Starting phenix.real_space_refine on Mon Mar 11 08:13:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yai_33713/03_2024/7yai_33713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yai_33713/03_2024/7yai_33713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yai_33713/03_2024/7yai_33713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yai_33713/03_2024/7yai_33713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yai_33713/03_2024/7yai_33713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yai_33713/03_2024/7yai_33713_updated.pdb" } resolution = 3.14 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= 0.005 sd= 0.049 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 S 55 5.16 5 C 4880 2.51 5 N 1287 2.21 5 O 1452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 240": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 413": "OD1" <-> "OD2" Residue "A TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 475": "OE1" <-> "OE2" Residue "A TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 681": "OD1" <-> "OD2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A PHE 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 860": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 893": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7678 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 878, 6704 Classifications: {'peptide': 878} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 842} Chain breaks: 2 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 942 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ACP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.79, per 1000 atoms: 0.62 Number of scatterers: 7678 At special positions: 0 Unit cell: (85.695, 84.71, 135.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 1 19.99 S 55 16.00 P 3 15.00 O 1452 8.00 N 1287 7.00 C 4880 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 128 " distance=2.04 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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1850 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 9 sheets defined 45.6% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 37 Processing helix chain 'A' and resid 48 through 58 removed outlier: 3.570A pdb=" N HIS A 53 " --> pdb=" O CYS A 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 3.933A pdb=" N GLN A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N PHE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS A 80 " --> pdb=" O ILE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 100 through 134 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 243 through 250 removed outlier: 3.653A pdb=" N GLN A 249 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 287 Processing helix chain 'A' and resid 291 through 305 Processing helix chain 'A' and resid 310 through 327 Processing helix chain 'A' and resid 335 through 343 removed outlier: 4.115A pdb=" N GLU A 339 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 341 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLY A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 410 Processing helix chain 'A' and resid 425 through 437 removed outlier: 3.575A pdb=" N LEU A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 3.568A pdb=" N ASP A 445 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 489 removed outlier: 3.647A pdb=" N TYR A 489 " --> pdb=" O GLN A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 520 Processing helix chain 'A' and resid 552 through 561 Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 604 through 610 removed outlier: 3.663A pdb=" N GLN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 634 Processing helix chain 'A' and resid 650 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 683 through 723 removed outlier: 3.916A pdb=" N TYR A 696 " --> pdb=" O GLY A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 742 Processing helix chain 'A' and resid 744 through 747 No H-bonds generated for 'chain 'A' and resid 744 through 747' Processing helix chain 'A' and resid 757 through 760 No H-bonds generated for 'chain 'A' and resid 757 through 760' Processing helix chain 'A' and resid 773 through 798 Processing helix chain 'A' and resid 805 through 827 removed outlier: 3.643A pdb=" N ARG A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 836 No H-bonds generated for 'chain 'A' and resid 833 through 836' Processing helix chain 'A' and resid 842 through 860 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 903 removed outlier: 4.120A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing sheet with id= A, first strand: chain 'A' and resid 147 through 151 removed outlier: 4.087A pdb=" N HIS A 140 " --> pdb=" O CYS A 162 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR A 160 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 231 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU A 175 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 195 through 197 removed outlier: 4.355A pdb=" N LEU A 181 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 330 through 332 Processing sheet with id= D, first strand: chain 'A' and resid 346 through 349 removed outlier: 6.846A pdb=" N SER