236 (tm-30) REVERT: W 450 MET cc_start: 0.7369 (ttp) cc_final: 0.6212 (ptp) REVERT: X 355 MET cc_start: 0.8213 (mmp) cc_final: 0.7872 (mmm) REVERT: X 361 GLN cc_start: 0.8945 (tt0) cc_final: 0.7994 (tm-30) REVERT: X 384 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7617 (tm-30) REVERT: X 386 GLN cc_start: 0.9281 (tm-30) cc_final: 0.8869 (tm-30) REVERT: X 404 TYR cc_start: 0.7340 (OUTLIER) cc_final: 0.5197 (t80) REVERT: X 417 SER cc_start: 0.8752 (t) cc_final: 0.8245 (t) REVERT: X 418 GLU cc_start: 0.6368 (mm-30) cc_final: 0.6034 (mm-30) REVERT: X 421 ASP cc_start: 0.8572 (p0) cc_final: 0.8115 (p0) REVERT: X 427 TYR cc_start: 0.8707 (m-80) cc_final: 0.8453 (m-80) REVERT: X 450 MET cc_start: 0.8053 (ttp) cc_final: 0.6265 (ptp) REVERT: Y 371 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8432 (tp30) REVERT: Y 379 GLN cc_start: 0.8713 (tt0) cc_final: 0.7999 (tm-30) REVERT: Y 384 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7615 (tm-30) REVERT: Y 386 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8660 (tt0) REVERT: Y 404 TYR cc_start: 0.6680 (m-10) cc_final: 0.5510 (t80) REVERT: Y 421 ASP cc_start: 0.8676 (p0) cc_final: 0.8446 (p0) REVERT: Y 422 ASP cc_start: 0.8861 (p0) cc_final: 0.8554 (p0) REVERT: Y 503 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7222 (mp) REVERT: Z 358 SER cc_start: 0.7561 (OUTLIER) cc_final: 0.6358 (p) REVERT: Z 372 LYS cc_start: 0.9072 (pptt) cc_final: 0.8815 (pttm) REVERT: Z 379 GLN cc_start: 0.8982 (tt0) cc_final: 0.8459 (pp30) REVERT: Z 404 TYR cc_start: 0.7196 (m-10) cc_final: 0.5522 (t80) REVERT: Z 450 MET cc_start: 0.7571 (ttp) cc_final: 0.6551 (ptp) REVERT: a 355 MET cc_start: 0.8205 (mmp) cc_final: 0.7886 (tpt) REVERT: a 371 GLU cc_start: 0.8574 (tp30) cc_final: 0.8299 (tp30) REVERT: a 383 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8661 (tt) REVERT: a 418 GLU cc_start: 0.6839 (mp0) cc_final: 0.6438 (mp0) REVERT: a 450 MET cc_start: 0.6831 (ttp) cc_final: 0.6317 (ptp) REVERT: a 459 MET cc_start: 0.8616 (ptm) cc_final: 0.8295 (ptm) REVERT: a 503 ILE cc_start: 0.8092 (OUTLIER) cc_final: 0.7252 (mp) outliers start: 107 outliers final: 79 residues processed: 716 average time/residue: 0.2818 time to fit residues: 304.0582 Evaluate side-chains 737 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 646 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 370 GLU Chi-restraints excluded: chain N residue 424 THR Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 449 SER Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 485 VAL Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 424 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 364 ASN Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 424 THR Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 484 LEU Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 370 GLU Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 364 ASN Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER Chi-restraints excluded: chain Z residue 415 MET Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 20.0000 chunk 24 optimal weight: 0.5980 chunk 123 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 182 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN P 405 GLN T 461 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN X 373 GLN Y 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18942 Z= 0.203 Angle : 0.674 10.559 25536 Z= 0.339 Chirality : 0.046 0.143 2744 Planarity : 0.004 0.048 3304 Dihedral : 4.870 17.713 2492 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.70 % Allowed : 20.78 % Favored : 73.51 % 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: -1.74 (0.16), residues: 2240 helix: 1.45 (0.21), residues: 574 sheet: -0.42 (0.21), residues: 462 loop : -2.96 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 466 HIS 0.003 0.001 HIS T 389 PHE 0.025 0.001 PHE R 420 TYR 0.015 0.001 TYR P 403 ARG 0.011 0.001 ARG P 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 668 time to evaluate : 2.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9129 (tt0) cc_final: 0.8468 (tm-30) REVERT: N 404 TYR cc_start: 0.7164 (m-10) cc_final: 0.4948 (t80) REVERT: N 415 MET cc_start: 0.7928 (ttm) cc_final: 0.7478 (ttm) REVERT: N 418 GLU cc_start: 0.6658 (mp0) cc_final: 0.6213 (mp0) REVERT: N 450 MET cc_start: 0.7691 (ttp) cc_final: 0.6387 (ptp) REVERT: N 503 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.7371 (mp) REVERT: O 379 GLN cc_start: 0.8861 (tt0) cc_final: 0.8400 (tm-30) REVERT: O 386 GLN cc_start: 0.9304 (tm-30) cc_final: 0.9006 (tm-30) REVERT: O 404 TYR cc_start: 0.6332 (m-10) cc_final: 0.5168 (t80) REVERT: O 412 LYS cc_start: 0.8741 (mmmt) cc_final: 0.8461 (mmmt) REVERT: O 422 ASP cc_start: 0.8915 (p0) cc_final: 0.8545 (p0) REVERT: O 450 MET cc_start: 0.7755 (ttp) cc_final: 0.6305 (ptp) REVERT: P 358 SER cc_start: 0.8361 (OUTLIER) cc_final: 0.8043 (t) REVERT: P 364 ASN cc_start: 0.8601 (m-40) cc_final: 0.7593 (t0) REVERT: P 379 GLN cc_start: 0.8749 (tt0) cc_final: 0.7888 (tm-30) REVERT: P 384 GLU cc_start: 0.8297 (tm-30) cc_final: 0.8021 (pp20) REVERT: P 387 TYR cc_start: 0.9218 (t80) cc_final: 0.8757 (t80) REVERT: P 404 TYR cc_start: 0.7410 (m-10) cc_final: 0.6057 (t80) REVERT: P 422 ASP cc_start: 0.9148 (p0) cc_final: 0.8580 (p0) REVERT: P 464 LEU cc_start: 0.9297 (mp) cc_final: 0.8934 (mt) REVERT: P 485 VAL cc_start: 0.9227 (OUTLIER) cc_final: 0.8994 (p) REVERT: