Starting phenix.real_space_refine on Fri Mar 15 07:32:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/03_2024/7vsh_32111_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 58 5.16 5 C 7106 2.51 5 N 1800 2.21 5 O 2022 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 269": "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: 10992 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8300 Classifications: {'peptide': 1028} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 25, 'TRANS': 1002} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 25, 'TRANS': 298} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 1, '17F': 1, 'ALF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'17F:plan-5': 1, '17F:plan-1': 1, '17F:plan-2': 1, '17F:plan-3': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.04, per 1000 atoms: 0.55 Number of scatterers: 10992 At special positions: 0 Unit cell: (110.39, 87.15, 158.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 58 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 2022 8.00 N 1800 7.00 C 7106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 91 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 94 " - pdb=" SG CYS C 102 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " 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 Links applied ALPHA1-3 " NAG B 2 " - " MAN B 3 " BETA1-3 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN C 180 " " NAG C 401 " - " ASN C 294 " " NAG C 402 " - " ASN C 107 " Time building additional restraints: 4.18 Conformation dependent library (CDL) restraints added in 1.7 seconds 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2562 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 11 sheets defined 42.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.63 Creating SS restraints... Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 88 through 121 removed outlier: 5.387A pdb=" N LEU A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Proline residue: A 94 - end of helix removed outlier: 3.558A pdb=" N PHE A 97 " --> pdb=" O PRO A 94 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 98 " --> pdb=" O LEU A 95 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 99 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 101 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 102 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 109 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP A 110 " --> pdb=" O GLY A 107 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 113 " --> pdb=" O ASP A 110 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 119 " --> pdb=" O ALA A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 176 through 179 No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 283 through 315 removed outlier: 3.565A pdb=" N VAL A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 332 No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 359 through 376 removed outlier: 4.200A pdb=" N PHE A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N PHE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.613A pdb=" N GLY A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.510A pdb=" N ALA A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 575 through 590 removed outlier: 3.852A pdb=" N GLU A 579 " --> pdb=" O ASN A 575 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LEU A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL A 583 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 removed outlier: 3.531A pdb=" N ARG A 610 " --> pdb=" O ASP A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 632 Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.621A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 725 removed outlier: 3.940A pdb=" N GLU A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU A 718 " --> pdb=" O ARG A 714 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 760 Processing helix chain 'A' and resid 771 through 781 removed outlier: 3.923A pdb=" N LYS A 781 " --> pdb=" O GLN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 803 Processing helix chain 'A' and resid 821 through 826 Processing helix chain 'A' and resid 840 through 843 No H-bonds generated for 'chain 'A' and resid 840 through 843' Processing helix chain 'A' and resid 853 through 860 removed outlier: 3.508A pdb=" N LYS A 856 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 858 " --> pdb=" O LEU A 855 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 859 " --> pdb=" O LYS A 856 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 860 " --> pdb=" O LYS