Starting phenix.real_space_refine on Sun Apr 7 01:56:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vsg_32110/04_2024/7vsg_32110_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 P 1 5.49 5 S 45 5.16 5 Be 1 3.05 5 C 6072 2.51 5 N 1503 2.21 5 O 1699 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A PHE 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 383": "OE1" <-> "OE2" Residue "A PHE 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 820": "OD1" <-> "OD2" Residue "A TYR 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 903": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 907": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 927": "OE1" <-> "OE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 985": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B GLU 164": "OE1" <-> "OE2" Residue "B GLU 225": "OE1" <-> "OE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 244": "OD1" <-> "OD2" Residue "B TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 305": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9324 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6600 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 792} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Chain: "B" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2604 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 298} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 54 Unusual residues: {'17F': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.19, per 1000 atoms: 0.56 Number of scatterers: 9324 At special positions: 0 Unit cell: (102.09, 99.6, 135.29, 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 45 16.00 P 1 15.00 F 3 9.00 O 1699 8.00 N 1503 7.00 C 6072 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 91 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 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 ALPHA1-4 " NAG D 2 " - " MAN D 3 " BETA1-4 " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG B 401 " - " ASN B 107 " " NAG B 402 " - " ASN B 294 " " NAG D 1 " - " ASN B 180 " Time building additional restraints: 4.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2156 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 8 sheets defined 45.0% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.16 Creating SS restraints... Processing helix chain 'A' and resid 55 through 65 Processing helix chain 'A' and resid 67 through 81 Processing helix chain 'A' and resid 88 through 121 Proline residue: A 94 - end of helix Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' 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 283 through 315 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 357 through 376 removed outlier: 4.217A pdb=" N PHE A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N PHE A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE A 374 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER A 375 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 402 Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 678 through 687 removed outlier: 4.552A pdb=" N SER A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR A 684 " --> pdb=" O THR A 680 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N TYR A 686 " --> pdb=" O LYS A 682 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 687 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 725 removed outlier: 4.019A pdb=" N ARG A 723 " --> pdb=" O LEU A 719 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 724 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS A 725 " --> pdb=" O GLU A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 746 No H-bonds generated for 'chain 'A' and resid 744 through 746' Processing helix chain 'A' and resid 753 through 765 removed outlier: 3.942A pdb=" N SER A 763 " --> pdb=" O ILE A 759 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N GLN A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ASP A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 removed outlier: 4.151A 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 819 through 826 removed outlier: 3.659A pdb=" N SER A 822 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 825 " --> pdb=" O SER A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 844 removed outlier: 3.890A pdb=" N ASN A 844 " --> pdb=" O GLN A 840 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 