A 565 " --> pdb=" O ILE A 347 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N SER A 349 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LYS A 567 " --> pdb=" O SER A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 391 through 393 removed outlier: 4.302A pdb=" N VAL A 386 " --> pdb=" O VAL A 393 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N THR A 363 " --> pdb=" O VAL A 375 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 541 " --> pdb=" O LEU A 525 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 525 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 543 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ARG A 523 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 498 through 501 removed outlier: 7.158A pdb=" N LEU A 536 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR A 493 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N PHE A 538 " --> pdb=" O TYR A 493 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N SER A 495 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 592 through 595 removed outlier: 7.528A pdb=" N VAL A 594 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N PHE A 617 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 37 through 40 removed outlier: 3.500A pdb=" N THR C 110 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 105 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 147 through 149 removed outlier: 3.637A pdb=" N TRP C 66 " --> pdb=" O GLN C 131 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA C 82 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ARG C 71 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N PHE C 80 " --> pdb=" O ARG C 71 " (cutoff:3.500A) 380 hydrogen bonds defined for protein. 1101 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: 2.95 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2016 1.33 - 1.46: 1459 1.46 - 1.58: 4239 1.58 - 1.70: 2 1.70 - 1.82: 90 Bond restraints: 7806 Sorted by residual: bond pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 1.698 1.607 0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C3B ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sigma weight residual 1.875 1.794 0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" O5' ACP A1001 " pdb=" PA ACP A1001 " ideal model delta sigma weight residual 1.659 1.578 0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" N VAL A 31 " pdb=" CA VAL A 31 " ideal model delta sigma weight residual 1.461 1.498 -0.037 1.19e-02 7.06e+03 9.63e+00 bond pdb=" C LYS A 761 " pdb=" N PRO A 762 " ideal model delta sigma weight residual 1.329 1.365 -0.036 1.18e-02 7.18e+03 9.35e+00 ... (remaining 7801 not shown) Histogram of bond angle deviations from ideal: 98.90 - 105.96: 181 105.96 - 113.01: 4358 113.01 - 120.07: 2550 120.07 - 127.13: 3414 127.13 - 134.19: 71 Bond angle restraints: 10574 Sorted by residual: angle pdb=" PA ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sigma weight residual 125.06 109.97 15.09 3.00e+00 1.11e-01 2.53e+01 angle pdb=" CA MET A 247 " pdb=" CB MET A 247 " pdb=" CG MET A 247 " ideal model delta sigma weight residual 114.10 122.05 -7.95 2.00e+00 2.50e-01 1.58e+01 angle pdb=" C LYS C 108 " pdb=" N ASN C 109 " pdb=" CA ASN C 109 " ideal model delta sigma weight residual 122.46 127.99 -5.53 1.41e+00 5.03e-01 1.54e+01 angle pdb=" CA LEU A 29 " pdb=" C LEU A 29 " pdb=" N PRO A 30 " ideal model delta sigma weight residual 117.67 121.50 -3.83 1.01e+00 9.80e-01 1.44e+01 angle pdb=" C VAL C 111 " pdb=" CA VAL C 111 " pdb=" CB VAL C 111 " ideal model delta sigma weight residual 110.91 115.37 -4.46 1.24e+00 6.50e-01 1.29e+01 ... (remaining 10569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.07: 4425 26.07 - 52.13: 281 52.13 - 78.20: 28 78.20 - 104.26: 6 104.26 - 130.33: 2 Dihedral angle restraints: 4742 sinusoidal: 1870 harmonic: 2872 Sorted by residual: dihedral pdb=" CB CYS C 55 " pdb=" SG CYS C 55 " pdb=" SG CYS C 128 " pdb=" CB CYS C 128 " ideal model delta sinusoidal sigma weight residual -86.00 -18.81 -67.19 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" O1A ACP A1001 " pdb=" O3A ACP A1001 " pdb=" PA ACP A1001 " pdb=" PB ACP A1001 " ideal model delta sinusoidal sigma weight residual -48.75 81.58 -130.33 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" O1B ACP A1001 " pdb=" C3B ACP A1001 " pdb=" PB ACP A1001 " pdb=" PG ACP A1001 " ideal model delta sinusoidal sigma weight residual -52.82 60.34 -113.16 1 3.00e+01 1.11e-03 1.49e+01 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1081 0.064 - 0.128: 156 0.128 - 0.192: 11 0.192 - 0.255: 1 0.255 - 0.319: 1 Chirality restraints: 1250 Sorted by residual: chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB ILE A 803 " pdb=" CA ILE A 803 " pdb=" CG1 ILE A 803 " pdb=" CG2 ILE A 803 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA LEU A 29 " pdb=" N LEU A 29 " pdb=" C LEU A 29 " pdb=" CB LEU A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 1247 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 760 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.73e+00 pdb=" C ARG A 760 " 0.041 2.00e-02 2.50e+03 pdb=" O ARG A 760 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS A 761 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 648 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C ASP A 648 " 0.037 2.00e-02 2.50e+03 pdb=" O ASP A 648 " -0.014 2.00e-02 2.50e+03 pdb=" N ALA A 649 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 28 " 0.010 2.00e-02 2.50e+03 2.04e-02 4.15e+00 pdb=" C GLU A 28 " -0.035 2.00e-02 2.50e+03 pdb=" O GLU A 28 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 29 " 0.012 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 82 2.64 - 3.21: 6987 3.21 - 3.77: 12430 3.77 - 4.34: 16886 4.34 - 4.90: 27760 Nonbonded interactions: 64145 Sorted by model distance: nonbonded pdb=" O VAL A 303 " pdb=" OD1 ASN A 738 " model vdw 2.075 3.040 nonbonded pdb=" O ARG A 417 " pdb=" OG1 THR A 420 " model vdw 2.217 2.440 nonbonded pdb=" OE2 GLU A 308 " pdb=" ND2 ASN A 738 " model vdw 2.260 2.520 nonbonded pdb=" OG SER A 368 " pdb=" OH TYR A 510 " model vdw 2.286 2.440 nonbonded pdb=" OG SER A 27 " pdb=" OE1 GLN A 202 " model vdw 2.303 2.440 ... (remaining 64140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.000 Extract box with map and model: 2.280 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 26.360 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 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 : 0.004 0.091 7806 Z= 0.288 Angle : 0.779 15.091 10574 Z= 0.430 Chirality : 0.046 0.319 1250 Planarity : 0.005 0.048 1331 Dihedral : 16.329 130.326 2889 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.35 % Allowed : 20.78 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.25), residues: 991 helix: 1.06 (0.22), residues: 479 sheet: 0.05 (0.45), residues: 126 loop : -0.26 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 149 HIS 0.002 0.001 HIS C 86 PHE 0.017 0.001 PHE A 454 TYR 0.013 0.001 TYR C 70 ARG 0.004 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 121 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: C 69 TRP cc_start: 0.7571 (OUTLIER) cc_final: 0.7090 (m-10) outliers start: 3 outliers final: 1 residues processed: 121 average time/residue: 0.1918 time to fit residues: 32.1603 Evaluate side-chains 120 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 118 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 TRP Chi-restraints excluded: chain C residue 146 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 0.0670 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 20.0000 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.0495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7806 Z= 0.156 Angle : 0.500 10.258 10574 Z= 0.252 Chirality : 0.040 0.129 1250 Planarity : 0.003 0.042 1331 Dihedral : 8.481 120.093 1096 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.24 % Allowed : 20.31 % Favored : 77.45 % 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: 1.12 (0.26), residues: 991 helix: 1.70 (0.23), residues: 479 sheet: -0.01 (0.44), residues: 125 loop : -0.12 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 69 HIS 0.001 0.000 HIS C 86 PHE 0.008 0.001 PHE A 176 TYR 0.007 0.001 TYR C 112 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 0.817 Fit side-chains REVERT: A 149 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7236 (m-70) REVERT: A 262 MET cc_start: 0.7629 (mmt) cc_final: 0.7307 (mmt) REVERT: A 691 GLU cc_start: 0.7181 (OUTLIER) cc_final: 0.6621 (mp0) outliers start: 19 outliers final: 10 residues processed: 132 average time/residue: 0.1804 time to fit residues: 33.0369 Evaluate side-chains 127 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 80 optimal weight: 0.0470 chunk 89 optimal weight: 30.0000 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.0170 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN C 114 GLN C 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7806 Z= 0.169 Angle : 0.488 9.790 10574 Z= 0.247 Chirality : 0.040 0.128 1250 Planarity : 0.004 0.041 1331 Dihedral : 7.967 121.511 1092 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.95 % Allowed : 19.83 % Favored : 77.21 % 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: 1.34 (0.26), residues: 991 helix: 1.94 (0.23), residues: 472 sheet: 0.38 (0.47), residues: 115 loop : -0.16 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 149 HIS 0.001 0.000 HIS A 624 PHE 0.012 0.001 PHE A 383 TYR 0.007 0.001 TYR C 112 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 118 time to evaluate : 0.907 Fit side-chains REVERT: A 149 HIS cc_start: 0.7480 (OUTLIER) cc_final: 0.7234 (m-70) REVERT: A 464 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.7039 (mppt) REVERT: A 691 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6505 (mp0) outliers start: 25 outliers final: 14 residues processed: 133 average time/residue: 0.1848 time to fit residues: 34.2742 Evaluate side-chains 129 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 9.9990 chunk 95 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 7806 Z= 0.249 Angle : 0.535 9.619 10574 Z= 0.268 Chirality : 0.042 0.134 1250 Planarity : 0.004 0.044 1331 Dihedral : 8.112 124.835 1092 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.31 % Allowed : 19.83 % Favored : 76.86 % 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: 