A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 894 removed outlier: 3.599A pdb=" N GLN A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 884 " --> pdb=" O LYS A 880 " (cutoff:3.500A) Proline residue: A 887 - end of helix removed outlier: 4.160A pdb=" N GLN A 892 " --> pdb=" O GLN A 888 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N PHE A 893 " --> pdb=" O PHE A 889 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N PHE A 894 " --> pdb=" O LEU A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 913 removed outlier: 4.803A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.670A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 945 No H-bonds generated for 'chain 'A' and resid 942 through 945' Processing helix chain 'A' and resid 949 through 951 No H-bonds generated for 'chain 'A' and resid 949 through 951' Processing helix chain 'A' and resid 953 through 975 removed outlier: 3.596A pdb=" N PHE A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 979 No H-bonds generated for 'chain 'A' and resid 977 through 979' Processing helix chain 'A' and resid 992 through 1014 Processing helix chain 'A' and resid 1020 through 1040 removed outlier: 3.635A pdb=" N LEU A1030 " --> pdb=" O ILE A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 Processing helix chain 'A' and resid 1064 through 1077 Processing helix chain 'A' and resid 1079 through 1089 removed outlier: 3.543A pdb=" N ILE A1085 " --> pdb=" O GLU A1081 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 74 Proline residue: C 52 - end of helix removed outlier: 4.319A pdb=" N ILE C 62 " --> pdb=" O GLY C 58 " (cutoff:3.500A) Proline residue: C 63 - end of helix Processing helix chain 'C' and resid 90 through 94 removed outlier: 4.024A pdb=" N LYS C 93 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 No H-bonds generated for 'chain 'C' and resid 132 through 135' Processing helix chain 'C' and resid 147 through 151 removed outlier: 3.566A pdb=" N LEU C 151 " --> pdb=" O SER C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 147 through 151' Processing helix chain 'C' and resid 155 through 160 Proline residue: C 159 - end of helix Processing helix chain 'C' and resid 173 through 176 No H-bonds generated for 'chain 'C' and resid 173 through 176' Processing helix chain 'C' and resid 207 through 211 Processing helix chain 'C' and resid 223 through 226 No H-bonds generated for 'chain 'C' and resid 223 through 226' Processing helix chain 'C' and resid 240 through 242 No H-bonds generated for 'chain 'C' and resid 240 through 242' Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 255 through 261 Processing helix chain 'C' and resid 302 through 304 No H-bonds generated for 'chain 'C' and resid 302 through 304' Processing helix chain 'C' and resid 323 through 349 Processing sheet with id= A, first strand: chain 'A' and resid 20 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 124 through 128 Processing sheet with id= C, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.577A pdb=" N VAL A 260 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASP A 158 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 185 through 188 removed outlier: 3.620A pdb=" N TYR A 172 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 669 through 672 removed outlier: 6.607A pdb=" N VAL A 829 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY A 815 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE A 831 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR A 847 " --> pdb=" O GLY A 832 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 419 through 422 removed outlier: 3.604A pdb=" N ALA A 647 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 519 through 521 removed outlier: 6.905A pdb=" N ILE A 550 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N THR A 537 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N SER A 548 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 696 through 700 Processing sheet with id= I, first strand: chain 'A' and resid 598 through 600 removed outlier: 3.693A pdb=" N GLY A 644 " --> pdb=" O VAL A 598 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N PHE A 600 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU A 642 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 77 through 81 removed outlier: 3.558A pdb=" N ARG C 307 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N TYR C 122 " --> pdb=" O LEU C 272 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU C 272 " --> pdb=" O TYR C 122 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N LEU C 124 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ARG