840 through 844' Processing helix chain 'A' and resid 853 through 894 removed outlier: 3.503A pdb=" N LYS A 856 " --> pdb=" O LYS A 853 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 859 " --> pdb=" O LYS A 856 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 860 " --> pdb=" O LYS A 857 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A 861 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N HIS A 862 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY A 863 " --> pdb=" O LEU A 860 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N HIS A 864 " --> pdb=" O ALA A 861 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 866 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 869 " --> pdb=" O TYR A 866 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 871 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS A 872 " --> pdb=" O ARG A 869 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 874 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN A 875 " --> pdb=" O HIS A 872 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 878 " --> pdb=" O GLN A 875 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN A 881 " --> pdb=" O PHE A 878 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 882 " --> pdb=" O TYR A 879 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 886 " --> pdb=" O CYS A 883 " (cutoff:3.500A) Proline residue: A 887 - end of helix Processing helix chain 'A' and resid 905 through 913 removed outlier: 4.697A pdb=" N ASN A 912 " --> pdb=" O LEU A 908 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 925 Processing helix chain 'A' and resid 932 through 937 removed outlier: 3.763A pdb=" N THR A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 943 removed outlier: 3.554A pdb=" N TYR A 942 " --> pdb=" O PRO A 939 " (cutoff:3.500A) 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 979 removed outlier: 3.622A pdb=" N GLN A 979 " --> pdb=" O TYR A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 1014 Processing helix chain 'A' and resid 1020 through 1040 Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1064 through 1089 Proline residue: A1080 - end of helix removed outlier: 3.552A pdb=" N ASN A1089 " --> pdb=" O ILE A1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 74 Proline residue: B 52 - end of helix removed outlier: 3.692A pdb=" N PHE B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Proline residue: B 63 - end of helix removed outlier: 3.519A pdb=" N THR B 71 " --> pdb=" O GLY B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 4.133A pdb=" N LYS B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 140 through 143 No H-bonds generated for 'chain 'B' and resid 140 through 143' Processing helix chain 'B' and resid 147 through 151 removed outlier: 3.690A pdb=" N LEU B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 147 through 151' Processing helix chain 'B' and resid 173 through 176 No H-bonds generated for 'chain 'B' and resid 173 through 176' Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 223 through 226 No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 240 through 242 No H-bonds generated for 'chain 'B' and resid 240 through 242' Processing helix chain 'B' and resid 255 through 261 Processing helix chain 'B' and resid 323 through 348 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 125 through 129 Processing sheet with id= C, first strand: chain 'A' and resid 146 through 149 removed outlier: 4.018A pdb=" N SER A 163 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N VAL A 260 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LEU A 161 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 170 through 174 Processing sheet with id= E, first strand: chain 'A' and resid 669 through 671 removed outlier: 6.681A pdb=" N VAL A 829 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLY A 815 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 831 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR A 847 " --> pdb=" O GLY A 832 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 696 through 700 Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.300A pdb=" N TYR B 122 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU B 272 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 124 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG B 270 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 104 through 109 removed outlier: 4.766A pdb=" N ARG B 290 " --> pdb=" O ILE B 188 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 188 " --> pdb=" O ARG B 290 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 184 " --> pdb=" O ASN B 294 " (cutoff:3.500A) 346 hydrogen bonds defined for protein. 