Starting phenix.real_space_refine (version: 1.21rc1) on Thu Jul 6 01:14:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_2023/7vsh_32111_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_2023/7vsh_32111.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_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_32111/07_2023/7vsh_32111_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_2023/7vsh_32111_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_2023/7vsh_32111.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_2023/7vsh_32111.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_2023/7vsh_32111_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsh_32111/07_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 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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 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: 5.83, per 1000 atoms: 0.53 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: 4.37 Conformation dependent library (CDL) restraints added in 1.4 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: 3.44 Time building geometry restraints manager: 4.68 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 - 17.14: 5992 17.14 - 34.28: 534 34.28 - 51.43: 103 51.43 - 68.57: 20 68.57 - 85.71: 9 Dihedral angle restraints: 6658 sinusoidal: 2689 harmonic: 3969 Sorted by residual: dihedral pdb=" CA THR A 51 " pdb=" C THR A 51 " pdb=" N LEU A 52 " pdb=" CA LEU A 52 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 941 " pdb=" C LEU A 941 " pdb=" N TYR A 942 " pdb=" CA TYR A 942 " ideal model delta harmonic sigma weight residual 180.00 -162.57 -17.43 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA PHE A 894 " pdb=" C PHE A 894 " pdb=" N CYS A 895 " pdb=" CA CYS A 895 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 6655 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: 0.890 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: 4.310 Check model and map are aligned: 0.190 Set scattering table: 0.100 Process input model: 30.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.480 ------------------------------------------------------------------------------- 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 : 13.548 85.712 4087 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 : 1.229 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 146 average time/residue: 0.2405 time to fit residues: 50.2283 Evaluate side-chains 112 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.254 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1015 time to fit residues: 1.9276 ------------------------------------------------------------------------------- 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: 0.8028 moved from start: 0.0982 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= 0.215 Angle : 0.564 6.649 15232 Z= 0.293 Chirality : 0.043 0.290 1723 Planarity : 0.004 0.042 1917 Dihedral : 5.471 53.880 1480 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % 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: -0.01 (0.21), residues: 581 sheet: -0.16 (0.36), residues: 197 loop : -1.70 (0.25), residues: 564 *********************** 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 129 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.241 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 127 average time/residue: 0.2383 time to fit residues: 43.5490 Evaluate side-chains 115 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1472 time to fit residues: 4.4243 ------------------------------------------------------------------------------- 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: 2.9990 chunk 101 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 121 optimal weight: 0.0970 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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: 0.8043 moved from start: 0.1283 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= 0.240 Angle : 0.552 7.069 15232 Z= 0.284 Chirality : 0.043 0.296 1723 Planarity : 0.004 0.036 1917 Dihedral : 5.397 56.746 1480 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % 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: -1.02 (0.22), residues: 1342 helix: 0.21 (0.21), residues: 579 sheet: -0.29 (0.35), residues: 210 loop : -1.75 (0.25), residues: 553 *********************** 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 : 1.408 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 123 average time/residue: 0.2429 time to fit residues: 43.3341 Evaluate side-chains 107 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 106 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0997 time to fit residues: 1.9344 ------------------------------------------------------------------------------- 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: 3.9990 chunk 91 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 864 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 11243 Z= 0.259 Angle : 0.546 6.653 15232 Z= 0.282 Chirality : 0.044 0.277 1723 Planarity : 0.004 0.034 1917 Dihedral : 5.341 58.024 1480 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 0.67 % 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: -0.93 (0.22), residues: 1342 helix: 0.27 (0.21), residues: 575 sheet: -0.07 (0.36), residues: 197 loop : -1.74 (0.25), residues: 570 *********************** 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 118 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.304 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 114 average time/residue: 0.2429 time to fit residues: 40.0737 Evaluate side-chains 107 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 104 time to evaluate : 1.297 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1043 time to fit residues: 2.4866 ------------------------------------------------------------------------------- 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: 9.