1.05 (0.26), residues: 991 helix: 1.68 (0.23), residues: 479 sheet: -0.03 (0.45), residues: 125 loop : -0.21 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 149 HIS 0.003 0.001 HIS A 364 PHE 0.013 0.001 PHE A 383 TYR 0.009 0.001 TYR A 483 ARG 0.002 0.000 ARG C 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.890 Fit side-chains REVERT: A 149 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.7215 (m-70) REVERT: A 464 LYS cc_start: 0.7507 (OUTLIER) cc_final: 0.7022 (mppt) REVERT: A 691 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6625 (mp0) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 0.1819 time to fit residues: 34.2726 Evaluate side-chains 131 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7806 Z= 0.177 Angle : 0.498 10.068 10574 Z= 0.252 Chirality : 0.040 0.132 1250 Planarity : 0.004 0.042 1331 Dihedral : 7.956 121.032 1092 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.07 % Allowed : 20.43 % Favored : 76.51 % 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: 1.32 (0.27), residues: 991 helix: 1.95 (0.23), residues: 474 sheet: 0.05 (0.45), residues: 136 loop : -0.10 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.012 0.001 PHE A 383 TYR 0.008 0.001 TYR A 696 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.919 Fit side-chains REVERT: A 149 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7225 (m-70) REVERT: A 464 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7003 (mppt) REVERT: A 691 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6496 (mp0) outliers start: 26 outliers final: 19 residues processed: 130 average time/residue: 0.1843 time to fit residues: 33.3877 Evaluate side-chains 130 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 632 LEU Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 512 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN A 855 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 7806 Z= 0.522 Angle : 0.671 9.070 10574 Z= 0.345 Chirality : 0.049 0.170 1250 Planarity : 0.005 0.058 1331 Dihedral : 8.677 127.085 1092 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.19 % Allowed : 19.72 % Favored : 75.09 % 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: 0.09 (0.26), residues: 991 helix: 0.68 (0.23), residues: 480 sheet: 0.01 (0.48), residues: 122 loop : -0.57 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 60 HIS 0.006 0.001 HIS A 364 PHE 0.023 0.002 PHE A 705 TYR 0.017 0.002 TYR A 483 ARG 0.003 0.001 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 120 time to evaluate : 0.901 Fit side-chains REVERT: A 277 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8356 (mt) REVERT: A 464 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7120 (mppt) REVERT: A 691 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: A 693 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7379 (mmtp) REVERT: A 902 ARG cc_start: 0.6753 (OUTLIER) cc_final: 0.6437 (ttp80) outliers start: 44 outliers final: 31 residues processed: 152 average time/residue: 0.2068 time to fit residues: 42.2820 Evaluate side-chains 155 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 55 CYS Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 59 optimal weight: 0.6980 chunk 58 optimal weight: 0.0000 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 505 GLN A 512 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 747 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7806 Z= 0.157 Angle : 0.512 10.631 10574 Z= 0.260 Chirality : 0.040 0.131 1250 Planarity : 0.004 0.043 1331 Dihedral : 8.084 118.269 1092 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.54 % Allowed : 22.08 % Favored : 74.38 % 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: 0.92 (0.26), residues: 991 helix: 1.61 (0.23), residues: 478 sheet: 0.21 (0.48), residues: 122 loop : -0.46 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 736 HIS 0.001 0.000 HIS A 624 PHE 0.015 0.001 PHE A 383 TYR 0.008 0.001 TYR C 112 ARG 0.002 0.000 ARG A 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7437 (OUTLIER) cc_final: 0.7172 (m-70) REVERT: A 464 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7021 (mppt) REVERT: A 691 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6516 (mp0) REVERT: A 693 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7171 (mmtp) REVERT: A 902 ARG cc_start: 0.6684 (OUTLIER) cc_final: 0.6397 (ttp80) outliers start: 30 outliers final: 18 residues processed: 150 average time/residue: 0.2068 time to fit residues: 42.4238 Evaluate side-chains 141 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.0970 chunk 28 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7806 Z= 0.179 Angle : 0.513 10.196 10574 Z= 0.259 Chirality : 0.040 0.130 1250 Planarity : 0.004 0.043 1331 Dihedral : 8.039 118.603 1092 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 3.07 % Allowed : 22.43 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 991 helix: 1.80 (0.23), residues: 479 sheet: 0.26 (0.49), residues: 110 loop : -0.40 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.022 0.001 PHE A 454 TYR 0.008 0.001 TYR C 112 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 149 