P 497 LEU cc_start: 0.7964 (mt) cc_final: 0.7611 (mt) REVERT: P 503 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7330 (mp) REVERT: Q 370 GLU cc_start: 0.8166 (pp20) cc_final: 0.7841 (tm-30) REVERT: Q 403 TYR cc_start: 0.9073 (m-80) cc_final: 0.8470 (m-10) REVERT: Q 421 ASP cc_start: 0.8536 (p0) cc_final: 0.8000 (p0) REVERT: Q 427 TYR cc_start: 0.8965 (m-80) cc_final: 0.8654 (m-80) REVERT: Q 459 MET cc_start: 0.8106 (mtp) cc_final: 0.7769 (mtp) REVERT: Q 468 ARG cc_start: 0.9079 (ttp80) cc_final: 0.8380 (ttp-170) REVERT: R 384 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8158 (tm-30) REVERT: R 385 THR cc_start: 0.9323 (m) cc_final: 0.8916 (t) REVERT: R 386 GLN cc_start: 0.8890 (tm-30) cc_final: 0.8479 (pp30) REVERT: R 443 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8028 (mm-40) REVERT: R 497 LEU cc_start: 0.7742 (mp) cc_final: 0.7414 (mt) REVERT: S 364 ASN cc_start: 0.8106 (t0) cc_final: 0.7805 (t0) REVERT: S 372 LYS cc_start: 0.8415 (pptt) cc_final: 0.7914 (mtpt) REVERT: S 384 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8250 (tm-30) REVERT: S 417 SER cc_start: 0.8703 (t) cc_final: 0.8188 (t) REVERT: S 418 GLU cc_start: 0.7061 (mp0) cc_final: 0.6700 (mm-30) REVERT: S 422 ASP cc_start: 0.8907 (p0) cc_final: 0.8489 (p0) REVERT: S 436 GLN cc_start: 0.9449 (tp40) cc_final: 0.6400 (pm20) REVERT: S 452 ASP cc_start: 0.8080 (p0) cc_final: 0.7811 (p0) REVERT: T 367 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8089 (pttm) REVERT: T 379 GLN cc_start: 0.8571 (tt0) cc_final: 0.7749 (pp30) REVERT: T 384 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8173 (tm-30) REVERT: T 405 GLN cc_start: 0.8869 (pt0) cc_final: 0.8488 (pt0) REVERT: T 456 ASP cc_start: 0.8567 (t0) cc_final: 0.8292 (t0) REVERT: T 503 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7555 (mp) REVERT: U 365 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8281 (ptpt) REVERT: U 379 GLN cc_start: 0.9077 (tt0) cc_final: 0.8133 (tm-30) REVERT: U 384 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8203 (pp20) REVERT: U 404 TYR cc_start: 0.7167 (m-10) cc_final: 0.5465 (t80) REVERT: U 418 GLU cc_start: 0.5905 (mp0) cc_final: 0.5292 (mp0) REVERT: U 421 ASP cc_start: 0.8564 (p0) cc_final: 0.8008 (p0) REVERT: U 422 ASP cc_start: 0.9249 (p0) cc_final: 0.8964 (p0) REVERT: U 450 MET cc_start: 0.7666 (ttp) cc_final: 0.7233 (ptp) REVERT: U 503 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.7168 (mp) REVERT: V 355 MET cc_start: 0.8096 (mmp) cc_final: 0.7765 (tpt) REVERT: V 356 MET cc_start: 0.7771 (mmp) cc_final: 0.7271 (ptt) REVERT: V 361 GLN cc_start: 0.8064 (pp30) cc_final: 0.7713 (tm-30) REVERT: V 377 LEU cc_start: 0.8645 (tp) cc_final: 0.7992 (pp) REVERT: V 384 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7272 (tm-30) REVERT: V 386 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8839 (tm-30) REVERT: V 450 MET cc_start: 0.6965 (ttp) cc_final: 0.5456 (ptp) REVERT: W 377 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8467 (pp) REVERT: W 379 GLN cc_start: 0.9037 (tt0) cc_final: 0.8238 (tm-30) REVERT: W 450 MET cc_start: 0.7408 (ttp) cc_final: 0.6189 (ptp) REVERT: X 355 MET cc_start: 0.8193 (mmp) cc_final: 0.7848 (mmm) REVERT: X 361 GLN cc_start: 0.8986 (tt0) cc_final: 0.8017 (tm-30) REVERT: X 373 GLN cc_start: 0.8523 (tp40) cc_final: 0.8272 (tp-100) REVERT: X 377 LEU cc_start: 0.8675 (tp) cc_final: 0.8112 (pp) REVERT: X 386 GLN cc_start: 0.9301 (tm-30) cc_final: 0.8878 (tm-30) REVERT: X 404 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5219 (t80) REVERT: X 417 SER cc_start: 0.8713 (t) cc_final: 0.8216 (t) REVERT: X 418 GLU cc_start: 0.6398 (mm-30) cc_final: 0.6040 (mm-30) REVERT: X 421 ASP cc_start: 0.8555 (p0) cc_final: 0.8142 (p0) REVERT: X 427 TYR cc_start: 0.8706 (m-80) cc_final: 0.8430 (m-80) REVERT: X 450 MET cc_start: 0.8076 (ttp) cc_final: 0.6290 (ptp) REVERT: Y 371 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8455 (tp30) REVERT: Y 379 GLN cc_start: 0.8721 (tt0) cc_final: 0.7999 (tm-30) REVERT: Y 384 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7602 (tm-30) REVERT: Y 386 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8665 (tt0) REVERT: Y 404 TYR cc_start: 0.6090 (OUTLIER) cc_final: 0.4939 (t80) REVERT: Y 421 ASP cc_start: 0.8689 (p0) cc_final: 0.8458 (p0) REVERT: Y 422 ASP cc_start: 0.8848 (p0) cc_final: 0.8537 (p0) REVERT: Y 485 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8948 (p) REVERT: Y 503 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7244 (mp) REVERT: Z 358 SER cc_start: 0.7030 (OUTLIER) cc_final: 0.6811 (t) REVERT: Z 372 LYS cc_start: 0.9060 (pptt) cc_final: 0.8807 (pttm) REVERT: Z 379 GLN cc_start: 0.8993 (tt0) cc_final: 0.8485 (pp30) REVERT: Z 404 TYR cc_start: 0.7262 (m-10) cc_final: 0.5497 (t80) REVERT: Z 450 MET cc_start: 0.7608 (ttp) cc_final: 0.6598 (ptp) REVERT: a 355 MET cc_start: 0.8199 (mmp) cc_final: 0.7880 (tpt) REVERT: a 371 GLU cc_start: 0.8554 (tp30) cc_final: 0.8149 (tp30) REVERT: a 383 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8739 (tt) REVERT: a 418 GLU cc_start: 0.6807 (mp0) cc_final: 0.6308 (mp0) REVERT: a 450 MET cc_start: 0.6886 (ttp) cc_final: 0.6325 (ptp) REVERT: a 459 MET cc_start: 0.8674 (ptm) cc_final: 0.8288 (ptm) REVERT: a 464 LEU cc_start: 0.9501 (mp) cc_final: 0.9222 (mp) REVERT: a 503 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7318 (mp) outliers start: 115 outliers