C 270 " --> pdb=" O LEU C 124 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 104 through 109 removed outlier: 4.520A pdb=" N ARG C 290 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C 182 " --> pdb=" O THR C 296 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1074 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: 3.89 Time building geometry restraints manager: 4.58 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: 3451 1.34 - 1.46: 2146 1.46 - 1.58: 5555 1.58 - 1.70: 0 1.70 - 1.82: 91 Bond restraints: 11243 Sorted by residual: bond pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.684 1.801 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.798 -0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.685 1.797 -0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" F4 ALF A1101 " pdb="AL ALF A1101 " ideal model delta sigma weight residual 1.686 1.797 -0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C3 NAG B 1 " pdb=" O3 NAG B 1 " ideal model delta sigma weight residual 1.403 1.443 -0.040 2.00e-02 2.50e+03 3.90e+00 ... (remaining 11238 not shown) Histogram of bond angle deviations from ideal: 89.58 - 107.59: 361 107.59 - 125.60: 14716 125.60 - 143.61: 153 143.61 - 161.62: 0 161.62 - 179.62: 2 Bond angle restraints: 15232 Sorted by residual: angle pdb=" F1 ALF A1101 " pdb="AL ALF A1101 " pdb=" F2 ALF A1101 " ideal model delta sigma weight residual 108.68 179.62 -70.94 3.00e+00 1.11e-01 5.59e+02 angle pdb=" F3 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 109.63 179.50 -69.87 3.00e+00 1.11e-01 5.42e+02 angle pdb=" C21 17F A1102 " pdb=" C22 17F A1102 " pdb=" C23 17F A1102 " ideal model delta sigma weight residual 152.67 120.82 31.85 3.00e+00 1.11e-01 1.13e+02 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F4 ALF A1101 " ideal model delta sigma weight residual 110.21 90.06 20.15 3.00e+00 1.11e-01 4.51e+01 angle pdb=" F2 ALF A1101 " pdb="AL ALF A1101 " pdb=" F3 ALF A1101 " ideal model delta sigma weight residual 109.59 89.58 20.01 3.00e+00 1.11e-01 4.45e+01 ... (remaining 15227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.22: 6339 23.22 - 46.44: 346 46.44 - 69.66: 44 69.66 - 92.88: 17 92.88 - 116.10: 11 Dihedral angle restraints: 6757 sinusoidal: 2788 harmonic: 3969 Sorted by residual: dihedral pdb=" O2 MAN B 3 " pdb=" C2 MAN B 3 " pdb=" C3 MAN B 3 " pdb=" O3 MAN B 3 " ideal model delta sinusoidal sigma weight residual -57.63 58.47 -116.10 1 3.00e+01 1.11e-03 1.54e+01 dihedral pdb=" C4 MAN B 3 " pdb=" C2 MAN B 3 " pdb=" C3 MAN B 3 " pdb=" O2 MAN B 3 " ideal model delta sinusoidal sigma weight residual -64.75 -179.48 114.73 1 3.00e+01 1.11e-03 1.51e+01 dihedral pdb=" C1 MAN B 3 " pdb=" C2 MAN B 3 " pdb=" C3 MAN B 3 " pdb=" O3 MAN B 3 " ideal model delta sinusoidal sigma weight residual -176.02 -62.95 -113.07 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 6754 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1561 0.072 - 0.145: 155 0.145 - 0.217: 5 0.217 - 0.289: 1 0.289 - 0.362: 1 Chirality restraints: 1723 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O3 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-02 2.50e+03 3.27e+02 chirality pdb=" C1 MAN B 3 " pdb=" O3 NAG B 2 " pdb=" C2 MAN B 3 " pdb=" O5 MAN B 3 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.50e+01 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 294 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1720 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 401 " -0.320 2.00e-02 2.50e+03 2.74e-01 9.36e+02 pdb=" C7 NAG C 401 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG C 401 " -0.173 2.00e-02 2.50e+03 pdb=" N2 NAG C 401 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG C 401 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 402 " 0.317 2.00e-02 2.50e+03 2.66e-01 8.84e+02 pdb=" C7 NAG C 402 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG C 402 " 0.194 2.00e-02 2.50e+03 pdb=" N2 NAG C 402 " -0.456 2.00e-02 2.50e+03 pdb=" O7 NAG C 402 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.218 2.00e-02 2.50e+03 1.85e-01 4.30e+02 pdb=" C7 NAG B 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.303 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.169 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 52 2.55 - 3.14: 8717 3.14 - 3.73: 16645 3.73 - 4.31: 24291 4.31 - 4.90: 39998 Nonbonded interactions: 89703 Sorted by model distance: nonbonded pdb="MG MG A1100 " pdb=" F1 ALF A1101 " model vdw 1.964 2.120 nonbonded pdb=" OH TYR A 311 " pdb=" OD2 ASP A 343 " model vdw 2.235 2.440 nonbonded pdb=" ND2 ASN C 176 " pdb=" OD1 