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.7229 (m-70) REVERT: A 464 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7052 (mppt) REVERT: A 691 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6515 (mp0) REVERT: A 693 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7085 (mmtp) REVERT: A 902 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6391 (ttp80) outliers start: 26 outliers final: 20 residues processed: 137 average time/residue: 0.2070 time to fit residues: 38.2761 Evaluate side-chains 142 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 50.0000 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7806 Z= 0.339 Angle : 0.594 9.827 10574 Z= 0.303 Chirality : 0.043 0.142 1250 Planarity : 0.004 0.047 1331 Dihedral : 8.319 123.963 1092 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.54 % Allowed : 22.43 % Favored : 74.03 % 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: 0.60 (0.26), residues: 991 helix: 1.25 (0.23), residues: 485 sheet: 0.15 (0.49), residues: 111 loop : -0.52 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 149 HIS 0.003 0.001 HIS A 364 PHE 0.017 0.002 PHE A 454 TYR 0.011 0.001 TYR A 483 ARG 0.003 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 118 time to evaluate : 0.906 Fit side-chains REVERT: A 149 HIS cc_start: 0.7544 (OUTLIER) cc_final: 0.7208 (m-70) REVERT: A 464 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7129 (mppt) REVERT: A 691 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6539 (mp0) REVERT: A 693 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7292 (mmtp) REVERT: A 902 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.6400 (ttp80) outliers start: 30 outliers final: 24 residues processed: 138 average time/residue: 0.2243 time to fit residues: 42.5175 Evaluate side-chains 146 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 117 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 0.4980 chunk 48 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 83 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN A 512 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7806 Z= 0.150 Angle : 0.525 10.398 10574 Z= 0.264 Chirality : 0.040 0.130 1250 Planarity : 0.004 0.042 1331 Dihedral : 7.996 116.358 1092 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.19 % Allowed : 22.67 % Favored : 74.14 % 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: 1.17 (0.27), residues: 991 helix: 1.83 (0.23), residues: 480 sheet: 0.69 (0.52), residues: 99 loop : -0.44 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.021 0.001 PHE A 454 TYR 0.008 0.001 TYR C 112 ARG 0.002 0.000 ARG A 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1982 Ramachandran restraints generated. 991 Oldfield, 0 Emsley, 991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 0.883 Fit side-chains REVERT: A 149 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7231 (m-70) REVERT: A 464 LYS cc_start: 0.7516 (OUTLIER) cc_final: 0.7061 (mppt) REVERT: A 691 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6462 (mp0) REVERT: A 693 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7032 (mmtp) REVERT: A 902 ARG cc_start: 0.6687 (OUTLIER) cc_final: 0.6384 (ttp80) REVERT: C 78 ARG cc_start: 0.6980 (ttm170) cc_final: 0.6570 (ttt180) outliers start: 27 outliers final: 22 residues processed: 137 average time/residue: 0.2119 time to fit residues: 39.4714 Evaluate side-chains 142 residues out of total 851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 141 CYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 HIS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 475 GLU Chi-restraints excluded: chain A residue 505 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 646 VAL Chi-restraints excluded: chain A residue 650 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 693 LYS Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 797 GLU Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 902 ARG Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 0.0870 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 9.9990 chunk 78 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 chunk 80 optimal weight: 7.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 GLN ** A 633 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.202042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157293 restraints weight = 8268.907| |-----------------------------------------------------------------------------| r_work (start): 0.3872 rms_B_bonded: 2.15 r_work: 0.3545 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7806 Z= 0.163 Angle : 0.531 10.235 10574 Z= 0.268 Chirality : 0.040 0.127 1250 Planarity : 0.004 0.042 1331 Dihedral : 7.983 116.559 1092 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.19 % Allowed : 23.14 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 991 helix: 1.92 (0.23), residues: 480 sheet: 0.37 (0.49), residues: 110 loop : -0.35 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 736 HIS 0.001 0.000 HIS A 364 PHE 0.020 0.001 PHE A 454 TYR 0.007 0.001 TYR C 112 ARG 0.002 0.000 ARG A 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1917.37 seconds wall clock time: 35 minutes 38.35 seconds (2138.35 seconds total)