final: 88 residues processed: 721 average time/residue: 0.2836 time to fit residues: 310.3396 Evaluate side-chains 759 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 655 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 364 ASN Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 485 VAL Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 424 THR Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain R residue 472 ILE Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 421 ASP Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 362 ILE Chi-restraints excluded: chain T residue 388 VAL Chi-restraints excluded: chain T residue 424 THR Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 364 ASN Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 424 THR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 355 MET Chi-restraints excluded: chain W residue 358 SER Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 383 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 415 MET Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 424 THR Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 439 ILE Chi-restraints excluded: chain X residue 441 VAL Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 364 ASN Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 386 GLN Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 358 SER Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 364 ASN Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER Chi-restraints excluded: chain Z residue 424 THR Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 439 ILE Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 169 optimal weight: 0.0070 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN N 436 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN R 364 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 373 GLN Y 405 GLN Z 500 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18942 Z= 0.186 Angle : 0.686 11.190 25536 Z= 0.343 Chirality : 0.046 0.147 2744 Planarity : 0.005 0.060 3304 Dihedral : 4.709 21.150 2492 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.76 % Allowed : 22.02 % Favored : 73.21 % 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: -1.61 (0.17), residues: 2240 helix: 1.54 (0.22), residues: 574 sheet: -0.27 (0.21), residues: 462 loop : -2.91 (0.15), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP a 466 HIS 0.003 0.001 HIS N 413 PHE 0.025 0.001 PHE R 420 TYR 0.018 0.001 TYR Z 506 ARG 0.014 0.001 ARG a 410 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 692 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9130 (tt0) cc_final: 0.8465 (tm-30) REVERT: N 404 TYR cc_start: 0.7128 (m-10) cc_final: 0.4845 (t80) REVERT: N 405 GLN cc_start: 0.8360 (pt0) cc_final: 0.7896 (pt0) REVERT: N 415 MET cc_start: 0.8325 (ttm) cc_final: 0.7957 (ttm) REVERT: N 450 MET cc_start: 0.7281 (ttp) cc_final: 0.5959 (ptp) REVERT: N 503 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7384 (mp) REVERT: O 366 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7613 (tm-30) REVERT: O 379 GLN cc_start: 0.8869 (tt0) cc_final: 0.8133 (pp30) REVERT: O 386 GLN cc_start: 0.9303 (tm-30) cc_final: 0.8975 (tm-30) REVERT: O 404 TYR cc_start: 0.7231 (m-10) cc_final: 0.5786 (t80) REVERT: O 422 ASP cc_start: 0.8898 (p0) cc_final: 0.8581 (p0) REVERT: O 450 MET cc_start: 0.7713 (ttp) cc_final: 0.6259 (ptp) REVERT: P 358 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.8017 (t) REVERT: P 364 ASN cc_start: 0.8602 (m-40) cc_final: 0.7605 (t0) REVERT: P 379 GLN cc_start: 0.8743 (tt0) cc_final: 0.7882 (tm-30) REVERT: P 384 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8026 (pp20) REVERT: P 404 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5357 (t80) REVERT: P 422 ASP cc_start: 0.9133 (p0) cc_final: 0.8543 (p0) REVERT: P 464 LEU cc_start: 0.9268 (mp) cc_final: 0.8892 (mt) REVERT: P 485 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.9013 (p) REVERT: P 503 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.7311 (mp) REVERT: Q 356 MET cc_start: 0.6070 (tmm) cc_final: 0.5703 (tmm) REVERT: Q 403 TYR cc_start: 0.9013 (m-80) cc_final: 0.8393 (m-10) REVERT: Q 421 ASP cc_start: 0.8491 (p0) cc_final: 0.7976 (p0) REVERT: Q 427 TYR cc_start: 0.8993 (m-80) cc_final: 0.8704 (m-80) REVERT: Q 459 MET cc_start: 0.8028 (mtp) cc_final: 0.7711 (mtp) REVERT: Q 468 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8344 (ttp-170) REVERT: R 375 ILE cc_start: 0.8944 (mm) cc_final: 0.8665 (pt) REVERT: R 384 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8090 (tm-30) REVERT: R 385 THR cc_start: 0.9331 (m) cc_final: 0.8957 (t) REVERT: R 386 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8488 (pp30) REVERT: R 443 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: R 497 LEU cc_start: 0.7683 (mp) cc_final: 0.7375 (mt) REVERT: S 367 LYS cc_start: 0.8109 (ptmt) cc_final: 0.7608 (pttm) REVERT: S 372 LYS cc_start: 0.8535 (pptt) cc_final: 0.8062 (mtpt) REVERT: S 373 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7603 (tm-30) REVERT: S 384 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8401 (tm-30) REVERT: S 410 ARG cc_start: 0.7392 (ptp-110) cc_final: 0.7073 (ptm160) REVERT: S 417 SER cc_start: 0.8708 (t) cc_final: 0.7862 (t) REVERT: S 418 GLU cc_start: 0.7034 (mp0) cc_final: 0.6593 (mp0) REVERT: S 422 ASP cc_start: 0.8901 (p0) cc_final: 0.8461 (p0) REVERT: S 436 GLN cc_start: 