939 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: 3.23 Time building geometry restraints manager: 4.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1547 1.32 - 1.45: 2610 1.45 - 1.57: 5323 1.57 - 1.69: 2 1.69 - 1.81: 71 Bond restraints: 9553 Sorted by residual: bond pdb=" F3 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.529 1.765 -0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.535 1.752 -0.217 2.00e-02 2.50e+03 1.17e+02 bond pdb=" F1 BFD A 409 " pdb="BE BFD A 409 " ideal model delta sigma weight residual 1.542 1.755 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" CG BFD A 409 " pdb=" OD1 BFD A 409 " ideal model delta sigma weight residual 1.269 1.454 -0.185 2.00e-02 2.50e+03 8.51e+01 bond pdb=" C17 17F A1101 " pdb=" O9 17F A1101 " ideal model delta sigma weight residual 1.434 1.343 0.091 2.00e-02 2.50e+03 2.09e+01 ... (remaining 9548 not shown) Histogram of bond angle deviations from ideal: 95.46 - 103.30: 100 103.30 - 111.14: 3750 111.14 - 118.99: 3922 118.99 - 126.83: 5054 126.83 - 134.67: 127 Bond angle restraints: 12953 Sorted by residual: angle pdb=" C21 17F A1101 " pdb=" C22 17F A1101 " pdb=" C23 17F A1101 " ideal model delta sigma weight residual 152.67 125.64 27.03 3.00e+00 1.11e-01 8.12e+01 angle pdb=" O BFD A 409 " pdb=" C BFD A 409 " pdb=" N LYS A 410 " ideal model delta sigma weight residual 123.00 134.67 -11.67 1.60e+00 3.91e-01 5.32e+01 angle pdb=" F2 BFD A 409 " pdb="BE BFD A 409 " pdb=" F3 BFD A 409 " ideal model delta sigma weight residual 112.60 95.57 17.03 3.00e+00 1.11e-01 3.22e+01 angle pdb=" CA BFD A 409 " pdb=" C BFD A 409 " pdb=" O BFD A 409 " ideal model delta sigma weight residual 120.80 111.22 9.58 1.70e+00 3.46e-01 3.18e+01 angle pdb=" OD1 BFD A 409 " pdb="BE BFD A 409 " pdb=" F1 BFD A 409 " ideal model delta sigma weight residual 102.38 118.58 -16.20 3.00e+00 1.11e-01 2.92e+01 ... (remaining 12948 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.74: 5311 22.74 - 45.47: 314 45.47 - 68.21: 40 68.21 - 90.95: 23 90.95 - 113.69: 31 Dihedral angle restraints: 5719 sinusoidal: 2376 harmonic: 3343 Sorted by residual: dihedral pdb=" CB CYS B 91 " pdb=" SG CYS B 91 " pdb=" SG CYS B 104 " pdb=" CB CYS B 104 " ideal model delta sinusoidal sigma weight residual 93.00 156.03 -63.03 1 1.00e+01 1.00e-02 5.25e+01 dihedral pdb=" C2 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" C4 NAG D 2 " pdb=" O4 NAG D 2 " ideal model delta sinusoidal sigma weight residual 175.11 61.42 113.69 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" O2 MAN D 3 " pdb=" C1 MAN D 3 " pdb=" C2 MAN D 3 " pdb=" O5 MAN D 3 " ideal model delta sinusoidal sigma weight residual 67.84 -179.23 -112.93 1 3.00e+01 1.11e-03 1.48e+01 ... (remaining 5716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1297 0.060 - 0.120: 158 0.120 - 0.180: 8 0.180 - 0.240: 1 0.240 - 0.300: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG B 401 " pdb=" ND2 ASN B 107 " pdb=" C2 NAG B 401 " pdb=" O5 NAG B 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 294 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN B 180 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 1463 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " 0.292 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" C7 NAG D 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " 0.190 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " -0.411 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " -0.213 2.00e-02 2.50e+03 1.81e-01 4.08e+02 pdb=" C7 NAG D 1 " 0.047 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.038 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " 0.294 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 402 " 0.175 2.00e-02 2.50e+03 1.45e-01 2.62e+02 pdb=" C7 NAG B 402 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG B 402 " 0.129 2.00e-02 2.50e+03 pdb=" N2 NAG B 402 " -0.234 2.00e-02 2.50e+03 pdb=" O7 NAG B 402 " -0.022 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1010 2.75 - 3.29: 9646 3.29 - 3.82: 15488 3.82 - 4.36: 18926 4.36 - 4.90: 31297 Nonbonded interactions: 76367 Sorted by model distance: nonbonded pdb=" OG SER A 763 " pdb=" NZ LYS A 772 " model vdw 2.210 2.520 nonbonded pdb=" O LEU A 983 " pdb=" OG SER A1063 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR A 907 " pdb=" OG SER A1037 " model vdw 2.260 2.440 nonbonded pdb=" O LEU A 758 " pdb=" OG SER A 762 " model vdw 2.266 2.440 nonbonded pdb=" O PHE A 915 " pdb=" OG SER A1029 " model vdw 2.268 2.440 ... (remaining 76362 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.990 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 29.270 Find NCS groups from input model: 0.260 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.006 0.236 9553 Z= 0.419 Angle : 0.768 27.031 12953 Z= 0.360 Chirality : 0.041 0.300 1466 Planarity : 0.010 0.243 1612 Dihedral : 17.234 113.687 3554 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.15 (0.24), residues: 1126 helix: 0.59 (0.22), residues: 498 sheet: 0.69 (0.45), residues: 137 loop : -1.01 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 PHE 0.014 0.001 PHE A1047 TYR 0.016 0.001 TYR A 318 ARG 0.004 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.996 Fit side-chains REVERT: A 45 ILE cc_start: 0.6976 (pt) cc_final: 0.6122 (pt) REVERT: A 145 ASP cc_start: 0.8244 (t70) cc_final: 0.7881 (t70) REVERT: A 285 GLU cc_start: 0.7538 (tt0) cc_final: 0.7327 (tt0) REVERT: A 395 ASP cc_start: 0.7834 (m-30) cc_final: 0.7478 (t0) REVERT: A 816 ASP cc_start: 0.6971 (p0) cc_final: 0.6537 (p0) REVERT: A 846 ASP cc_start: 0.8086 (m-30) cc_final: 0.7827 (m-30) REVERT: B 31 THR cc_start: 0.8069 (m) cc_final: 0.7837 (p) REVERT: B 197 ILE cc_start: 0.8262 (mp) cc_final: 0.7750 (tp) REVERT: B 337 PHE cc_start: 0.7259 (t80) cc_final: 0.6943 (t80) outliers start: 1 outliers final: 0 residues processed: 165 average time/residue: 0.2257 time to fit residues: 51.8845 Evaluate side-chains 111 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 88 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN B 130 ASN B 131 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9553 Z= 0.195 Angle : 0.584 10.282 12953 Z= 0.290 Chirality : 0.043 0.263 1466 Planarity : 0.004 0.040 1612 Dihedral : 15.462 108.640 1373 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.77 % Allowed : 7.38 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.12 (0.25), residues: 1126 helix: 0.94 (0.23), residues: 492 sheet: 0.43 (0.43), residues: 148 loop : -0.88 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 313 HIS 0.007 0.001 HIS A 864 PHE 0.018 0.002 PHE A 775 TYR 0.014 0.001 TYR B 121 ARG 0.003 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.038 Fit side-chains REVERT: A 143 VAL cc_start: 0.7055 (OUTLIER) cc_final: 0.6784 (p) REVERT: A 145 ASP cc_start: 0.8358 (t70) cc_final: 0.8007 (t70) REVERT: A 790 MET cc_start: 0.8660 (mmm) cc_final: 0.8325 (mtp) REVERT: A 816 ASP cc_start: 0.7174 (p0) cc_final: 0.6769 (p0) REVERT: A 846 ASP cc_start: 0.8105 (m-30) cc_final: 0.7784 (m-30) REVERT: B 197 ILE cc_start: 0.8268 (mp) cc_final: 0.7779 (tp) REVERT: B 337 PHE cc_start: 0.7294 (t80) cc_final: 0.6813 (t80) outliers start: 18 outliers final: 11 residues processed: 127 average time/residue: 0.2008 time to fit residues: 37.0226 Evaluate side-chains 114 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 102 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN B 126 ASN B 235 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9553 Z= 0.215 Angle : 0.579 9.526 12953 Z= 0.281 Chirality : 0.043 0.247 1466 Planarity : 0.004 0.037 1612 Dihedral : 11.619 88.450 1373 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.26 % Allowed : 11.12 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.01 (0.25), residues: 1126 helix: 0.88 (0.24), residues: 496 sheet: 0.25 (0.42), residues: 153 loop : -1.00 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1067 HIS 0.006 0.001 HIS A1023 PHE 0.012 0.002 PHE A 775 TYR 0.015 0.001 TYR B 241 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.966 Fit side-chains REVERT: A 145 ASP cc_start: 0.8296 (t70) cc_final: 0.7974 (t70) REVERT: A 790 MET cc_start: 0.8653 (mmm) cc_final: 0.8337 (mtp) REVERT: A 800 ARG cc_start: 0.7238 (ttm170) cc_final: 0.6974 (ttm110) REVERT: A 816 ASP cc_start: 0.7149 (p0) cc_final: 0.6773 (p0) REVERT: A 846 ASP cc_start: 0.8108 (m-30) cc_final: 0.7724 (m-30) REVERT: B 197 ILE cc_start: 0.8255 (mp) cc_final: 0.7849 (tp) REVERT: B 337 PHE cc_start: 0.7263 (t80) cc_final: 0.6731 (t80) outliers start: 23 outliers final: 17 residues processed: 120 average time/residue: 0.2004 time to fit residues: 34.7401 Evaluate side-chains 112 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 95 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 0.0670 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 90 optimal weight: 0.