Starting phenix.real_space_refine (version: dev) on Mon Feb 20 00:28:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_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_32111/02_2023/7vsh_32111_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/02_2023/7vsh_32111_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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-4877/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: 1 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: 24 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 chiralities: 3 Time building chain proxies: 6.37, per 1000 atoms: 0.58 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: 4.71 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: 1.56 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: 3.45 Time building geometry restraints manager: 4.89 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=" C22 17F A1102 " pdb=" C23 17F A1102 " ideal model delta sigma weight residual 1.548 1.510 0.038 2.00e-02 2.50e+03 3.68e+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=" C2 NAG C 401 " pdb=" C1 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sigma weight residual 109.64 114.97 -5.33 5.38e-01 3.45e+00 9.82e+01 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 ... (remaining 15227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.06: 6243 22.06 - 44.12: 386 44.12 - 66.18: 46 66.18 - 88.24: 14 88.24 - 110.31: 3 Dihedral angle restraints: 6692 sinusoidal: 2723 harmonic: 3969 Sorted by residual: dihedral pdb=" C2 NAG C 402 " pdb=" C3 NAG C 402 " pdb=" C4 NAG C 402 " pdb=" C5 NAG C 402 " ideal model delta sinusoidal sigma weight residual 50.00 -52.10 102.10 1 2.00e+01 2.50e-03 2.90e+01 dihedral pdb=" C1 NAG C 402 " pdb=" C2 NAG C 402 " pdb=" C3 NAG C 402 " pdb=" C4 NAG C 402 " ideal model delta sinusoidal sigma weight residual -50.00 41.02 -91.02 1 2.00e+01 2.50e-03 2.44e+01 dihedral pdb=" C3 NAG C 401 " pdb=" C1 NAG C 401 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " ideal model delta sinusoidal sigma weight residual -50.00 38.09 -88.09 1 2.00e+01 2.50e-03 2.32e+01 ... (remaining 6689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1560 0.072 - 0.145: 156 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 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. 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: 0.770 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: 4.490 Check model and map are aligned: 0.160 Process input model: 30.940 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 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= 0.304 Angle : 1.100 70.944 15232 Z= 0.475 Chirality : 0.044 0.362 1723 Planarity : 0.011 0.274 1917 Dihedral : 14.072 110.306 4121 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 % 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 *********************** 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 : 1.317 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.2482 time to fit residues: 51.9670 Evaluate side-chains 112 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0962 time to fit residues: 1.9635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8296 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 11243 Z= 0.223 Angle : 0.553 6.659 15232 Z= 0.294 Chirality : 0.043 0.267 1723 Planarity : 0.004 0.043 1917 Dihedral : 8.478 100.714 1514 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 1.08 % 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 (0.22), residues: 1342 helix: -0.02 (0.21), residues: 576 sheet: -0.18 (0.36), residues: 197 loop : -1.65 (0.25), residues: 569 *********************** 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 131 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 1.194 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 129 average time/residue: 0.2441 time to fit residues: 45.6276 Evaluate side-chains 114 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 1.213 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1642 time to fit residues: 4.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 82 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 0.0770 chunk 131 optimal weight: 0.9990 chunk 108 optimal weight: 0.0030 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 overall best weight: 0.7352 ------------------------------------------------------------------------------- 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 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.067 11243 Z= 0.160 Angle : 0.497 7.364 15232 Z= 0.261 Chirality : 0.041 0.246 1723 Planarity : 0.004 0.033 1917 Dihedral : 8.339 103.130 1514 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer Outliers : 0.50 % 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: -0.78 (0.23), residues: 1342 helix: 0.38 (0.21), residues: 579 sheet: -0.02 (0.37), residues: 196 loop : -1.63 (0.26), residues: 567 *********************** 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 125 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.309 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 122 average time/residue: 0.2255 time to fit residues: 40.5256 Evaluate side-chains 103 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 100 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1078 time to fit residues: 2.3446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.0370 chunk 129 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 overall best weight: 1.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** A 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 11243 Z= 0.244 Angle : 0.527 6.295 15232 Z= 0.277 Chirality : 0.043 0.233 1723 Planarity : 0.004 0.034 1917 Dihedral : 8.375 103.585 1514 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.58 % 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: -0.81 (0.22), residues: 1342 helix: 0.40 (0.21), residues: 576 sheet: -0.05 (0.36), residues: 204 loop : -1.70 (0.25), residues: 562 *********************** 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 117 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 110 time to evaluate : 1.338 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 114 average time/residue: 0.2493 time to fit residues: 41.4969 Evaluate side-chains 108 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 106 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1073 time to fit residues: 2.3185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8333 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 11243 Z= 0.304 Angle : 0.549 6.664 15232 Z= 0.288 Chirality : 0.044 0.253 1723 Planarity : 0.004 0.034 1917 Dihedral : 8.377 105.006 1514 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.92 % 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: -0.88 (0.22), residues: 1342 helix: 0.38 (0.21), residues: 570 