0.9442 (tp40) cc_final: 0.6343 (pm20) REVERT: S 452 ASP cc_start: 0.8067 (p0) cc_final: 0.7788 (p0) REVERT: T 367 LYS cc_start: 0.8680 (ptmt) cc_final: 0.8098 (pttm) REVERT: T 379 GLN cc_start: 0.8635 (tt0) cc_final: 0.7826 (pp30) REVERT: T 384 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8153 (tm-30) REVERT: T 405 GLN cc_start: 0.8786 (pt0) cc_final: 0.8425 (pt0) REVERT: T 456 ASP cc_start: 0.8522 (t0) cc_final: 0.8224 (t0) REVERT: T 503 ILE cc_start: 0.8422 (OUTLIER) cc_final: 0.7538 (mp) REVERT: U 365 LYS cc_start: 0.8612 (ptpp) cc_final: 0.8250 (ptpt) REVERT: U 379 GLN cc_start: 0.9075 (tt0) cc_final: 0.8150 (tm-30) REVERT: U 384 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7866 (tm-30) REVERT: U 404 TYR cc_start: 0.7689 (m-10) cc_final: 0.5695 (t80) REVERT: U 418 GLU cc_start: 0.5599 (mp0) cc_final: 0.5122 (mp0) REVERT: U 421 ASP cc_start: 0.8566 (p0) cc_final: 0.8008 (p0) REVERT: U 450 MET cc_start: 0.7598 (ttp) cc_final: 0.7109 (ptp) REVERT: U 503 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7160 (mp) REVERT: V 355 MET cc_start: 0.8061 (mmp) cc_final: 0.7779 (tpt) REVERT: V 377 LEU cc_start: 0.8658 (tp) cc_final: 0.8132 (pp) REVERT: V 384 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7234 (tm-30) REVERT: V 386 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8849 (tm-30) REVERT: V 450 MET cc_start: 0.7121 (ttp) cc_final: 0.5666 (ptp) REVERT: W 377 LEU cc_start: 0.9057 (tt) cc_final: 0.8465 (pp) REVERT: W 379 GLN cc_start: 0.9058 (tt0) cc_final: 0.8250 (tm-30) REVERT: W 404 TYR cc_start: 0.7096 (m-80) cc_final: 0.6754 (m-80) REVERT: W 450 MET cc_start: 0.7324 (ttp) cc_final: 0.6127 (ptp) REVERT: W 485 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8907 (p) REVERT: X 355 MET cc_start: 0.8147 (mmp) cc_final: 0.7819 (mmm) REVERT: X 361 GLN cc_start: 0.8983 (tt0) cc_final: 0.8022 (tm-30) REVERT: X 373 GLN cc_start: 0.8477 (tp40) cc_final: 0.8185 (tp-100) REVERT: X 377 LEU cc_start: 0.8664 (tp) cc_final: 0.8103 (pp) REVERT: X 384 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7691 (tm-30) REVERT: X 386 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8828 (tm-30) REVERT: X 403 TYR cc_start: 0.8981 (m-80) cc_final: 0.8355 (m-10) REVERT: X 404 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.5208 (t80) REVERT: X 417 SER cc_start: 0.8686 (t) cc_final: 0.8183 (t) REVERT: X 418 GLU cc_start: 0.6357 (mm-30) cc_final: 0.5994 (mm-30) REVERT: X 421 ASP cc_start: 0.8520 (p0) cc_final: 0.8081 (p0) REVERT: X 427 TYR cc_start: 0.8689 (m-80) cc_final: 0.8481 (m-80) REVERT: X 450 MET cc_start: 0.8047 (ttp) cc_final: 0.6300 (ptp) REVERT: Y 371 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8482 (tp30) REVERT: Y 379 GLN cc_start: 0.8729 (tt0) cc_final: 0.8006 (tm-30) REVERT: Y 403 TYR cc_start: 0.9161 (m-80) cc_final: 0.8906 (m-10) REVERT: Y 404 TYR cc_start: 0.6456 (OUTLIER) cc_final: 0.5741 (t80) REVERT: Y 485 VAL cc_start: 0.9238 (OUTLIER) cc_final: 0.8961 (p) REVERT: Z 356 MET cc_start: 0.8181 (tmm) cc_final: 0.7791 (mmp) REVERT: Z 372 LYS cc_start: 0.9051 (pptt) cc_final: 0.8753 (pttm) REVERT: Z 379 GLN cc_start: 0.9007 (tt0) cc_final: 0.8487 (pp30) REVERT: Z 384 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7987 (tm-30) REVERT: Z 404 TYR cc_start: 0.7303 (m-10) cc_final: 0.5451 (t80) REVERT: Z 450 MET cc_start: 0.7585 (ttp) cc_final: 0.6544 (ptp) REVERT: a 355 MET cc_start: 0.8343 (mmp) cc_final: 0.8051 (tpt) REVERT: a 371 GLU cc_start: 0.8568 (tp30) cc_final: 0.8135 (tp30) REVERT: a 383 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8686 (tt) REVERT: a 386 GLN cc_start: 0.9330 (tm-30) cc_final: 0.8833 (tm-30) REVERT: a 418 GLU cc_start: 0.6778 (mp0) cc_final: 0.6303 (mp0) REVERT: a 450 MET cc_start: 0.6798 (ttp) cc_final: 0.6271 (ptp) REVERT: a 459 MET cc_start: 0.8760 (ptm) cc_final: 0.8481 (ptm) REVERT: a 461 ASN cc_start: 0.8751 (t0) cc_final: 0.8455 (t0) REVERT: a 464 LEU cc_start: 0.9457 (mp) cc_final: 0.9125 (mp) REVERT: a 503 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7451 (mp) outliers start: 96 outliers final: 68 residues processed: 732 average time/residue: 0.2802 time to fit residues: 309.1300 Evaluate side-chains 743 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 661 time to evaluate : 2.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 424 THR Chi-restraints excluded: chain O residue 459 MET Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 358 SER Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 404 TYR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 485 VAL Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 370 GLU Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 421 ASP Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 388 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 364 ASN Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 355 MET Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 415 MET Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 415 MET Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 4.9990 chunk 206 optimal weight: 0.9990 chunk 188 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 121 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 181 optimal weight: 0.7980 chunk 190 optimal weight: 0.0270 chunk 200 optimal weight: 0.0980 overall best weight: 0.