Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 21:56:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/04_2023/6oeg_20020_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/04_2023/6oeg_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_20020/04_2023/6oeg_20020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/04_2023/6oeg_20020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/04_2023/6oeg_20020_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oeg_20020/04_2023/6oeg_20020_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-1.21rc1-4938/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: 9.09, per 1000 atoms: 0.49 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: 6.97 Conformation dependent library (CDL) restraints added in 2.8 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: 0.97 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: 5.26 Time building geometry restraints manager: 7.59 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: 6.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 29.720 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 45.560 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.130 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.910 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.480 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 outliers start: 112 outliers final: 30 residues processed: 856 average time/residue: 0.3189 time to fit residues: 398.7187 Evaluate side-chains 633 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 603 time to evaluate : 2.402 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 30 outliers final: 1 residues processed: 30 average time/residue: 0.1621 time to fit residues: 12.1142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 114 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 175 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.3463 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= 0.201 Angle : 0.674 7.667 25536 Z= 0.351 Chirality : 0.047 0.176 2744 Planarity : 0.006 0.045 3304 Dihedral : 5.915 22.413 2492 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 4.12 % 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: -3.83 (0.14), residues: 2240 helix: -1.34 (0.19), residues: 574 sheet: -2.48 (0.18), residues: 462 loop : -3.27 (0.14), residues: 1204 *********************** 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 766 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 683 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 65 residues processed: 714 average time/residue: 0.2989 time to fit residues: 319.7008 Evaluate side-chains 675 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 610 time to evaluate : 2.452 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 3 residues processed: 65 average time/residue: 0.1737 time to fit residues: 24.2340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.0030 chunk 169 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 220 optimal weight: 5.9990 chunk 181 optimal weight: 0.9990 chunk 202 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 163 optimal weight: 0.7980 overall best weight: 1.0994 ------------------------------------------------------------------------------- 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 O 500 ASN P 386 GLN P 461 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 500 ASN S 500 ASN U 500 ASN V 364 ASN V 443 GLN V 500 ASN W 500 ASN X 373 GLN X 405 GLN ** X 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 413 HIS Y 461 ASN Y 500 ASN Z 500 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4092 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= 0.219 Angle : 0.676 9.078 25536 Z= 0.347 Chirality : 0.046 0.150 2744 Planarity : 0.005 0.037 3304 Dihedral : 5.569 20.669 2492 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer Outliers : 2.48 % 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: -2.96 (0.15), residues: 2240 helix: 0.18 (0.21), residues: 546 sheet: -1.63 (0.18), residues: 434 loop : -3.26 (0.14), residues: 1260 *********************** 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 711 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 661 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 29 residues processed: 678 average time/residue: 0.3041 time to fit residues: 310.1529 Evaluate side-chains 646 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 617 time to evaluate : 2.831 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2072 time to fit residues: 14.6040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 0.0010 chunk 153 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 0.0670 chunk 204 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 361 GLN R 405 GLN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 413 HIS X 373 GLN X 413 HIS a 500 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 18942 Z= 0.167 Angle : 0.649 9.455 25536 Z= 0.328 Chirality : 0.045 0.143 2744 Planarity : 0.005 0.036 3304 Dihedral : 5.089 18.658 2492 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer Outliers : 2.93 % 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: 0.61 (0.21), residues: 574 sheet: -1.41 (0.19), residues: 462 loop : -3.07 (0.15), residues: 1204 *********************** 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 725 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 666 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 37 residues processed: 688 average time/residue: 0.3023 time to fit residues: 313.7570 Evaluate side-chains 661 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 624 time to evaluate : 2.417 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.1681 time to fit residues: 14.6506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 161 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 184 optimal weight: 0.0170 chunk 149 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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 ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 461 ASN V 364 ASN ** 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: 0.7688 moved from start: 0.4755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18942 Z= 0.183 Angle : 0.663 9.999 25536 Z= 0.336 Chirality : 0.045 0.156 2744 Planarity : 0.005 0.034 3304 Dihedral : 4.931 18.596 2492 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 2.03 % 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: -2.16 (0.16), residues: 2240 helix: 0.99 (0.21), residues: 574 sheet: -0.99 (0.19), residues: 462 loop : -3.01 (0.15), residues: 1204 *********************** 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 693 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 652 time to evaluate : 2.