Starting phenix.real_space_refine on Sun Sep 13 13:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.map 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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wyx_32897/09_2026/7wyx_32897.cif" } 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 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= 0.004 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 32 5.49 5 Mg 2 5.21 5 S 118 5.16 5 Na 2 4.78 5 C 14694 2.51 5 N 3528 2.21 5 O 4338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22714 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 477 Unusual residues: {' MG': 1, ' NA': 1, '7Q2': 1, 'ATP': 1, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'CLR': 1, 'PCW': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: C, D, E, K, L, M, N Time building chain proxies: 11.39, per 1000 atoms: 0.50 Number of scatterers: 22714 At special positions: 0 Unit cell: (216.276, 181.844, 104.372, 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 118 16.00 P 32 15.00 Mg 2 11.99 Na 2 11.00 O 4338 8.00 N 3528 7.00 C 14694 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA H 3 " - " MAN H 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 6 " BETA1-2 " MAN H 4 " - " NAG H 5 " " MAN L 4 " - " NAG L 5 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " BETA1-6 " NAG F 1 " - " FUC F 6 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 5 " " NAG K 1 " - " FUC K 6 " " NAG M 1 " - " FUC M 5 " NAG-ASN " NAG F 1 " - " ASN B 114 " " NAG H 1 " - " ASN B 159 " " NAG I 1 " - " ASN B 194 " " NAG J 1 " - " ASN B 267 " " NAG K 1 " - " ASN D 114 " " NAG L 1 " - " ASN D 159 " " NAG M 1 " - " ASN D 194 " " NAG N 1 " - " ASN D 267 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 49.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 47 through 56 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 87 through 97 removed outlier: 3.654A pdb=" N LYS A 91 " --> pdb=" O PRO A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 122 Processing helix chain 'A' and resid 127 through 160 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 261 through 264 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 282 through 313 Processing helix chain 'A' and resid 316 through 331 removed outlier: 3.659A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.598A pdb=" N THR A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 removed outlier: 3.948A pdb=" N VAL A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 361 through 364' Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 415 through 428 removed outlier: 3.677A pdb=" N SER A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 464 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 510 through 516 Processing helix chain 'A' and resid 531 through 548 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.827A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 649 Processing helix chain 'A' and resid 656 through 660 removed outlier: 3.672A pdb=" N ALA A 660 " --> pdb=" O PRO A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 671 Processing helix chain 'A' and resid 674 through 685 Processing helix chain 'A' and resid 694 through 707 Processing helix chain 'A' and resid 718 through 720 No H-bonds generated for 'chain 'A' and resid 718 through 720' Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.641A pdb=" N LYS A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 746 Processing helix chain 'A' and resid 755 through 782 removed outlier: 4.296A pdb=" N VAL A 759 " --> pdb=" O PHE A 755 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 786 Processing helix chain 'A' and resid 787 through 797 Processing helix chain 'A' and resid 803 through 812 removed outlier: 3.505A pdb=" N ILE A 807 " --> pdb=" O GLY A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 Processing helix chain 'A' and resid 823 through 825 No H-bonds generated for 'chain 'A' and resid 823 through 825' Processing helix chain 'A' and resid 846 through 854 removed outlier: 3.657A pdb=" N ILE A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 876 Processing helix chain 'A' and resid 879 through 884 removed outlier: 4.252A pdb=" N ILE A 884 " --> pdb=" O PRO A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 892 Processing helix chain 'A' and resid 907 through 939 removed outlier: 4.035A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A 939 " --> pdb=" O ILE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 948 Processing helix chain 'A' and resid 951 through 971 removed outlier: 3.553A pdb=" N ILE A 955 " --> pdb=" O ASN A 951 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 978 Processing helix chain 'A' and resid 986 through 990 removed outlier: 3.793A pdb=" N PHE A 989 " --> pdb=" O SER A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1012 removed outlier: 3.527A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1022 Processing helix chain 'B' and resid 29 through 62 removed outlier: 3.879A pdb=" N TRP B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 62 " --> pdb=" O LEU B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 99 through 111 removed outlier: 3.558A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.934A pdb=" N ALA B 204 " --> pdb=" O GLU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 225 removed outlier: 4.383A pdb=" N LYS B 225 " --> pdb=" O GLU B 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 225' Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.746A pdb=" N TYR B 237 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 245 No H-bonds generated for 'chain 'B' and resid 243 through 245' Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.162A pdb=" N LEU B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 13 Processing helix chain 'G' and resid 15 through 40 Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 47 through 56 Processing helix chain 'C' and resid 64 through 76 Processing helix chain 'C' and resid 87 through 97 removed outlier: 3.654A pdb=" N LYS C 91 " --> pdb=" O PRO C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 122 Processing helix chain 'C' and resid 127 through 160 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 261 through 264 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 282 through 313 Processing helix chain 'C' and resid 316 through 331 removed outlier: 3.659A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.599A pdb=" N THR C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 364 removed outlier: 3.948A pdb=" N VAL C 364 " --> pdb=" O LEU C 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 361 through 364' Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 415 through 428 removed outlier: 3.679A pdb=" N SER C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 464 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 510 through 516 Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'C' and resid 598 through 609 Processing helix chain 'C' and resid 620 through 632 removed outlier: 3.827A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 649 Processing helix chain 'C' and resid 656 through 660 removed outlier: 3.673A pdb=" N ALA C 660 " --> pdb=" O PRO C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 671 Processing helix chain 'C' and resid 674 through 685 Processing helix chain 'C' and resid 694 through 707 Processing helix chain 'C' and resid 718 through 720 No H-bonds generated for 'chain 'C' and resid 718 through 720' Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.641A pdb=" N LYS C 727 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 746 Processing helix chain 'C' and resid 755 through 782 removed outlier: 4.296A pdb=" N VAL C 759 " --> pdb=" O PHE C 755 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 786 Processing helix chain 'C' and resid 787 through 797 Processing helix chain 'C' and resid 803 through 812 removed outlier: 3.505A pdb=" N ILE C 807 " --> pdb=" O GLY C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 822 Processing helix chain 'C' and resid 823 through 825 No H-bonds generated for 'chain 'C' and resid 823 through 825' Processing helix chain 'C' and resid 846 through 854 removed outlier: 3.658A pdb=" N ILE C 850 " --> pdb=" O ASN C 846 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 876 Processing helix chain 'C' and resid 879 through 884 removed outlier: 4.252A pdb=" N ILE C 884 " --> pdb=" O PRO C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 892 Processing helix chain 'C' and resid 907 through 939 removed outlier: 4.035A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N THR C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 948 Processing helix chain 'C' and resid 951 through 971 removed outlier: 3.554A pdb=" N ILE C 955 " --> pdb=" O ASN C 951 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 978 Processing helix chain 'C' and resid 986 through 990 removed outlier: 3.793A pdb=" N PHE C 989 " --> pdb=" O SER C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 991 through 1012 removed outlier: 3.525A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1022 Processing helix chain 'D' and resid 29 through 62 removed outlier: 3.879A pdb=" N TRP D 33 " --> pdb=" O THR D 29 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 98 Processing helix chain 'D' and resid 99 through 111 removed outlier: 3.558A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 removed outlier: 3.934A pdb=" N ALA D 204 " --> pdb=" O GLU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 225 removed outlier: 4.383A pdb=" N LYS D 225 " --> pdb=" O GLU D 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 225' Processing helix chain 'D' and resid 233 through 237 removed outlier: 3.746A pdb=" N TYR D 237 " --> pdb=" O LEU D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 245 No H-bonds generated for 'chain 'D' and resid 243 through 245' Processing helix chain 'D' and resid 248 through 253 removed outlier: 4.161A pdb=" N LEU D 252 " --> pdb=" O TYR D 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 15 through 40 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.758A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N THR A 253 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA A 208 " --> pdb=" O THR A 253 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG A 255 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP A 202 " --> pdb=" O VAL A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 226 removed outlier: 4.097A pdb=" N ASN A 248 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.706A pdb=" N VAL A 712 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N VAL A 732 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL A 714 " --> pdb=" O VAL A 732 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N MET A 734 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY A 716 " --> pdb=" O MET A 734 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A 373 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL A 616 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER A 375 " --> pdb=" O VAL A 616 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL A 613 " --> pdb=" O ILE A 688 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N PHE A 690 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET A 615 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS A 663 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ALA A 691 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL A 665 " --> pdb=" O ALA A 691 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 392 Processing sheet with id=AA5, first strand: chain 'A' and resid 432 through 433 removed outlier: 3.849A pdb=" N VAL A 432 " --> pdb=" O ALA A 448 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 476 through 480 removed outlier: 6.495A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS A 557 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE A 585 " --> pdb=" O HIS A 557 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA A 559 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N LEU A 583 " --> pdb=" O ALA A 559 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE A 585 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE A 521 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLY A 587 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 11.584A pdb=" N LEU A 523 " --> pdb=" O GLY A 587 " (cutoff:3.500A) removed outlier: 17.098A pdb=" N MET A 589 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 898 through 899 Processing sheet with id=AA8, first strand: chain 'B' and resid 78 through 80 removed outlier: 6.986A pdb=" N LEU B 268 " --> pdb=" O ILE B 226 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE B 226 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 88 through 91 Processing sheet with id=AB1, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.759A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR C 253 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA C 208 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ARG C 255 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP C 202 " --> pdb=" O VAL C 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 225 through 226 removed outlier: 4.096A pdb=" N ASN C 248 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.705A pdb=" N VAL C 712 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N VAL C 732 " --> pdb=" O VAL C 712 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL C 714 " --> pdb=" O VAL C 732 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N MET C 734 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY C 716 " --> pdb=" O MET C 734 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C 373 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL C 616 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N SER C 375 " --> pdb=" O VAL C 616 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL C 613 " --> pdb=" O ILE C 688 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N PHE C 690 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET C 615 " --> pdb=" O PHE C 690 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N CYS C 663 " --> pdb=" O VAL C 689 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA C 691 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL C 665 " --> pdb=" O ALA C 691 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 390 through 392 Processing sheet with id=AB6, first strand: chain 'C' and resid 432 through 433 removed outlier: 3.850A pdb=" N VAL C 432 " --> pdb=" O ALA C 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 476 through 480 removed outlier: 6.495A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS C 557 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE C 585 " --> pdb=" O HIS C 557 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ALA C 559 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N LEU C 583 " --> pdb=" O ALA C 559 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE C 585 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE C 521 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLY C 587 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 11.584A pdb=" N LEU C 523 " --> pdb=" O GLY C 587 " (cutoff:3.500A) removed outlier: 17.100A pdb=" N MET C 589 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 898 through 899 Processing sheet with id=AB9, first strand: chain 'D' and resid 78 through 80 removed outlier: 6.987A pdb=" N LEU D 268 " --> pdb=" O ILE D 226 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ILE D 226 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 88 through 91 Processing sheet with id=AC2, first strand: chain 'D' and resid 124 through 125 1006 hydrogen bonds defined for protein. 2916 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: 4.77 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6867 1.35 - 1.47: 5216 1.47 - 1.59: 10823 1.59 - 1.70: 70 1.70 - 1.82: 172 Bond restraints: 23148 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.509 0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C39 PCW G1304 " pdb=" C40 PCW G1304 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C39 PCW E1304 " pdb=" C40 PCW E1304 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C19 PCW A1109 " pdb=" C20 PCW A1109 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 23143 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 28921 2.33 - 4.65: 1835 4.65 - 6.98: 334 6.98 - 9.30: 118 9.30 - 11.63: 44 Bond angle restraints: 31252 Sorted by residual: angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 101.00 7.67 1.55e+00 4.16e-01 2.45e+01 angle pdb=" N GLY A 855 " pdb=" CA GLY A 855 " pdb=" C GLY A 855 " ideal model delta sigma weight residual 113.18 124.49 -11.31 2.37e+00 1.78e-01 2.28e+01 angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" C LYS D 158 " ideal model delta sigma weight residual 110.80 120.96 -10.16 2.13e+00 2.20e-01 2.28e+01 angle