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 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 0.030 9553 Z= 0.129 Angle : 0.522 9.178 12953 Z= 0.250 Chirality : 0.040 0.208 1466 Planarity : 0.003 0.035 1612 Dihedral : 9.470 81.858 1373 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.18 % Allowed : 13.78 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.19 (0.25), residues: 1126 helix: 1.05 (0.24), residues: 500 sheet: 0.37 (0.42), residues: 152 loop : -0.92 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 PHE 0.018 0.001 PHE A 368 TYR 0.012 0.001 TYR A 324 ARG 0.002 0.000 ARG B 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.089 Fit side-chains REVERT: A 72 PHE cc_start: 0.7465 (m-80) cc_final: 0.7151 (m-80) REVERT: A 145 ASP cc_start: 0.8337 (t70) cc_final: 0.8005 (t70) REVERT: A 348 MET cc_start: 0.7991 (tpt) cc_final: 0.7754 (tpp) REVERT: A 714 ARG cc_start: 0.7019 (mmm160) cc_final: 0.6719 (mmp80) REVERT: A 790 MET cc_start: 0.8585 (mmm) cc_final: 0.8372 (mtp) REVERT: A 800 ARG cc_start: 0.7287 (ttm170) cc_final: 0.7041 (ttm110) REVERT: A 846 ASP cc_start: 0.8002 (m-30) cc_final: 0.7735 (m-30) REVERT: B 185 LEU cc_start: 0.8891 (mm) cc_final: 0.8676 (mm) REVERT: B 197 ILE cc_start: 0.8212 (mp) cc_final: 0.7885 (tp) REVERT: B 337 PHE cc_start: 0.7242 (t80) cc_final: 0.6733 (t80) outliers start: 12 outliers final: 6 residues processed: 130 average time/residue: 0.2127 time to fit residues: 39.4505 Evaluate side-chains 111 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 105 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain B residue 157 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 2.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 GLN B 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9553 Z= 0.291 Angle : 0.614 9.926 12953 Z= 0.303 Chirality : 0.043 0.244 1466 Planarity : 0.004 0.037 1612 Dihedral : 9.057 98.412 1373 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.05 % Allowed : 13.98 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.13 (0.25), residues: 1126 helix: 0.87 (0.24), residues: 498 sheet: 0.17 (0.44), residues: 146 loop : -1.16 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1067 HIS 0.008 0.001 HIS A1023 PHE 0.016 0.002 PHE A 97 TYR 0.016 0.002 TYR A 311 ARG 0.005 0.001 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 104 time to evaluate : 1.091 Fit side-chains REVERT: A 145 ASP cc_start: 0.8280 (t70) cc_final: 0.7941 (t70) REVERT: A 790 MET cc_start: 0.8636 (mmm) cc_final: 0.8351 (mtp) REVERT: A 816 ASP cc_start: 0.7379 (p0) cc_final: 0.6957 (p0) REVERT: A 826 GLU cc_start: 0.6902 (tp30) cc_final: 0.6162 (tp30) REVERT: A 846 ASP cc_start: 0.8074 (m-30) cc_final: 0.7675 (m-30) REVERT: B 126 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (t0) REVERT: B 197 ILE cc_start: 0.8359 (mp) cc_final: 0.7923 (tp) REVERT: B 224 GLU cc_start: 0.6391 (tp30) cc_final: 0.6130 (tp30) REVERT: B 337 PHE cc_start: 0.7263 (t80) cc_final: 0.6746 (t80) outliers start: 31 outliers final: 24 residues processed: 128 average time/residue: 0.2102 time to fit residues: 39.3067 Evaluate side-chains 121 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 96 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 127 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9553 Z= 0.222 Angle : 0.559 9.366 12953 Z= 0.276 Chirality : 0.042 0.229 1466 Planarity : 0.004 0.038 1612 Dihedral : 8.828 100.734 1373 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.56 % Allowed : 15.35 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.15 (0.25), residues: 1126 helix: 0.89 (0.24), residues: 491 sheet: 0.09 (0.45), residues: 143 loop : -1.15 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 313 HIS 0.006 0.001 HIS A1023 PHE 0.019 0.002 PHE A 368 TYR 0.015 0.001 TYR A 311 ARG 0.003 0.000 ARG B 133 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.100 