ASN C 235 " model vdw 2.239 2.520 nonbonded pdb=" OG1 THR A 484 " pdb=" O ALA A 487 " model vdw 2.251 2.440 nonbonded pdb=" OH TYR A 879 " pdb=" OE1 GLU A 966 " model vdw 2.281 2.440 ... (remaining 89698 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.950 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.590 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.050 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.117 11243 Z= 0.311 Angle : 1.103 70.944 15232 Z= 0.458 Chirality : 0.044 0.362 1723 Planarity : 0.011 0.274 1917 Dihedral : 15.263 116.102 4186 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.25 % Allowed : 0.08 % Favored : 99.67 % 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: -1.53 (0.22), residues: 1342 helix: -0.57 (0.21), residues: 565 sheet: -0.13 (0.37), residues: 192 loop : -1.70 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.005 0.001 HIS A 470 PHE 0.029 0.002 PHE A 978 TYR 0.016 0.002 TYR A1054 ARG 0.004 0.001 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.226 Fit side-chains REVERT: A 205 LEU cc_start: 0.7316 (tp) cc_final: 0.7008 (tp) REVERT: A 629 MET cc_start: 0.6772 (mmp) cc_final: 0.5886 (mtp) outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.2364 time to fit residues: 48.9909 Evaluate side-chains 113 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 0.0030 chunk 63 optimal weight: 5.9990 chunk 78 optimal weight: 0.0060 chunk 121 optimal weight: 0.2980 overall best weight: 1.4610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 536 HIS A 584 HIS ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 283 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11243 Z= 0.219 Angle : 0.579 7.683 15232 Z= 0.296 Chirality : 0.043 0.259 1723 Planarity : 0.004 0.043 1917 Dihedral : 9.601 77.090 1581 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.17 % Allowed : 5.41 % Favored : 93.42 % 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: -1.09 (0.22), residues: 1342 helix: 0.00 (0.21), residues: 577 sheet: -0.16 (0.36), residues: 197 loop : -1.65 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.013 0.001 HIS A 536 PHE 0.019 0.001 PHE A 633 TYR 0.017 0.001 TYR A 324 ARG 0.003 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 110 ASP cc_start: 0.8121 (t0) cc_final: 0.7909 (t0) REVERT: A 628 LYS cc_start: 0.7556 (ttpp) cc_final: 0.7349 (ttpp) REVERT: A 629 MET cc_start: 0.6889 (mmp) cc_final: 0.5905 (mtp) REVERT: A 678 MET cc_start: 0.8215 (tmm) cc_final: 0.7953 (tmm) REVERT: C 55 PHE cc_start: 0.7149 (m-80) cc_final: 0.6762 (m-80) outliers start: 14 outliers final: 12 residues processed: 132 average time/residue: 0.2787 time to fit residues: 53.5155 Evaluate side-chains 118 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 106 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 536 HIS Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 131 optimal weight: 4.9990 chunk 108 optimal weight: 0.0010 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 536 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11243 Z= 0.177 Angle : 0.530 7.262 15232 Z= 0.269 Chirality : 0.042 0.200 1723 Planarity : 0.004 0.033 1917 Dihedral : 7.433 74.245 1581 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 1.00 % Allowed : 8.33 % Favored : 90.67 % 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: -0.85 (0.22), residues: 1342 helix: 0.34 (0.21), residues: 578 sheet: -0.10 (0.37), residues: 196 loop : -1.67 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.004 0.001 HIS A 716 PHE 0.018 0.001 PHE A 633 TYR 0.016 0.001 TYR A 324 ARG 0.002 0.000 ARG A 572 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.286 Fit side-chains REVERT: A 628 LYS cc_start: 0.7558 (ttpp) cc_final: 0.7299 (ttpp) REVERT: A 629 MET cc_start: 0.6850 (mmp) cc_final: 0.5980 (mtp) REVERT: A 678 MET cc_start: 0.8232 (tmm) cc_final: 0.7968 (tmm) REVERT: C 55 PHE cc_start: 0.7036 (m-80) cc_final: 0.6767 (m-80) REVERT: C 60 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7935 (mt) REVERT: C 303 TYR cc_start: 0.7803 (m-80) cc_final: 0.7464 (m-80) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.2388 time to fit residues: 44.8654 Evaluate side-chains 116 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 60 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11243 Z= 0.259 Angle : 0.552 6.749 15232 Z= 0.282 Chirality : 0.043 0.183 1723 Planarity : 0.004 0.034 1917 Dihedral : 7.168 73.332 1581 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.50 % Allowed : 11.07 % Favored : 87.43 % 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: -0.84 (0.22), residues: 1342 helix: 0.36 (0.21), residues: 576 sheet: 0.05 (0.36), residues: 196 loop : -1.74 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 716 PHE 0.020 0.002 PHE A 421 TYR 0.017 0.002 TYR A 311 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.130 Fit side-chains REVERT: A 628 LYS cc_start: 0.7587 (ttpp) cc_final: 0.7295 (ttpp) REVERT: A 678 MET cc_start: 0.8213 (tmm) cc_final: 0.7886 (tmm) REVERT: A 722 TYR cc_start: 0.5290 (t80) cc_final: 0.5059 (t80) REVERT: C 55 PHE cc_start: 0.6984 (m-80) cc_final: 0.6709 (m-80) outliers start: 18 outliers final: 13 residues processed: 126 average time/residue: 0.2482 time to fit residues: 45.2416 Evaluate side-chains 118 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11243 Z= 0.319 Angle : 0.579 6.910 15232 Z= 0.298 Chirality : 0.045 0.194 1723 Planarity : 0.004 0.035 1917 Dihedral : 7.148 72.967 1581 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 1.58 % Allowed : 12.57 % Favored : 85.85 % 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: -0.96 (0.22), residues: 1342 helix: 0.27 (0.21), residues: 574 sheet: -0.03 (0.36), residues: 197 loop : -1.80 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.005 0.001 HIS A 828 PHE 0.020 0.002 PHE A 633 TYR 0.019 0.002 TYR A 311 ARG 0.003 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.267 Fit side-chains REVERT: A 628 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7405 (ttpp) REVERT: C 55 PHE cc_start: 0.7016 (m-80) cc_final: 0.6740 (m-80) outliers start: 19 outliers final: 16 residues processed: 128 average time/residue: 0.2401 time to fit residues: 44.4196 Evaluate side-chains 121 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 0.5980 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 129 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11243 Z= 0.174 Angle : 0.506 6.918 15232 Z= 0.260 Chirality : 0.042 0.180 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.850 71.936 1581 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 1.67 % Allowed : 12.91 % Favored : 85.43 % 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: -0.75 (0.23), residues: 1342 helix: 0.55 (0.22), residues: 568 sheet: 0.02 (0.36), residues: 197 loop : -1.75 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.003 0.001 HIS A 864 PHE 0.015 0.001 PHE A 633 TYR 0.025 0.001 TYR A 722 ARG 0.003 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.151 Fit side-chains REVERT: A 145 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7766 (p0) REVERT: A 628 LYS cc_start: 0.7676 (ttpp) cc_final: 0.7383 (ttpp) REVERT: C 55 PHE cc_start: 0.7004 (m-80) cc_final: 0.6778 (m-80) REVERT: C 303 TYR cc_start: 0.7832 (m-80) cc_final: 0.7564 (m-80) outliers start: 20 outliers final: 17 residues processed: 125 average time/residue: 0.2492 time to fit residues: 43.9764 Evaluate side-chains 121 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 chunk 59 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11243 Z= 0.232 Angle : 0.533 6.833 15232 Z= 0.274 Chirality : 0.043 0.181 1723 Planarity : 0.004 0.047 1917 Dihedral : 6.765 71.803 1581 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.26 % Favored : 93.67 % Rotamer: Outliers : 2.08 % Allowed : 12.99 % Favored : 84.93 % 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: -0.82 (0.22), residues: 1342 helix: 0.50 (0.21), residues: 572 sheet: -0.05 (0.36), residues: 199 loop : -1.82 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 323 HIS 0.004 0.001 HIS A 716 PHE 0.017 0.001 PHE A 633 TYR 0.025 0.001 TYR A 722 ARG 0.002 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.246 Fit side-chains REVERT: A 145 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7786 (p0) REVERT: A 252 LYS cc_start: 0.7749 (tppt) cc_final: 0.7498 (tmtt) REVERT: A 628 LYS cc_start: 0.7683 (ttpp) cc_final: 0.7379 (ttpp) REVERT: C 44 ILE cc_start: 0.7648 (tp) cc_final: 0.7201 (tp) REVERT: C 55 PHE cc_start: 0.6970 (m-80) cc_final: 0.6750 (m-80) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 0.2369 time to fit residues: 43.8869 Evaluate side-chains 127 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 106 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11243 Z= 0.177 Angle : 0.505 6.917 15232 Z= 0.259 Chirality : 0.042 0.175 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.557 71.136 1581 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.92 % Allowed : 13.16 % Favored : 84.93 % 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: -0.62 (0.23), residues: 1342 helix: 0.75 (0.22), residues: 563 sheet: 0.06 (0.37), residues: 191 loop : -1.75 