pdb=" N GLY C 855 " pdb=" CA GLY C 855 " pdb=" C GLY C 855 " ideal model delta sigma weight residual 113.18 124.46 -11.28 2.37e+00 1.78e-01 2.26e+01 ... (remaining 31247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12792 35.90 - 71.81: 684 71.81 - 107.71: 30 107.71 - 143.61: 24 143.61 - 179.51: 2 Dihedral angle restraints: 13532 sinusoidal: 5876 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW G1303 " pdb=" C31 PCW G1303 " pdb=" C32 PCW G1303 " pdb=" O2 PCW G1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.34 -179.51 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW E1303 " pdb=" C31 PCW E1303 " pdb=" C32 PCW E1303 " pdb=" O2 PCW E1303 " ideal model delta sinusoidal sigma weight residual -168.17 11.29 -179.46 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1112 " pdb=" C31 PCW A1112 " pdb=" C32 PCW A1112 " pdb=" O2 PCW A1112 " ideal model delta sinusoidal sigma weight residual -168.17 -29.70 -138.47 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 13529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2967 0.078 - 0.157: 455 0.157 - 0.235: 62 0.235 - 0.314: 30 0.314 - 0.392: 18 Chirality restraints: 3532 Sorted by residual: chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.38e+01 chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.37e+01 chirality pdb=" C1 FUC K 6 " pdb=" O6 NAG K 1 " pdb=" C2 FUC K 6 " pdb=" O5 FUC K 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.13e+01 ... (remaining 3529 not shown) Planarity restraints: 3820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.088 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO B 123 " 0.239 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.076 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.088 5.00e-02 4.00e+02 1.38e-01 3.05e+01 pdb=" N PRO D 123 " -0.239 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.076 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 124 " 0.063 5.00e-02 4.00e+02 9.58e-02 1.47e+01 pdb=" N PRO A 125 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " 0.052 5.00e-02 4.00e+02 ... (remaining 3817 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 102 2.49 - 3.10: 15861 3.10 - 3.70: 31118 3.70 - 4.30: 47965 4.30 - 4.90: 77914 Nonbonded interactions: 172960 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.893 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.893 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1202 " model vdw 1.973 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 1.976 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 2.007 2.170 ... (remaining 172955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } 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: 1.220 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 29.420 Find NCS groups from input model: 0.180 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: 0.010 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.011 0.308 23192 Z= 0.561 Angle : 1.376 17.146 31378 Z= 0.656 Chirality : 0.066 0.392 3532 Planarity : 0.009 0.138 3812 Dihedral : 19.009 179.514 8602 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.68 % Allowed : 8.35 % Favored : 90.97 % Rotamer: Outliers : 10.43 % Allowed : 8.58 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.31 (0.14), residues: 2636 helix: -1.58 (0.13), residues: 1190 sheet: -2.36 (0.28), residues: 260 loop : -2.77 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 596 TYR 0.030 0.002 TYR B 40 PHE 0.024 0.002 PHE D 297 TRP 0.025 0.002 TRP A 894 HIS 0.009 0.002 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.01117 / 0.56 (23148) covalent geometry : angle 1.35287 / 0.65 (31252) SS BOND : bond 0.00285 / 0.15 ( 6) SS BOND : angle 1.88477 / 1.10 ( 12) hydrogen bonds : bond 0.16816 / 11.18 ( 1006) hydrogen bonds : angle 7.20162 / 5.01 ( 2916) link_ALPHA1-3 : bond 0.00761 / 0.38 ( 6) link_ALPHA1-3 : angle 3.10940 / 1.61 ( 18) link_ALPHA1-6 : bond 0.00662 / 0.33 ( 4) link_ALPHA1-6 : angle 1.33610 / 0.74 ( 12) link_BETA1-2 : bond 0.00827 / 0.41 ( 2) link_BETA1-2 : angle 5.40621 / 2.59 ( 6) link_BETA1-4 : bond 0.00894 / 0.53 ( 14) link_BETA1-4 : angle 5.98292 / 3.41 ( 42) link_BETA1-6 : bond 0.00247 / 0.13 ( 4) link_BETA1-6 : angle 1.09944 / 0.69 ( 12) link_NAG-ASN : bond 0.01434 / 0.71 ( 8) link_NAG-ASN : angle 3.54590 / 1.72 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 236 poor density : 446 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.5629 (OUTLIER) cc_final: 0.5247 (m-40) REVERT: A 127 ASN cc_start: 0.6712 (OUTLIER) cc_final: 0.6026 (m110) REVERT: A 248 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7113 (p0) REVERT: A 267 MET cc_start: 0.8414 (ppp) cc_final: 0.7750 (ttt) REVERT: A 308 ILE cc_start: 0.8619 (mp) cc_final: 0.8368 (mm) REVERT: A 350 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7235 (mtt180) REVERT: A 460 ILE cc_start: 0.8305 (mm) cc_final: 0.8001 (mt) REVERT: A 484 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6633 (p) REVERT: A 708 GLN cc_start: 0.8040 (OUTLIER) cc_final: 0.7253 (mm-40) REVERT: A 846 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7504 (p0) REVERT: A 1007 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7780 (t80) REVERT: B 26 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8472 (mt) REVERT: B 32 SER cc_start: 0.8101 (OUTLIER) cc_final: 0.7755 (t) REVERT: B 73 VAL cc_start: 0.7355 (OUTLIER) cc_final: 0.7150 (m) REVERT: B 154 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.8045 (ttt180) REVERT: B 156 TRP cc_start: 0.8775 (OUTLIER) cc_final: 0.8309 (m-10) REVERT: C 65 ASN cc_start: 0.5754 (OUTLIER) cc_final: 0.5400 (m-40) REVERT: C 127 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.5957 (m110) REVERT: C 267 MET cc_start: 0.8412 (ppp) cc_final: 0.7797 (ttt) REVERT: C 308 ILE cc_start: 0.8592 (mp) cc_final: 0.8333 (mm) REVERT: C 350 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7331 (mtt180) REVERT: C 442 ILE cc_start: 0.7700 (mt) cc_final: 0.7447 (tt) REVERT: C 460 ILE cc_start: 0.8405 (mm) cc_final: 0.8093 (mt) REVERT: C 484 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.6895 (p) REVERT: C 708 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7204 (mm-40) REVERT: C 949 MET cc_start: 0.8357 (mmm) cc_final: 0.8101 (mtp) REVERT: C 1007 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7707 (t80) REVERT: D 26 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8508 (mt) REVERT: D 32 SER cc_start: 0.8223 (OUTLIER) cc_final: 0.7859 (t) REVERT: D 73 VAL cc_start: 0.7467 (OUTLIER) cc_final: 0.7202 (p) outliers start: 236 outliers final: 50 residues processed: 621 average time/residue: 0.1928 time to fit residues: 177.1079 Evaluate side-chains 284 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 212 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 445 ARG Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 692 ARG Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 127 ASN Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 332 VAL Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 445 ARG Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 708 GLN Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 269 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.0060 chunk 155 optimal weight: 0.0070 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 5.9990 overall best weight: 1.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS A 225 GLN A 620 HIS A 683 HIS A 904 GLN B 56 GLN B 203 GLN B 258 GLN B 271 ASN C 52 HIS C 225 GLN C 566 ASN C 620 HIS C 904 GLN D 56 GLN D 203 GLN D 258 GLN D 271 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.133620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.093909 restraints weight = 37878.996| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.65 r_work: 0.3060 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23192 Z= 0.156 Angle : 0.687 11.280 31378 Z= 0.330 Chirality : 0.045 0.432 3532 Planarity : 0.006 0.069 3812 Dihedral : 15.992 171.523 3792 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.76 % Allowed : 13.04 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.15), residues: 2636 helix: 0.28 (0.15), residues: 1214 sheet: -1.92 (0.27), residues: 256 loop : -1.94 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 137 TYR 0.019 0.001 TYR B 40 PHE 0.017 0.002 PHE C 793 TRP 0.018 0.002 TRP A 392 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (23148) covalent geometry : angle 0.66536 / 0.33 (31252) SS BOND : bond 0.00093 / 0.05 ( 6) SS BOND : angle 0.96496 / 0.44 ( 12) hydrogen bonds : bond 0.06049 / 4.00 ( 1006) hydrogen bonds : angle 5.07807 / 3.53 ( 2916) link_ALPHA1-3 : bond 0.00799 / 0.44 ( 6) link_ALPHA1-3 : angle 3.09604 / 1.74 ( 18) link_ALPHA1-6 : bond 0.00554 / 0.27 ( 4) link_ALPHA1-6 : angle 1.60810 / 0.95 ( 12) link_BETA1-2 : bond 0.00801 / 0.40 ( 2) link_BETA1-2 : angle 4.22392 / 2.05 ( 6) link_BETA1-4 : bond 0.00895 / 0.53 ( 14) link_BETA1-4 : angle 3.60634 / 2.08 ( 42) link_BETA1-6 : bond 0.00336 / 0.16 ( 4) link_BETA1-6 : angle 1.62033 / 0.93 ( 12) link_NAG-ASN : bond 0.00657 / 0.32 ( 8) link_NAG-ASN : angle 2.00114 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: A 217 SER cc_start: 0.8932 (t) cc_final: 0.8589 (p) REVERT: A 267 MET cc_start: 0.8432 (ppp) cc_final: 0.8033 (ttt) REVERT: A 308 ILE cc_start: 0.8797 (mp) cc_final: 0.8528 (mp) REVERT: A 350 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7433 (mtt180) REVERT: A 392 TRP cc_start: 0.7663 (t60) cc_final: 0.7215 (t60) REVERT: A 470 MET cc_start: 0.8346 (mmm) cc_final: 0.7247 (mpp) REVERT: A 488 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7315 (p90) REVERT: A 833 LYS cc_start: 0.8882 (mptt) cc_final: 0.8538 (mptt) REVERT: A 1007 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.8075 (t80) REVERT: B 26 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 32 SER cc_start: 0.8043 (OUTLIER) cc_final: 0.7620 (t) REVERT: B 73 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.7806 (p) REVERT: B 156 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.7749 (m-10) REVERT: C 58 ASP cc_start: 0.7285 (t0) cc_final: 0.6897 (m-30) REVERT: C 100 PHE cc_start: 0.7432 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 181 ASN cc_start: 0.7072 (OUTLIER) cc_final: 0.6083 (t0) REVERT: C 267 MET cc_start: 0.8532 (ppp) cc_final: 0.8236 (ttt) REVERT: C 308 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8615 (mp) REVERT: C 350 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7433 (mtt180) REVERT: C 470 MET cc_start: 0.8381 (mmm) cc_final: 0.7178 (mpp) REVERT: C 488 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.7412 (p90) REVERT: C 900 ASP cc_start: 0.8976 (p0) cc_final: 0.8567 (p0) REVERT: C 1007 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.8054 (t80) REVERT: D 26 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8508 (mt) REVERT: D 32 SER cc_start: 0.8173 (OUTLIER) cc_final: 0.7710 (t) REVERT: D 73 VAL cc_start: 0.8302 (OUTLIER) cc_final: 0.7944 (p) REVERT: D 223 ARG cc_start: 0.7704 (ttm110) cc_final: 0.7294 (mtt180) REVERT: D 255 LYS cc_start: 0.8745 (mttt) cc_final: 0.8289 (mmtm) outliers start: 85 outliers final: 47 residues processed: 308 average time/residue: 0.1818 time to fit residues: 85.5541 Evaluate side-chains 235 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 171 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 350 ARG Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain C residue 91 LYS Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 15 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 36 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 chunk 164 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 180 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 121 optimal weight: 5.9990 chunk 46 optimal weight: 40.