Fit side-chains REVERT: A 72 PHE cc_start: 0.7496 (m-80) cc_final: 0.7138 (m-80) REVERT: A 145 ASP cc_start: 0.8321 (t70) cc_final: 0.7968 (t70) REVERT: A 790 MET cc_start: 0.8604 (mmm) cc_final: 0.8371 (mtp) REVERT: A 816 ASP cc_start: 0.7392 (p0) cc_final: 0.6993 (p0) REVERT: A 846 ASP cc_start: 0.7995 (m-30) cc_final: 0.7649 (m-30) REVERT: B 197 ILE cc_start: 0.8330 (mp) cc_final: 0.7911 (tp) REVERT: B 337 PHE cc_start: 0.7232 (t80) cc_final: 0.6704 (t80) outliers start: 26 outliers final: 23 residues processed: 125 average time/residue: 0.2138 time to fit residues: 38.3435 Evaluate side-chains 124 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9553 Z= 0.252 Angle : 0.569 9.506 12953 Z= 0.282 Chirality : 0.042 0.224 1466 Planarity : 0.004 0.037 1612 Dihedral : 8.778 102.798 1373 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.25 % Allowed : 15.26 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.22 (0.25), residues: 1126 helix: 0.83 (0.24), residues: 490 sheet: 0.10 (0.47), residues: 133 loop : -1.18 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1067 HIS 0.006 0.001 HIS A1023 PHE 0.018 0.002 PHE A 76 TYR 0.017 0.002 TYR A 311 ARG 0.004 0.001 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 1.048 Fit side-chains REVERT: A 72 PHE cc_start: 0.7502 (m-80) cc_final: 0.7131 (m-80) REVERT: A 145 ASP cc_start: 0.8323 (t70) cc_final: 0.7970 (t70) REVERT: A 714 ARG cc_start: 0.7285 (mmm160) cc_final: 0.6913 (mmp80) REVERT: A 790 MET cc_start: 0.8619 (mmm) cc_final: 0.8394 (mtp) REVERT: A 816 ASP cc_start: 0.7351 (p0) cc_final: 0.7099 (p0) REVERT: A 846 ASP cc_start: 0.7891 (m-30) cc_final: 0.7559 (m-30) REVERT: B 197 ILE cc_start: 0.8314 (mp) cc_final: 0.7943 (tp) REVERT: B 310 MET cc_start: 0.8569 (tmm) cc_final: 0.8102 (tmm) REVERT: B 337 PHE cc_start: 0.7208 (t80) cc_final: 0.6704 (t80) outliers start: 33 outliers final: 31 residues processed: 126 average time/residue: 0.1907 time to fit residues: 35.3715 Evaluate side-chains 123 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 301 THR Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 820 ASP Chi-restraints excluded: chain A residue 823 MET Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1004 VAL Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1086 VAL Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 292 SER Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 21 optimal weight: 20.0000 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9553 Z= 0.135 Angle : 0.508 9.305 12953 Z= 0.250 Chirality : 0.040 0.189 1466 Planarity : 0.003 0.041 1612 Dihedral : 8.294 99.225 1373 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.07 % Allowed : 16.44 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.05 (0.25), residues: 1126 helix: 1.10 (0.25), residues: 484 sheet: 0.25 (0.46), residues: 141 loop : -1.09 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 PHE 0.021 0.001 PHE A 368 TYR 0.013 0.001 TYR A 188 ARG 0.002 0.000 ARG A 723 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.131 Fit side-chains REVERT: A 72 PHE cc_start: 0.7450 (m-80) cc_final: 0.7106 (m-80) REVERT: A 145 ASP cc_start: 0.8312 (t70) cc_final: 0.7917 (t70) REVERT: A 714 ARG cc_start: 0.7215 (mmm160) cc_final: 0.6835 (mmp80) REVERT: A 816 ASP cc_start: 0.7201 (p0) cc_final: 0.6928 (p0) REVERT: A 846 ASP cc_start: 0.7949 (m-30) cc_final: 0.7623 (m-30) REVERT: B 197 ILE cc_start: 0.8258 (mp) cc_final: 0.7961 (tp) REVERT: B 337 PHE cc_start: 0.7163 (t80) cc_final: 0.6656 (t80) outliers start: 21 outliers final: 13 residues processed: 125 average time/residue: 0.2095 time to fit residues: 37.7970 Evaluate side-chains 114 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 157 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 104 optimal weight: 0.0870 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 79 optimal weight: 4.9990 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9553 Z= 0.135 Angle : 0.513 9.444 12953 Z= 0.251 Chirality : 0.039 0.190 1466 Planarity : 0.003 0.042 1612 Dihedral : 7.834 95.840 1373 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.77 % Allowed : 16.83 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.17 (0.26), residues: 1126 helix: 1.17 (0.25), residues: 485 sheet: 0.33 (0.46), residues: 141 loop : -1.00 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 