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.003 0.001 HIS A 716 PHE 0.015 0.001 PHE A 633 TYR 0.016 0.001 TYR A 324 ARG 0.002 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.321 Fit side-chains REVERT: A 145 ASP cc_start: 0.8004 (OUTLIER) cc_final: 0.7753 (p0) REVERT: A 252 LYS cc_start: 0.7744 (tppt) cc_final: 0.7262 (tmtt) REVERT: A 596 LEU cc_start: 0.7460 (mp) cc_final: 0.7198 (mp) REVERT: A 628 LYS cc_start: 0.7649 (ttpp) cc_final: 0.7294 (ttpp) REVERT: C 303 TYR cc_start: 0.7837 (m-80) cc_final: 0.7575 (m-80) outliers start: 23 outliers final: 18 residues processed: 132 average time/residue: 0.2398 time to fit residues: 45.0273 Evaluate side-chains 126 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 0.0570 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11243 Z= 0.193 Angle : 0.511 6.886 15232 Z= 0.262 Chirality : 0.042 0.176 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.484 71.082 1579 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.67 % Allowed : 14.15 % Favored : 84.18 % 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: -0.59 (0.23), residues: 1342 helix: 0.80 (0.22), residues: 558 sheet: 0.03 (0.37), residues: 192 loop : -1.74 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 323 HIS 0.003 0.001 HIS A 716 PHE 0.017 0.001 PHE A 633 TYR 0.016 0.001 TYR A 311 ARG 0.002 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 1.245 Fit side-chains REVERT: A 145 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7796 (p0) REVERT: A 252 LYS cc_start: 0.7781 (tppt) cc_final: 0.7293 (tmtt) REVERT: A 628 LYS cc_start: 0.7595 (ttpp) cc_final: 0.7311 (ttpp) REVERT: A 649 GLU cc_start: 0.7185 (tp30) cc_final: 0.6931 (tt0) outliers start: 20 outliers final: 18 residues processed: 127 average time/residue: 0.2490 time to fit residues: 45.1533 Evaluate side-chains 127 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11243 Z= 0.312 Angle : 0.575 6.812 15232 Z= 0.295 Chirality : 0.045 0.192 1723 Planarity : 0.004 0.035 1917 Dihedral : 6.720 71.611 1579 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.00 % Allowed : 14.07 % Favored : 83.93 % 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: -0.83 (0.22), residues: 1342 helix: 0.51 (0.21), residues: 568 sheet: -0.07 (0.35), residues: 206 loop : -1.85 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 323 HIS 0.005 0.001 HIS A 864 PHE 0.018 0.002 PHE A 633 TYR 0.019 0.002 TYR A 311 ARG 0.003 0.000 ARG C 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2684 Ramachandran restraints generated. 1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 113 time to evaluate : 1.230 Fit side-chains REVERT: A 145 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7836 (p0) REVERT: A 193 THR cc_start: 0.7656 (p) cc_final: 0.7329 (p) REVERT: A 628 LYS cc_start: 0.7625 (ttpp) cc_final: 0.7373 (ttpp) REVERT: A 631 LYS cc_start: 0.7676 (ttpt) cc_final: 0.7124 (mtmt) REVERT: C 44 ILE cc_start: 0.7637 (tp) cc_final: 0.7175 (tp) outliers start: 24 outliers final: 20 residues processed: 131 average time/residue: 0.2224 time to fit residues: 42.1808 Evaluate side-chains 131 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 152 ASP Chi-restraints excluded: chain A residue 222 VAL Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 494 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 918 LEU Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain C residue 290 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 0.0470 chunk 98 optimal weight: 0.0000 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 overall best weight: 0.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 844 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.156121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.121256 restraints weight = 14141.260| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.33 r_work: 0.3157 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11243 Z= 0.138 Angle : 0.494 6.944 15232 Z= 0.254 Chirality : 0.041 0.181 1723 Planarity : 0.003 0.034 1917 Dihedral : 6.439 70.700 1579 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.25 % Allowed : 14.82 % Favored : 83.93 % 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: -0.49 (0.23), residues: 1342 helix: 0.88 (0.22), residues: 558 sheet: 0.04 (0.37), residues: 191 loop : -1.66 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 323 HIS 0.003 0.001 HIS A 716 PHE 0.014 0.001 PHE C 54 TYR 0.016 0.001 TYR A 324 ARG 0.002 0.000 ARG A 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.51 seconds wall clock time: 42 minutes 25.43 seconds (2545.43 seconds total)