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN P 500 ASN ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN Y 373 GLN Y 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18942 Z= 0.213 Angle : 0.721 12.838 25536 Z= 0.362 Chirality : 0.047 0.169 2744 Planarity : 0.005 0.066 3304 Dihedral : 4.763 19.350 2492 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 4.37 % Allowed : 23.12 % Favored : 72.52 % 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: -1.56 (0.17), residues: 2240 helix: 1.62 (0.21), residues: 574 sheet: -0.52 (0.21), residues: 490 loop : -2.81 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 466 HIS 0.003 0.001 HIS T 389 PHE 0.024 0.001 PHE R 420 TYR 0.031 0.001 TYR Z 403 ARG 0.015 0.001 ARG Y 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 672 time to evaluate : 2.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9139 (tt0) cc_final: 0.8464 (tm-30) REVERT: N 404 TYR cc_start: 0.7302 (m-10) cc_final: 0.4807 (t80) REVERT: N 405 GLN cc_start: 0.8301 (pt0) cc_final: 0.7852 (pt0) REVERT: N 415 MET cc_start: 0.8427 (ttm) cc_final: 0.8064 (ttm) REVERT: N 450 MET cc_start: 0.7600 (ttp) cc_final: 0.5908 (ptp) REVERT: N 503 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7374 (mp) REVERT: O 379 GLN cc_start: 0.8875 (tt0) cc_final: 0.8210 (pp30) REVERT: O 386 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9017 (tm-30) REVERT: O 404 TYR cc_start: 0.7298 (m-10) cc_final: 0.5778 (t80) REVERT: O 418 GLU cc_start: 0.6048 (mp0) cc_final: 0.5257 (mp0) REVERT: O 422 ASP cc_start: 0.8969 (p0) cc_final: 0.8618 (p0) REVERT: O 450 MET cc_start: 0.7784 (ttp) cc_final: 0.6269 (ptp) REVERT: P 364 ASN cc_start: 0.8614 (m-40) cc_final: 0.7610 (t0) REVERT: P 379 GLN cc_start: 0.8747 (tt0) cc_final: 0.7908 (tm-30) REVERT: P 384 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7870 (tm-30) REVERT: P 404 TYR cc_start: 0.6639 (m-10) cc_final: 0.5640 (t80) REVERT: P 422 ASP cc_start: 0.9167 (p0) cc_final: 0.8553 (p0) REVERT: P 464 LEU cc_start: 0.9294 (mp) cc_final: 0.8949 (mt) REVERT: P 485 VAL cc_start: 0.9222 (OUTLIER) cc_final: 0.8888 (p) REVERT: P 503 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.7306 (mp) REVERT: Q 356 MET cc_start: 0.6340 (tmm) cc_final: 0.6137 (tmm) REVERT: Q 403 TYR cc_start: 0.9057 (m-80) cc_final: 0.8420 (m-10) REVERT: Q 421 ASP cc_start: 0.8550 (p0) cc_final: 0.8091 (p0) REVERT: Q 427 TYR cc_start: 0.8963 (m-80) cc_final: 0.8664 (m-80) REVERT: Q 459 MET cc_start: 0.8053 (mtp) cc_final: 0.7720 (mtp) REVERT: Q 468 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8313 (ttp-170) REVERT: R 384 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8147 (tm-30) REVERT: R 385 THR cc_start: 0.9254 (m) cc_final: 0.8897 (t) REVERT: R 386 GLN cc_start: 0.8920 (tm-30) cc_final: 0.8542 (pp30) REVERT: R 443 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7792 (mm-40) REVERT: R 497 LEU cc_start: 0.7782 (mp) cc_final: 0.7449 (mt) REVERT: S 367 LYS cc_start: 0.8193 (ptmt) cc_final: 0.7691 (pttm) REVERT: S 372 LYS cc_start: 0.8626 (pptt) cc_final: 0.8079 (mtpt) REVERT: S 373 GLN cc_start: 0.7933 (tm-30) cc_final: 0.7655 (tm-30) REVERT: S 384 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8000 (tm-30) REVERT: S 410 ARG cc_start: 0.7452 (ptp-110) cc_final: 0.7168 (ptm160) REVERT: S 417 SER cc_start: 0.8687 (t) cc_final: 0.8419 (t) REVERT: S 436 GLN cc_start: 0.9448 (tp40) cc_final: 0.6351 (pm20) REVERT: S 452 ASP cc_start: 0.7958 (p0) cc_final: 0.7695 (p0) REVERT: T 367 LYS cc_start: 0.8711 (ptmt) cc_final: 0.8078 (pttm) REVERT: T 379 GLN cc_start: 0.8621 (tt0) cc_final: 0.7739 (pp30) REVERT: T 384 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8159 (tm-30) REVERT: T 405 GLN cc_start: 0.8805 (pt0) cc_final: 0.8453 (pt0) REVERT: T 418 GLU cc_start: 0.6986 (mp0) cc_final: 0.6704 (mp0) REVERT: T 425 PHE cc_start: 0.7969 (m-10) cc_final: 0.6646 (m-10) REVERT: T 456 ASP cc_start: 0.8516 (t0) cc_final: 0.8244 (t0) REVERT: T 503 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.7531 (mp) REVERT: U 365 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8271 (ptpt) REVERT: U 369 ARG cc_start: 0.7229 (ttp80) cc_final: 0.7025 (ttp80) REVERT: U 379 GLN cc_start: 0.9130 (tt0) cc_final: 0.8180 (tm-30) REVERT: U 384 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7854 (tm-30) REVERT: U 404 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.5710 (t80) REVERT: U 421 ASP cc_start: 0.8515 (p0) cc_final: 0.7924 (p0) REVERT: U 450 MET cc_start: 0.7251 (ttp) cc_final: 0.6669 (ptp) REVERT: U 503 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.7262 (mp) REVERT: V 355 MET cc_start: 0.8068 (mmp) cc_final: 0.7788 (tpt) REVERT: V 377 LEU cc_start: 0.8682 (tp) cc_final: 0.8143 (pp) REVERT: V 384 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7246 (tm-30) REVERT: V 386 GLN cc_start: 0.9216 (tm-30) cc_final: 0.8856 (tm-30) REVERT: V 450 MET cc_start: 0.7158 (ttp) cc_final: 0.5754 (ptp) REVERT: W 372 LYS cc_start: 0.8970 (mmmt) cc_final: 0.8726 (mmtp) REVERT: W 377 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8488 (pp) REVERT: W 379 GLN cc_start: 0.9088 (tt0) cc_final: 0.8198 (tm-30) REVERT: W 450 MET cc_start: 0.7373 (ttp) cc_final: 0.6123 (ptp) REVERT: X 355 MET cc_start: 0.8158 (mmp) cc_final: 0.7839 (mmm) REVERT: X 361 GLN cc_start: 0.9018 (tt0) cc_final: 0.8030 (tm-30) REVERT: X 386 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8838 (tm-30) REVERT: X 403 TYR cc_start: 0.8980 (m-80) cc_final: 0.8452 (m-10) REVERT: X 