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS B 243 GLN B 284 ASN C 52 HIS D 243 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.122778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.083355 restraints weight = 38342.461| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.89 r_work: 0.2833 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 23192 Z= 0.329 Angle : 0.812 11.574 31378 Z= 0.396 Chirality : 0.051 0.425 3532 Planarity : 0.006 0.050 3812 Dihedral : 15.703 157.290 3709 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.47 % Allowed : 12.91 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.15), residues: 2636 helix: 0.33 (0.14), residues: 1212 sheet: -1.24 (0.31), residues: 248 loop : -1.45 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.001 ARG C 61 TYR 0.039 0.003 TYR B 44 PHE 0.034 0.003 PHE A 793 TRP 0.022 0.003 TRP C 392 HIS 0.007 0.002 HIS C 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00809 / 0.33 (23148) covalent geometry : angle 0.79495 / 0.39 (31252) SS BOND : bond 0.00342 / 0.19 ( 6) SS BOND : angle 1.32365 / 0.65 ( 12) hydrogen bonds : bond 0.08262 / 5.48 ( 1006) hydrogen bonds : angle 5.01478 / 3.52 ( 2916) link_ALPHA1-3 : bond 0.00819 / 0.41 ( 6) link_ALPHA1-3 : angle 2.83340 / 1.72 ( 18) link_ALPHA1-6 : bond 0.00349 / 0.17 ( 4) link_ALPHA1-6 : angle 1.93063 / 1.09 ( 12) link_BETA1-2 : bond 0.00539 / 0.27 ( 2) link_BETA1-2 : angle 3.77630 / 1.86 ( 6) link_BETA1-4 : bond 0.00574 / 0.35 ( 14) link_BETA1-4 : angle 3.45327 / 1.91 ( 42) link_BETA1-6 : bond 0.00718 / 0.36 ( 4) link_BETA1-6 : angle 1.84369 / 1.01 ( 12) link_NAG-ASN : bond 0.00469 / 0.21 ( 8) link_NAG-ASN : angle 2.12015 / 1.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 180 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7120 (t0) cc_final: 0.6593 (m-30) REVERT: A 128 ASP cc_start: 0.7437 (m-30) cc_final: 0.7177 (p0) REVERT: A 217 SER cc_start: 0.9041 (t) cc_final: 0.8788 (p) REVERT: A 248 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7137 (p0) REVERT: A 470 MET cc_start: 0.8262 (mmm) cc_final: 0.7424 (mpp) REVERT: A 488 TYR cc_start: 0.8081 (p90) cc_final: 0.7852 (p90) REVERT: A 678 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7772 (tt) REVERT: B 37 PHE cc_start: 0.8424 (t80) cc_final: 0.7997 (t80) REVERT: B 55 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7775 (tp) REVERT: B 73 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8479 (m) REVERT: B 156 TRP cc_start: 0.8977 (OUTLIER) cc_final: 0.7781 (m-90) REVERT: C 58 ASP cc_start: 0.7309 (t0) cc_final: 0.6847 (m-30) REVERT: C 128 ASP cc_start: 0.7432 (m-30) cc_final: 0.7150 (p0) REVERT: C 385 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7237 (ttp80) REVERT: C 392 TRP cc_start: 0.7874 (t60) cc_final: 0.7437 (t60) REVERT: C 470 MET cc_start: 0.8406 (mmm) cc_final: 0.7356 (mpp) REVERT: C 534 MET cc_start: 0.7567 (mmm) cc_final: 0.7348 (mmm) REVERT: C 678 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8096 (tt) REVERT: D 37 PHE cc_start: 0.8437 (t80) cc_final: 0.8022 (t80) REVERT: D 38 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8412 (tt) REVERT: D 55 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.7779 (tp) REVERT: D 73 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8451 (m) REVERT: D 156 TRP cc_start: 0.8967 (OUTLIER) cc_final: 0.8043 (m-10) outliers start: 101 outliers final: 58 residues processed: 266 average time/residue: 0.1695 time to fit residues: 70.3217 Evaluate side-chains 222 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 153 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 385 ARG Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 93 ILE Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 29 optimal weight: 0.7980 chunk 147 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 383 GLN A 493 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.127541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087495 restraints weight = 37446.798| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.52 r_work: 0.2954 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23192 Z= 0.118 Angle : 0.577 10.199 31378 Z= 0.275 Chirality : 0.042 0.412 3532 Planarity : 0.004 0.048 3812 Dihedral : 14.264 157.568 3683 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.03 % Allowed : 15.34 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.16), residues: 2636 helix: 1.10 (0.15), residues: 1222 sheet: -0.56 (0.31), residues: 268 loop : -1.32 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.012 0.001 TYR A 684 PHE 0.019 0.001 PHE A 967 TRP 0.010 0.001 TRP C 392 HIS 0.006 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (23148) covalent geometry : angle 0.55675 / 0.27 (31252) SS BOND : bond 0.00079 / 0.05 ( 6) SS BOND : angle 1.07480 / 0.65 ( 12) hydrogen bonds : bond 0.05365 / 3.55 ( 1006) hydrogen bonds : angle 4.39745 / 3.05 ( 2916) link_ALPHA1-3 : bond 0.00750 / 0.39 ( 6) link_ALPHA1-3 : angle 2.62969 / 1.56 ( 18) link_ALPHA1-6 : bond 0.00431 / 0.21 ( 4) link_ALPHA1-6 : angle 1.47741 / 0.86 ( 12) link_BETA1-2 : bond 0.00649 / 0.33 ( 2) link_BETA1-2 : angle 4.10455 / 2.03 ( 6) link_BETA1-4 : bond 0.00653 / 0.40 ( 14) link_BETA1-4 : angle 3.01434 / 1.65 ( 42) link_BETA1-6 : bond 0.00252 / 0.12 ( 4) link_BETA1-6 : angle 1.61973 / 0.95 ( 12) link_NAG-ASN : bond 0.00609 / 0.29 ( 8) link_NAG-ASN : angle 1.66139 / 0.89 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 165 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7093 (t0) cc_final: 0.6608 (m-30) REVERT: A 100 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7161 (m-80) REVERT: A 470 MET cc_start: 0.8276 (mmm) cc_final: 0.7537 (mpp) REVERT: A 488 TYR cc_start: 0.8100 (p90) cc_final: 0.7733 (p90) REVERT: A 678 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7869 (tt) REVERT: B 37 PHE cc_start: 0.8398 (t80) cc_final: 0.8162 (t80) REVERT: B 73 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8038 (p) REVERT: B 180 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8214 (ttpt) REVERT: C 58 ASP cc_start: 0.7537 (t0) cc_final: 0.6971 (m-30) REVERT: C 100 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: C 158 MET cc_start: 0.7055 (tpp) cc_final: 0.6656 (tmm) REVERT: C 392 TRP cc_start: 0.7845 (t60) cc_final: 0.7174 (t60) REVERT: C 470 MET cc_start: 0.8434 (mmm) cc_final: 0.7394 (mpp) REVERT: C 534 MET cc_start: 0.7640 (mmm) cc_final: 0.7427 (mmm) REVERT: C 678 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8090 (tt) REVERT: C 852 MET cc_start: 0.8530 (tpp) cc_final: 0.8311 (mmm) REVERT: D 37 PHE cc_start: 0.8410 (t80) cc_final: 0.8185 (t80) REVERT: D 73 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8122 (p) REVERT: D 180 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8187 (ttpt) outliers start: 46 outliers final: 32 residues processed: 206 average time/residue: 0.1670 time to fit residues: 54.2195 Evaluate side-chains 193 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 203 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 9 optimal weight: 20.0000 chunk 245 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 240 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 39 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 231 optimal weight: 8.9990 chunk 99 optimal weight: 0.0870 overall best weight: 2.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 181 ASN A 493 HIS B 284 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.125762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.086857 restraints weight = 37085.712| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.79 r_work: 0.2886 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23192 Z= 0.157 Angle : 0.599 9.435 31378 Z= 0.285 Chirality : 0.043 0.410 3532 Planarity : 0.004 0.045 3812 Dihedral : 13.543 147.053 3681 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.01 % Allowed : 15.30 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 2636 helix: 1.26 (0.15), residues: 1236 sheet: -0.83 (0.30), residues: 280 loop : -1.17 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 473 TYR 0.017 0.001 TYR B 40 PHE 0.023 0.002 PHE C 793 TRP 0.021 0.001 TRP A 392 HIS 0.004 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (23148) covalent geometry : angle 0.58086 / 0.28 (31252) SS BOND : bond 0.00108 / 0.06 ( 6) SS BOND : angle 0.83911 / 0.42 ( 12) hydrogen bonds : bond 0.05766 / 3.81 ( 1006) hydrogen bonds : angle 4.34382 / 3.02 ( 2916) link_ALPHA1-3 : bond 0.00735 / 0.39 ( 6) link_ALPHA1-3 : angle 2.63191 / 1.58 ( 18) link_ALPHA1-6 : bond 0.00340 / 0.17 ( 4) link_ALPHA1-6 : angle 1.61180 / 0.93 ( 12) link_BETA1-2 : bond 0.00589 / 0.30 ( 2) link_BETA1-2 : angle 4.04110 / 2.00 ( 6) link_BETA1-4 : bond 0.00588 / 0.35 ( 14) link_BETA1-4 : angle 2.89002 / 1.59 ( 42) link_BETA1-6 : bond 0.00323 / 0.16 ( 4) link_BETA1-6 : angle 1.69440 / 0.95 ( 12) link_NAG-ASN : bond 0.00422 / 0.19 ( 8) link_NAG-ASN : angle 1.59405 / 0.88 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 161 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.7160 (m-80) REVERT: A 158 MET cc_start: 0.7104 (tpp) cc_final: 0.6835 (tpp) REVERT: A 470 MET cc_start: 0.8180 (mmm) cc_final: 0.7425 (mpp) REVERT: A 488 TYR cc_start: 0.7949 (p90) cc_final: 0.7611 (p90) REVERT: A 678 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7889 (tt) REVERT: A 684 TYR cc_start: 0.7309 (m-80) cc_final: 0.7052 (m-80) REVERT: A 1007 PHE cc_start: 0.8335 (OUTLIER) cc_final: 0.8006 (t80) REVERT: B 37 PHE cc_start: 0.8323 (t80) cc_final: 0.8092 (t80) REVERT: B 55 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7562 (tp) REVERT: B 73 VAL cc_start: 0.8569 (OUTLIER) cc_final: 0.7913 (p) REVERT: C 58 ASP cc_start: 0.7563 (t0) cc_final: 0.6946 (m-30) REVERT: C 100 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: C 158 MET cc_start: 0.7084 (tpp) cc_final: 0.6772 (tmm) REVERT: C 392 TRP cc_start: 0.7820 (t60) cc_final: 0.7376 (t60) REVERT: C 470 MET cc_start: 0.8295 (mmm) cc_final: 0.7247 (mpp) REVERT: C 534 MET cc_start: 0.7639 (mmm) cc_final: 0.7430 (mmm) REVERT: C 578 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: C 615 MET cc_start: 0.8909 (tpp) cc_final: 0.8683 (ttt) REVERT: C 678 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8070 (tt) REVERT: C 1007 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.8057 (t80) REVERT: D 37 PHE cc_start: 0.8332 (t80) cc_final: 0.8082 (t80) REVERT: D 55 ILE cc_start: 0.8184 (OUTLIER) cc_final: 0.7552 (tp) REVERT: D 73 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.7981 (p) REVERT: D 156 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.7801 (m-10) REVERT: E 4 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5749 (pp20) outliers start: 68 outliers final: 47 residues processed: 218 average time/residue: 0.1588 time to fit residues: 55.1956 Evaluate side-chains 207 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 