sheet: -0.05 (0.36), residues: 199 loop : -1.77 (0.25), residues: 573 *********************** 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 122 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 1.288 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 117 average time/residue: 0.2429 time to fit residues: 41.0569 Evaluate side-chains 109 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 104 time to evaluate : 1.316 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1028 time to fit residues: 2.6553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 60 optimal weight: 0.0060 chunk 10 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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: 0.8279 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 11243 Z= 0.158 Angle : 0.483 6.462 15232 Z= 0.253 Chirality : 0.041 0.250 1723 Planarity : 0.004 0.034 1917 Dihedral : 8.191 106.637 1514 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.33 % 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: 0.68 (0.22), residues: 564 sheet: 0.13 (0.37), residues: 190 loop : -1.65 (0.25), residues: 588 *********************** 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 119 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.369 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 116 average time/residue: 0.2641 time to fit residues: 44.1549 Evaluate side-chains 106 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.219 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1237 time to fit residues: 2.0491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.1980 chunk 59 optimal weight: 20.0000 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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** ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 11243 Z= 0.247 Angle : 0.525 6.173 15232 Z= 0.275 Chirality : 0.043 0.237 1723 Planarity : 0.004 0.048 1917 Dihedral : 8.177 107.214 1514 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.04 % Rotamer Outliers : 0.50 % 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: -0.74 (0.23), residues: 1342 helix: 0.50 (0.21), residues: 574 sheet: -0.01 (0.36), residues: 204 loop : -1.72 (0.25), residues: 564 *********************** 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 116 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 110 time to evaluate : 1.318 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 115 average time/residue: 0.2539 time to fit residues: 42.1261 Evaluate side-chains 111 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 108 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1015 time to fit residues: 2.3873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 101 optimal weight: 0.0570 chunk 117 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 11243 Z= 0.156 Angle : 0.483 5.487 15232 Z= 0.252 Chirality : 0.041 0.245 1723 Planarity : 0.003 0.035 1917 Dihedral : 8.025 108.196 1514 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer Outliers : 0.25 % 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: 0.80 (0.22), residues: 558 sheet: 0.21 (0.37), residues: 191 loop : -1.63 (0.25), residues: 593 *********************** 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 119 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 116 time to evaluate : 1.397 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 117 average time/residue: 0.2646 time to fit residues: 44.3613 Evaluate side-chains 108 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 107 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1518 time to fit residues: 2.0328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 0.0370 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- 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: 0.8299 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11243 Z= 0.225 Angle : 0.522 8.724 15232 Z= 0.271 Chirality : 0.043 0.233 1723 Planarity : 0.004 0.035 1917 Dihedral : 8.056 108.651 1514 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 0.33 % 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: -0.65 (0.23), residues: 1342 helix: 0.69 (0.22), residues: 564 sheet: -0.01 (0.36), residues: 204 loop : -1.73 (0.25), residues: 574 *********************** 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 115 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.275 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 113 average time/residue: 0.2639 time to fit residues: 43.0097 Evaluate side-chains 111 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 107 time to evaluate : 1.345 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1096 time to fit residues: 2.6920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 133 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 0.0040 chunk 84 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 overall best weight: 1.5396 ------------------------------------------------------------------------------- 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: 0.8298 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11243 Z= 0.217 Angle : 0.515 7.423 15232 Z= 0.267 Chirality : 0.042 0.245 1723 Planarity : 0.004 0.034 1917 Dihedral : 8.026 108.957 1514 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer Outliers : 0.25 % 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: -0.57 (0.23), residues: 1342 helix: 0.77 (0.22), residues: 558 sheet: -0.03 (0.36), residues: 205 loop : -1.68 (0.25), residues: 579 ********************** 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 113 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.471 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 113 average time/residue: 0.2505 time to fit residues: 40.9937 Evaluate side-chains 104 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 2.9990 chunk 98 optimal weight: 0.0040 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 109 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 0.0670 overall best weight: 0.3428 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.158156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123572 restraints weight = 14154.983| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.07 r_work: 0.3195 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 11243 Z= 0.139 Angle : 0.484 8.806 15232 Z= 0.249 Chirality : 0.040 0.245 1723 Planarity : 0.003 0.035 1917 Dihedral : 7.901 109.674 1514 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.00 % 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: -0.34 (0.23), residues: 1342 helix: 0.94 (0.22), residues: 560 sheet: 0.07 (0.36), residues: 205 loop : -1.52 (0.26), residues: 577 =============================================================================== Job complete usr+sys time: 2320.00 seconds wall clock time: 43 minutes 19.97 seconds (2599.97 seconds total)