404 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.5076 (t80) REVERT: X 417 SER cc_start: 0.8676 (t) cc_final: 0.8166 (t) REVERT: X 418 GLU cc_start: 0.6398 (mm-30) cc_final: 0.6018 (mm-30) REVERT: X 421 ASP cc_start: 0.8547 (p0) cc_final: 0.8242 (p0) REVERT: X 427 TYR cc_start: 0.8690 (m-80) cc_final: 0.8482 (m-80) REVERT: X 450 MET cc_start: 0.8090 (ttp) cc_final: 0.6319 (ptp) REVERT: Y 379 GLN cc_start: 0.8767 (tt0) cc_final: 0.7989 (tm-30) REVERT: Y 384 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7725 (tm-30) REVERT: Y 404 TYR cc_start: 0.6283 (OUTLIER) cc_final: 0.5607 (t80) REVERT: Y 422 ASP cc_start: 0.9075 (p0) cc_final: 0.8692 (p0) REVERT: Y 485 VAL cc_start: 0.9186 (OUTLIER) cc_final: 0.8914 (p) REVERT: Y 503 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.7237 (mp) REVERT: Z 356 MET cc_start: 0.8088 (tmm) cc_final: 0.7820 (mmp) REVERT: Z 372 LYS cc_start: 0.9052 (pptt) cc_final: 0.8757 (pttm) REVERT: Z 379 GLN cc_start: 0.9017 (tt0) cc_final: 0.8472 (pp30) REVERT: Z 404 TYR cc_start: 0.7133 (m-10) cc_final: 0.5489 (t80) REVERT: Z 450 MET cc_start: 0.7618 (ttp) cc_final: 0.6531 (ptp) REVERT: a 355 MET cc_start: 0.8355 (mmp) cc_final: 0.8056 (tpt) REVERT: a 371 GLU cc_start: 0.8561 (tp30) cc_final: 0.8047 (tp30) REVERT: a 383 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8796 (tt) REVERT: a 386 GLN cc_start: 0.9309 (tm-30) cc_final: 0.9081 (tm-30) REVERT: a 418 GLU cc_start: 0.6797 (mp0) cc_final: 0.6304 (mp0) REVERT: a 450 MET cc_start: 0.6876 (ttp) cc_final: 0.6291 (ptp) REVERT: a 459 MET cc_start: 0.8831 (ptm) cc_final: 0.8566 (ptm) REVERT: a 461 ASN cc_start: 0.8756 (t0) cc_final: 0.8443 (t0) REVERT: a 464 LEU cc_start: 0.9465 (mp) cc_final: 0.9185 (mp) REVERT: a 503 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7488 (mp) outliers start: 88 outliers final: 70 residues processed: 708 average time/residue: 0.2782 time to fit residues: 297.8898 Evaluate side-chains 747 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 663 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 421 ASP Chi-restraints excluded: chain O residue 459 MET Chi-restraints excluded: chain O residue 484 LEU Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 485 VAL Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 417 SER Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 421 ASP Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 388 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 404 TYR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 449 SER Chi-restraints excluded: chain U residue 484 LEU Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 468 ARG Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 358 SER Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 411 SER Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 411 SER Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 370 GLU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9990 chunk 212 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 205 optimal weight: 0.3980 chunk 177 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 137 optimal weight: 0.0670 chunk 108 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 461 ASN O 500 ASN S 413 HIS ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18942 Z= 0.208 Angle : 0.730 13.516 25536 Z= 0.365 Chirality : 0.047 0.223 2744 Planarity : 0.005 0.062 3304 Dihedral : 4.716 20.264 2492 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.46 % Allowed : 22.92 % Favored : 72.62 % 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: -1.53 (0.17), residues: 2240 helix: 1.66 (0.21), residues: 574 sheet: -0.50 (0.21), residues: 490 loop : -2.79 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP X 466 HIS 0.003 0.001 HIS T 389 PHE 0.024 0.001 PHE R 420 TYR 0.025 0.001 TYR Z 403 ARG 0.016 0.001 ARG a 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4480 Ramachandran restraints generated. 2240 Oldfield, 0 Emsley, 2240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 681 time to evaluate : 2.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 379 GLN cc_start: 0.9146 (tt0) cc_final: 0.8463 (tm-30) REVERT: N 404 TYR cc_start: 0.7271 (m-10) cc_final: 0.4827 (t80) REVERT: N 405 GLN cc_start: 0.8240 (pt0) cc_final: 0.7864 (pt0) REVERT: N 415 MET cc_start: 0.8383 (ttm) cc_final: 0.8042 (ttm) REVERT: N 450 MET cc_start: 0.7713 (ttp) cc_final: 0.6389 (ptp) REVERT: N 503 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.7400 (mp) REVERT: O 379 GLN cc_start: 0.8880 (tt0) cc_final: 0.8318 (pp30) REVERT: O 386 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9000 (tm-30) REVERT: O 418 GLU cc_start: 0.5528 (mp0) cc_final: 0.4827 (mp0) REVERT: O 422 ASP cc_start: 0.8982 (p0) cc_final: 0.8651 (p0) REVERT: O 450 MET cc_start: 0.7774 (ttp) cc_final: 0.6224 (ptp) REVERT: O 503 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.7315 (mp) REVERT: P 364 ASN cc_start: 0.8604 (m-40) cc_final: 0.7672 (t0) REVERT: P 379 GLN cc_start: 0.8725 (tt0) cc_final: 0.7931 (tm-30) REVERT: P 404 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.5510 (t80) REVERT: P 422 ASP cc_start: 0.9169 (p0) cc_final: 0.8538 (p0) REVERT: P 464 LEU cc_start: 0.9296 (mp) cc_final: 0.8945 (mt) REVERT: P 503 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7316 (mp) REVERT: Q 403 TYR cc_start: 0.9094 (m-80) cc_final: 0.8347 (m-10) REVERT: Q 421 ASP cc_start: 0.8548 (p0) cc_final: 0.8033 (p0) REVERT: Q 427 TYR cc_start: 0.8973 (m-80) cc_final: 0.8685 (m-80) REVERT: Q 459 MET cc_start: 0.8054 (mtp) cc_final: 0.7722 (mtp) REVERT: Q 468 ARG cc_start: 0.8994 (ttp80) cc_final: 0.8279 (ttp-170) REVERT: R 356 MET cc_start: 0.6122 (tpp) cc_final: 0.5811 (tpp) REVERT: R 384 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8159 (tm-30) REVERT: R 385 THR cc_start: 0.9271 (m) cc_final: 0.8956 (t) REVERT: R 386 GLN cc_start: 0.8927 (tm-30) cc_final: 0.8549 (pp30) REVERT: R 443 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7729 (mm-40) REVERT: R 497 LEU cc_start: 0.7830 (mp) cc_final: 0.7571 (mt) REVERT: S 360 GLU cc_start: 0.7673 (mp0) cc_final: 0.7275 (mp0) REVERT: S 367 LYS cc_start: 0.8500 (ptmt) cc_final: 0.7919 (pttm) REVERT: S 372 LYS cc_start: 0.8652 (pptt) cc_final: 0.8093 (mtpt) REVERT: S 373 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7184 (tm-30) REVERT: S 384 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8018 (tm-30) REVERT: S 410 ARG cc_start: 0.7541 (ptp-110) cc_final: 0.7301 (ptm160) REVERT: S 417 SER cc_start: 0.8694 (t) cc_final: 0.8401 (t) REVERT: S 436 GLN cc_start: 0.9451 (tp40) cc_final: 0.6330 (pm20) REVERT: S 452 ASP cc_start: 0.7957 (p0) cc_final: 0.7719 (p0) REVERT: T 367 LYS cc_start: 0.8703 (ptmt) cc_final: 0.8050 (pttm) REVERT: T 379 GLN cc_start: 0.8662 (tt0) cc_final: 0.7893 (pp30) REVERT: T 384 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8167 (tm-30) REVERT: T 418 GLU cc_start: 0.7096 (mp0) cc_final: 0.6856 (mp0) REVERT: T 425 PHE cc_start: 0.8006 (m-10) cc_final: 0.6680 (m-10) REVERT: T 456 ASP cc_start: 0.8525 (t0) cc_final: 0.8203 (t0) REVERT: T 503 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.7541 (mp) REVERT: U 365 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8249 (ptpt) REVERT: U 379 GLN cc_start: 0.9132 (tt0) cc_final: 0.8313 (tm-30) REVERT: U 384 GLU cc_start: 0.8395 (tm-30) cc_final: 0.7825 (tm-30) REVERT: U 404 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.5700 (t80) REVERT: U 421 ASP cc_start: 0.8483 (p0) cc_final: 0.7821 (p0) REVERT: U 450 MET cc_start: 0.7202 (ttp) cc_final: 0.6627 (ptp) REVERT: U 503 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7246 (mp) REVERT: V 355 MET cc_start: 0.8061 (mmp) cc_final: 0.7778 (tpt) REVERT: V 377 LEU cc_start: 0.8702 (tp) cc_final: 0.8154 (pp) REVERT: V 384 GLU cc_start: 0.7791 (tm-30) cc_final: 0.7271 (tm-30) REVERT: V 386 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8859 (tm-30) REVERT: V 450 MET cc_start: 0.7174 (ttp) cc_final: 0.5701 (ptp) REVERT: W 372 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8700 (mmtp) REVERT: W 377 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8620 (pp) REVERT: W 379 GLN cc_start: 0.9067 (tt0) cc_final: 0.8284 (tm-30) REVERT: W 450 MET cc_start: 0.7533 (ttp) cc_final: 0.6325 (ptp) REVERT: X 355 MET cc_start: 0.8145 (mmp) cc_final: 0.7830 (mmm) REVERT: X 361 GLN cc_start: 0.9027 (tt0) cc_final: 0.8050 (tm-30) REVERT: X 373 GLN cc_start: 0.8600 (tp40) cc_final: 0.8350 (tp-100) REVERT: X 377 LEU cc_start: 0.8688 (tp) cc_final: 0.8093 (pp) REVERT: X 384 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7822 (tm-30) REVERT: X 386 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8834 (tm-30) REVERT: X 403 TYR cc_start: 0.8941 (m-80) cc_final: 0.8299 (m-10) REVERT: X 404 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.5092 (t80) REVERT: X 417 SER cc_start: 0.8733 (t) cc_final: 0.8187 (t) REVERT: X 418 GLU cc_start: 0.6397 (mm-30) cc_final: 0.6018 (mm-30) REVERT: X 421 ASP cc_start: 0.8534 (p0) cc_final: 0.8176 (p0) REVERT: X 427 TYR cc_start: 0.8742 (m-80) cc_final: 0.8480 (m-80) REVERT: X 450 MET cc_start: 0.8082 (ttp) cc_final: 0.6340 (ptp) REVERT: Y 379 GLN cc_start: 0.8757 (tt0) cc_final: 0.7962 (tm-30) REVERT: Y 384 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7701 (tm-30) REVERT: Y 404 TYR cc_start: 0.6012 (OUTLIER) cc_final: 0.5535 (t80) REVERT: Y 422 ASP cc_start: 0.9120 (p0) cc_final: 0.8779 (p0) REVERT: Y 485 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8906 (p) REVERT: Y 503 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.7264 (mp) REVERT: Z 372 LYS cc_start: 0.9011 (pptt) cc_final: 0.8754 (pttm) REVERT: Z 379 GLN cc_start: 0.8926 (tt0) cc_final: 0.8488 (pp30) REVERT: Z 404 TYR cc_start: 0.7053 (m-10) cc_final: 0.5437 (t80) REVERT: Z 450 MET cc_start: 0.7595 (ttp) cc_final: 0.6493 (ptp) REVERT: Z 504 LYS cc_start: 0.7985 (tptp) cc_final: 0.7770 (tttt) REVERT: a 355 MET cc_start: 0.8338 (mmp) cc_final: 0.8032 (tpt) REVERT: a 371 GLU cc_start: 0.8576 (tp30) cc_final: 0.8049 (tp30) REVERT: a 383 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8555 (tt) REVERT: a 386 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8783 (tm-30) REVERT: a 418 GLU cc_start: 0.6783 (mp0) cc_final: 0.6355 (mp0) REVERT: a 450 MET cc_start: 0.6862 (ttp) cc_final: 0.6291 (ptp) REVERT: a 459 MET cc_start: 0.8802 (ptm) cc_final: 0.8507 (ptm) REVERT: a 461 ASN cc_start: 0.8745 (t0) cc_final: 0.8453 (t0) REVERT: a 464 LEU cc_start: 0.9433 (mp) cc_final: 0.9113 (mp) REVERT: a 503 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7508 (mp) outliers start: 90 outliers final: 67 residues processed: 714 average time/residue: 0.2837 time to fit residues: 305.2565 Evaluate side-chains 751 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 669 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 