313 HIS 0.003 0.001 HIS A 864 PHE 0.014 0.001 PHE A 76 TYR 0.012 0.001 TYR B 241 ARG 0.002 0.000 ARG B 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.067 Fit side-chains REVERT: A 72 PHE cc_start: 0.7342 (m-80) cc_final: 0.6986 (m-80) REVERT: A 145 ASP cc_start: 0.8340 (t70) cc_final: 0.7970 (t70) REVERT: A 289 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7293 (t0) REVERT: A 714 ARG cc_start: 0.7197 (mmm160) cc_final: 0.6831 (mmp80) REVERT: A 816 ASP cc_start: 0.7196 (p0) cc_final: 0.6915 (p0) REVERT: A 846 ASP cc_start: 0.7859 (m-30) cc_final: 0.7557 (m-30) REVERT: B 197 ILE cc_start: 0.8270 (mp) cc_final: 0.7935 (tp) REVERT: B 310 MET cc_start: 0.8520 (tmm) cc_final: 0.8205 (tmm) REVERT: B 337 PHE cc_start: 0.7168 (t80) cc_final: 0.6677 (t80) outliers start: 18 outliers final: 14 residues processed: 121 average time/residue: 0.2086 time to fit residues: 36.7056 Evaluate side-chains 119 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 798 ILE Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 157 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 0.0270 chunk 112 optimal weight: 0.9980 chunk 103 optimal weight: 0.0040 chunk 89 optimal weight: 0.9990 chunk 9 optimal weight: 20.0000 chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 844 ASN ** A 881 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9553 Z= 0.134 Angle : 0.505 8.890 12953 Z= 0.248 Chirality : 0.039 0.198 1466 Planarity : 0.003 0.043 1612 Dihedral : 7.521 94.407 1373 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.48 % Allowed : 17.22 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.22 (0.26), residues: 1126 helix: 1.21 (0.25), residues: 490 sheet: 0.40 (0.46), residues: 140 loop : -1.00 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 PHE 0.018 0.001 PHE A 368 TYR 0.011 0.001 TYR A 188 ARG 0.005 0.000 ARG B 290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.018 Fit side-chains REVERT: A 72 PHE cc_start: 0.7313 (m-80) cc_final: 0.6963 (m-80) REVERT: A 145 ASP cc_start: 0.8280 (t70) cc_final: 0.7896 (t70) REVERT: A 289 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7298 (t0) REVERT: A 714 ARG cc_start: 0.7168 (mmm160) cc_final: 0.6815 (mmp80) REVERT: A 790 MET cc_start: 0.8689 (mmm) cc_final: 0.8347 (mtp) REVERT: A 816 ASP cc_start: 0.7244 (p0) cc_final: 0.6963 (p0) REVERT: A 846 ASP cc_start: 0.7844 (m-30) cc_final: 0.7562 (m-30) REVERT: B 197 ILE cc_start: 0.8258 (mp) cc_final: 0.7938 (tp) REVERT: B 337 PHE cc_start: 0.7171 (t80) cc_final: 0.6672 (t80) outliers start: 15 outliers final: 14 residues processed: 115 average time/residue: 0.2089 time to fit residues: 34.7969 Evaluate side-chains 116 residues out of total 1016 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 PHE Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 704 THR Chi-restraints excluded: chain A residue 750 ILE Chi-restraints excluded: chain A residue 786 LEU Chi-restraints excluded: chain A residue 980 THR Chi-restraints excluded: chain A residue 1045 TRP Chi-restraints excluded: chain A residue 1077 SER Chi-restraints excluded: chain A residue 1091 ARG Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 157 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 24 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 881 ASN ** 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 = 0.3930 r_free = 0.3930 target = 0.160890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123950 restraints weight = 12978.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123346 restraints weight = 12989.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.125418 restraints weight = 12555.528| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9553 Z= 0.139 Angle : 0.505 8.343 12953 Z= 0.248 Chirality : 0.039 0.197 1466 Planarity : 0.003 0.042 1612 Dihedral : 7.335 93.241 1373 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.57 % Allowed : 17.32 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.28 (0.26), residues: 1126 helix: 1.23 (0.25), residues: 492 sheet: 0.53 (0.46), residues: 138 loop : -0.98 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 313 HIS 0.004 0.001 HIS A 864 PHE 0.019 0.001 PHE A 368 TYR 0.011 0.001 TYR A 188 ARG 0.003 0.000 ARG B 290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1974.59 seconds wall clock time: 37 minutes 1.77 seconds (2221.77 seconds total)