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 18 residues processed: 670 average time/residue: 0.3069 time to fit residues: 309.4306 Evaluate side-chains 643 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 625 time to evaluate : 2.318 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1991 time to fit residues: 9.7322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 127 optimal weight: 0.0170 chunk 53 optimal weight: 4.9990 chunk 216 optimal weight: 0.5980 chunk 179 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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 O 461 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 413 HIS T 461 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Z 413 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.5074 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= 0.185 Angle : 0.673 10.097 25536 Z= 0.339 Chirality : 0.046 0.149 2744 Planarity : 0.005 0.039 3304 Dihedral : 4.820 18.636 2492 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 1.84 % 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: -1.87 (0.16), residues: 2240 helix: 1.26 (0.21), residues: 574 sheet: -0.61 (0.20), residues: 462 loop : -2.94 (0.15), residues: 1204 *********************** 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 686 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 649 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 657 average time/residue: 0.3005 time to fit residues: 297.4302 Evaluate side-chains 646 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 625 time to evaluate : 2.421 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.1587 time to fit residues: 9.5729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 123 optimal weight: 0.0030 chunk 158 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 0.0000 chunk 121 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 135 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 overall best weight: 0.3812 ------------------------------------------------------------------------------- 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 386 GLN O 461 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 443 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 18942 Z= 0.185 Angle : 0.693 10.318 25536 Z= 0.347 Chirality : 0.046 0.164 2744 Planarity : 0.005 0.058 3304 Dihedral : 4.645 17.783 2492 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.16), residues: 2240 helix: 1.39 (0.21), residues: 574 sheet: -0.30 (0.21), residues: 462 loop : -2.93 (0.15), residues: 1204 *********************** 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 669 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 649 time to evaluate : 2.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 658 average time/residue: 0.2989 time to fit residues: 297.2196 Evaluate side-chains 635 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 624 time to evaluate : 2.330 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1795 time to fit residues: 6.8142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 0.2980 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 chunk 106 optimal weight: 0.0000 chunk 20 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.4244 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** T 373 GLN T 461 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 373 GLN Y 373 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.5493 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= 0.193 Angle : 0.720 11.423 25536 Z= 0.358 Chirality : 0.046 0.159 2744 Planarity : 0.005 0.059 3304 Dihedral : 4.586 18.238 2492 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer Outliers : 0.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2240 helix: 1.53 (0.22), residues: 574 sheet: -0.06 (0.21), residues: 462 loop : -2.88 (0.15), residues: 1204 *********************** 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 667 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 647 time to evaluate : 2.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 652 average time/residue: 0.2962 time to fit residues: 290.9630 Evaluate side-chains 633 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 622 time to evaluate : 2.558 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1577 time to fit residues: 6.2480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 190 optimal weight: 0.6980 chunk 200 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 386 GLN O 461 ASN R 364 ASN ** R 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 373 GLN T 461 ASN ** V 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 443 GLN X 373 GLN Y 373 GLN Z 361 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 18942 Z= 0.205 Angle : 0.736 12.765 25536 Z= 0.367 Chirality : 0.046 0.162 2744 Planarity : 0.005 0.061 3304 Dihedral : 4.614 18.159 2492 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.17), residues: 2240 helix: 1.60 (0.22), residues: 574 sheet: 0.10 (0.22), residues: 462 loop : -2.86 (0.15), residues: 1204 *********************** 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 654 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 639 time to evaluate : 2.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 640 average time/residue: 0.2932 time to fit residues: 284.1267 Evaluate side-chains 625 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 614 time to evaluate : 2.151 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1712 time to fit residues: 6.5216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 0.0770 chunk 205 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 137 optimal weight: 0.0370 chunk 108 optimal weight: 0.0980 overall best weight: 0.4016 ------------------------------------------------------------------------------- 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 S 413 HIS T 373 GLN ** 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: 0.7633 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18942 Z= 0.204 Angle : 0.750 13.281 25536 Z= 0.372 Chirality : 0.046 0.220 2744 Planarity : 0.005 0.064 3304 Dihedral : 4.518 18.117 2492 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer Outliers : 0.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.17), residues: 2240 helix: 1.74 (0.22), residues: 574 sheet: 0.15 (0.22), residues: 462 loop : -2.85 (0.15), residues: 1204 ********************** 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 641 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 635 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 636 average time/residue: 0.3021 time to fit residues: 293.3195 Evaluate side-chains 629 residues out of total 2016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 626 time to evaluate : 2.472 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1723 time to fit residues: 4.1321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0070 chunk 163 optimal weight: 0.9980 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 182 optimal weight: 0.1980 chunk 22 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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 386 GLN O 461 ASN S 443 GLN T 373 GLN T 461 ASN ** V 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 413 HIS X 373 GLN Y 373 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.119469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.106979 restraints weight = 44297.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.108723 restraints weight = 20824.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.109782 restraints weight = 12261.017| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18942 Z= 0.209 Angle : 0.762 13.555 25536 Z= 0.378 Chirality : 0.046 0.196 2744 Planarity : 0.005 0.064 3304 Dihedral : 4.526 19.251 2492 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer Outliers : 0.35 % 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: -1.28 (0.17), residues: 2240 helix: 1.85 (0.22), residues: 574 sheet: 0.19 (0.22), residues: 462 loop : -2.83 (0.15), residues: 1204 =============================================================================== Job complete usr+sys time: 5479.68 seconds wall clock time: 99 minutes 31.41 seconds (5971.41 seconds total)