370 GLU Chi-restraints excluded: chain N residue 449 SER Chi-restraints excluded: chain N residue 485 VAL Chi-restraints excluded: chain N residue 503 ILE Chi-restraints excluded: chain O residue 370 GLU Chi-restraints excluded: chain O residue 459 MET Chi-restraints excluded: chain O residue 484 LEU Chi-restraints excluded: chain O residue 485 VAL Chi-restraints excluded: chain O residue 503 ILE Chi-restraints excluded: chain P residue 360 GLU Chi-restraints excluded: chain P residue 378 ASP Chi-restraints excluded: chain P residue 404 TYR Chi-restraints excluded: chain P residue 484 LEU Chi-restraints excluded: chain P residue 503 ILE Chi-restraints excluded: chain Q residue 360 GLU Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 469 VAL Chi-restraints excluded: chain Q residue 484 LEU Chi-restraints excluded: chain Q residue 485 VAL Chi-restraints excluded: chain R residue 443 GLN Chi-restraints excluded: chain R residue 460 THR Chi-restraints excluded: chain S residue 362 ILE Chi-restraints excluded: chain S residue 374 LYS Chi-restraints excluded: chain S residue 421 ASP Chi-restraints excluded: chain S residue 424 THR Chi-restraints excluded: chain S residue 449 SER Chi-restraints excluded: chain S residue 460 THR Chi-restraints excluded: chain T residue 370 GLU Chi-restraints excluded: chain T residue 388 VAL Chi-restraints excluded: chain T residue 448 LEU Chi-restraints excluded: chain T residue 460 THR Chi-restraints excluded: chain T residue 484 LEU Chi-restraints excluded: chain T residue 497 LEU Chi-restraints excluded: chain T residue 503 ILE Chi-restraints excluded: chain U residue 355 MET Chi-restraints excluded: chain U residue 360 GLU Chi-restraints excluded: chain U residue 370 GLU Chi-restraints excluded: chain U residue 374 LYS Chi-restraints excluded: chain U residue 378 ASP Chi-restraints excluded: chain U residue 404 TYR Chi-restraints excluded: chain U residue 439 ILE Chi-restraints excluded: chain U residue 484 LEU Chi-restraints excluded: chain U residue 485 VAL Chi-restraints excluded: chain U residue 503 ILE Chi-restraints excluded: chain V residue 370 GLU Chi-restraints excluded: chain V residue 388 VAL Chi-restraints excluded: chain V residue 411 SER Chi-restraints excluded: chain V residue 424 THR Chi-restraints excluded: chain V residue 439 ILE Chi-restraints excluded: chain V residue 449 SER Chi-restraints excluded: chain V residue 484 LEU Chi-restraints excluded: chain V residue 485 VAL Chi-restraints excluded: chain W residue 377 LEU Chi-restraints excluded: chain W residue 388 VAL Chi-restraints excluded: chain W residue 418 GLU Chi-restraints excluded: chain W residue 439 ILE Chi-restraints excluded: chain W residue 464 LEU Chi-restraints excluded: chain W residue 485 VAL Chi-restraints excluded: chain X residue 370 GLU Chi-restraints excluded: chain X residue 404 TYR Chi-restraints excluded: chain X residue 449 SER Chi-restraints excluded: chain X residue 485 VAL Chi-restraints excluded: chain Y residue 374 LYS Chi-restraints excluded: chain Y residue 378 ASP Chi-restraints excluded: chain Y residue 404 TYR Chi-restraints excluded: chain Y residue 424 THR Chi-restraints excluded: chain Y residue 484 LEU Chi-restraints excluded: chain Y residue 485 VAL Chi-restraints excluded: chain Y residue 503 ILE Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain Z residue 370 GLU Chi-restraints excluded: chain Z residue 378 ASP Chi-restraints excluded: chain Z residue 383 LEU Chi-restraints excluded: chain Z residue 484 LEU Chi-restraints excluded: chain Z residue 485 VAL Chi-restraints excluded: chain a residue 370 GLU Chi-restraints excluded: chain a residue 383 LEU Chi-restraints excluded: chain a residue 417 SER Chi-restraints excluded: chain a residue 448 LEU Chi-restraints excluded: chain a residue 484 LEU Chi-restraints excluded: chain a residue 497 LEU Chi-restraints excluded: chain a residue 503 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 163 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 182 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 32 optimal weight: 20.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 373 GLN ** O 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 500 ASN ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN X 500 ASN Y 373 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.106346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.093290 restraints weight = 44615.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.094905 restraints weight = 21177.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.095873 restraints weight = 12797.087| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18942 Z= 0.295 Angle : 0.776 13.365 25536 Z= 0.393 Chirality : 0.047 0.206 2744 Planarity : 0.005 0.064 3304 Dihedral : 5.223 21.823 2492 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 4.46 % Allowed : 23.86 % Favored : 71.68 % 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: -1.60 (0.17), residues: 2240 helix: 1.58 (0.21), residues: 574 sheet: -0.53 (0.21), residues: 490 loop : -2.83 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 466 HIS 0.005 0.001 HIS T 389 PHE 0.029 0.002 PHE X 425 TYR 0.028 0.002 TYR Z 403 ARG 0.014 0.001 ARG Y 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5579.27 seconds wall clock time: 100 minutes 42.30 seconds (6042.30 seconds total)