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 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: 0.8088 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 11243 Z= 0.338 Angle : 0.586 7.146 15232 Z= 0.303 Chirality : 0.045 0.263 1723 Planarity : 0.004 0.035 1917 Dihedral : 5.345 55.431 1480 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer Outliers : 1.00 % 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: -1.08 (0.22), residues: 1342 helix: 0.18 (0.21), residues: 575 sheet: -0.29 (0.35), residues: 210 loop : -1.80 (0.25), residues: 557 *********************** 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 125 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 113 time to evaluate : 1.279 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 118 average time/residue: 0.2393 time to fit residues: 41.2970 Evaluate side-chains 109 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 1.277 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1056 time to fit residues: 3.2248 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 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: 0.8041 moved from start: 0.1716 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= 0.195 Angle : 0.523 7.356 15232 Z= 0.270 Chirality : 0.042 0.271 1723 Planarity : 0.004 0.035 1917 Dihedral : 5.040 52.142 1480 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.66 % Favored : 94.26 % Rotamer Outliers : 0.75 % 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 (0.23), residues: 1342 helix: 0.42 (0.21), residues: 574 sheet: -0.12 (0.36), residues: 203 loop : -1.75 (0.25), residues: 565 *********************** 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: 9 poor density : 110 time to evaluate : 1.194 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 116 average time/residue: 0.2447 time to fit residues: 41.7321 Evaluate side-chains 111 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 1.279 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1087 time to fit residues: 2.6140 ------------------------------------------------------------------------------- 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: 2.9990 chunk 109 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 80 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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: 0.8036 moved from start: 0.1793 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= 0.196 Angle : 0.517 7.856 15232 Z= 0.266 Chirality : 0.042 0.272 1723 Planarity : 0.004 0.035 1917 Dihedral : 4.821 48.295 1480 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer Outliers : 0.83 % 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: 0.59 (0.21), residues: 566 sheet: -0.12 (0.36), residues: 210 loop : -1.76 (0.25), residues: 566 *********************** 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 124 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.279 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 121 average time/residue: 0.2394 time to fit residues: 42.4041 Evaluate side-chains 114 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 108 time to evaluate : 1.577 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1123 time to fit residues: 2.9891 ------------------------------------------------------------------------------- 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: 6.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 117 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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: 0.8010 moved from start: 0.1935 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= 0.159 Angle : 0.494 6.647 15232 Z= 0.254 Chirality : 0.042 0.276 1723 Planarity : 0.004 0.035 1917 Dihedral : 4.604 44.499 1480 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % 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: -0.60 (0.23), residues: 1342 helix: 0.76 (0.22), residues: 562 sheet: -0.01 (0.37), residues: 197 loop : -1.71 (0.25), residues: 583 *********************** 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 122 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.234 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 121 average time/residue: 0.2425 time to fit residues: 42.6158 Evaluate side-chains 109 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 106 time to evaluate : 1.296 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1248 time to fit residues: 2.5383 ------------------------------------------------------------------------------- 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: 2.9990 chunk 123 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 113 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 127 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.1984 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= 0.186 Angle : 0.504 6.574 15232 Z= 0.260 Chirality : 0.042 0.272 1723 Planarity : 0.004 0.035 1917 Dihedral : 4.558 42.970 1480 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.23), residues: 1342 helix: 0.79 (0.22), residues: 558 sheet: 0.03 (0.37), residues: 203 loop : -1.70 (0.25), residues: 581 *********************** 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 116 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 114 time to evaluate : 1.359 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.2560 time to fit residues: 42.9645 Evaluate side-chains 111 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1120 time to fit residues: 1.8336 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 0.0170 chunk 88 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 overall best weight: 0.7220 ------------------------------------------------------------------------------- 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: 0.7985 moved from start: 0.2114 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= 0.147 Angle : 0.485 6.589 15232 Z= 0.249 Chirality : 0.042 0.272 1723 Planarity : 0.003 0.035 1917 Dihedral : 4.367 40.113 1480 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % 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: -0.40 (0.23), residues: 1342 helix: 0.90 (0.22), residues: 559 sheet: 0.13 (0.37), residues: 197 loop : -1.58 (0.25), residues: 586 ********************** 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 120 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.282 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 119 average time/residue: 0.2588 time to fit residues: 44.6358 Evaluate side-chains 112 residues out of total 1204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 110 time to evaluate : 1.278 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2863 time to fit residues: 2.4759 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 0.0010 chunk 15 optimal weight: 10.0000 chunk 29 optimal weight: 0.3980 chunk 106 optimal weight: 0.9990 chunk 44 optimal weight: 10.0000 chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.3873 r_free = 0.3873 target = 0.157079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.122353 restraints weight = 14130.801| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.06 r_work: 0.3187 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2238 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 : 0.488 7.509 15232 Z= 0.249 Chirality : 0.041 0.272 1723 Planarity : 0.003 0.035 1917 Dihedral : 4.250 38.868 1480 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.17 % 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: -0.39 (0.23), residues: 1342 helix: 0.96 (0.22), residues: 557 sheet: 0.01 (0.36), residues: 209 loop : -1.59 (0.26), residues: 576 =============================================================================== Job complete usr+sys time: 2260.68 seconds wall clock time: 41 minutes 57.79 seconds (2517.79 seconds total)