148 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 524 ASN Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 116 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 164 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.088001 restraints weight = 37173.136| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.61 r_work: 0.2941 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23192 Z= 0.113 Angle : 0.550 10.237 31378 Z= 0.261 Chirality : 0.041 0.412 3532 Planarity : 0.004 0.048 3812 Dihedral : 12.936 144.063 3678 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.52 % Allowed : 15.43 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2636 helix: 1.53 (0.15), residues: 1240 sheet: -0.60 (0.30), residues: 292 loop : -1.16 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 473 TYR 0.014 0.001 TYR C 488 PHE 0.023 0.001 PHE C 967 TRP 0.017 0.001 TRP A 392 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (23148) covalent geometry : angle 0.53245 / 0.26 (31252) SS BOND : bond 0.00062 / 0.03 ( 6) SS BOND : angle 0.70397 / 0.38 ( 12) hydrogen bonds : bond 0.04997 / 3.31 ( 1006) hydrogen bonds : angle 4.16939 / 2.89 ( 2916) link_ALPHA1-3 : bond 0.00730 / 0.40 ( 6) link_ALPHA1-3 : angle 2.55120 / 1.51 ( 18) link_ALPHA1-6 : bond 0.00402 / 0.20 ( 4) link_ALPHA1-6 : angle 1.50481 / 0.88 ( 12) link_BETA1-2 : bond 0.00619 / 0.31 ( 2) link_BETA1-2 : angle 4.03272 / 1.99 ( 6) link_BETA1-4 : bond 0.00600 / 0.37 ( 14) link_BETA1-4 : angle 2.75261 / 1.51 ( 42) link_BETA1-6 : bond 0.00231 / 0.11 ( 4) link_BETA1-6 : angle 1.59913 / 0.92 ( 12) link_NAG-ASN : bond 0.00513 / 0.24 ( 8) link_NAG-ASN : angle 1.41287 / 0.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 153 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 470 MET cc_start: 0.8200 (mmm) cc_final: 0.7553 (mpp) REVERT: A 488 TYR cc_start: 0.8058 (p90) cc_final: 0.7647 (p90) REVERT: A 534 MET cc_start: 0.7542 (mmm) cc_final: 0.7183 (mmm) REVERT: A 585 PHE cc_start: 0.7601 (t80) cc_final: 0.6836 (t80) REVERT: A 684 TYR cc_start: 0.7491 (m-80) cc_final: 0.7193 (m-80) REVERT: A 1007 PHE cc_start: 0.8470 (OUTLIER) cc_final: 0.8205 (t80) REVERT: B 73 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.7928 (p) REVERT: C 158 MET cc_start: 0.7273 (tpp) cc_final: 0.6903 (tmm) REVERT: C 392 TRP cc_start: 0.7820 (t60) cc_final: 0.7372 (t60) REVERT: C 470 MET cc_start: 0.8283 (mmm) cc_final: 0.7264 (mpp) REVERT: C 534 MET cc_start: 0.7664 (mmm) cc_final: 0.7425 (mmm) REVERT: C 615 MET cc_start: 0.8936 (tpp) cc_final: 0.8727 (ttt) REVERT: C 678 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8099 (tt) REVERT: C 1007 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8198 (t80) REVERT: D 73 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8048 (p) REVERT: D 255 LYS cc_start: 0.8732 (mttt) cc_final: 0.8203 (mmtm) outliers start: 57 outliers final: 35 residues processed: 203 average time/residue: 0.1547 time to fit residues: 50.9200 Evaluate side-chains 188 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 203 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 57 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 247 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 946 GLN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.123672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082151 restraints weight = 37330.505| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.34 r_work: 0.2862 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.5083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 23192 Z= 0.260 Angle : 0.692 10.422 31378 Z= 0.334 Chirality : 0.047 0.417 3532 Planarity : 0.005 0.047 3812 Dihedral : 13.419 136.485 3676 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.09 % Allowed : 15.74 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.16), residues: 2636 helix: 1.17 (0.15), residues: 1228 sheet: -0.64 (0.33), residues: 246 loop : -1.15 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 473 TYR 0.025 0.002 TYR B 40 PHE 0.031 0.002 PHE A 793 TRP 0.017 0.002 TRP A 392 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00648 / 0.26 (23148) covalent geometry : angle 0.67606 / 0.33 (31252) SS BOND : bond 0.00174 / 0.09 ( 6) SS BOND : angle 0.84240 / 0.40 ( 12) hydrogen bonds : bond 0.06966 / 4.61 ( 1006) hydrogen bonds : angle 4.53242 / 3.17 ( 2916) link_ALPHA1-3 : bond 0.00770 / 0.41 ( 6) link_ALPHA1-3 : angle 2.65024 / 1.62 ( 18) link_ALPHA1-6 : bond 0.00201 / 0.10 ( 4) link_ALPHA1-6 : angle 1.75844 / 1.00 ( 12) link_BETA1-2 : bond 0.00457 / 0.23 ( 2) link_BETA1-2 : angle 3.98222 / 1.97 ( 6) link_BETA1-4 : bond 0.00532 / 0.32 ( 14) link_BETA1-4 : angle 2.86393 / 1.57 ( 42) link_BETA1-6 : bond 0.00531 / 0.26 ( 4) link_BETA1-6 : angle 1.90111 / 1.03 ( 12) link_NAG-ASN : bond 0.00461 / 0.21 ( 8) link_NAG-ASN : angle 1.73060 / 0.97 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 158 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6961 (t70) REVERT: A 46 LEU cc_start: 0.7367 (mp) cc_final: 0.7102 (mt) REVERT: A 128 ASP cc_start: 0.7628 (m-30) cc_final: 0.7300 (p0) REVERT: A 470 MET cc_start: 0.8206 (mmm) cc_final: 0.7492 (mpp) REVERT: A 488 TYR cc_start: 0.7980 (p90) cc_final: 0.7590 (p90) REVERT: B 37 PHE cc_start: 0.8518 (t80) cc_final: 0.8234 (t80) REVERT: B 55 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.7769 (tp) REVERT: C 33 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6654 (t70) REVERT: C 117 ILE cc_start: 0.8525 (mm) cc_final: 0.8293 (mt) REVERT: C 128 ASP cc_start: 0.7623 (m-30) cc_final: 0.7285 (p0) REVERT: C 158 MET cc_start: 0.7386 (tpp) cc_final: 0.7004 (tmm) REVERT: C 392 TRP cc_start: 0.7845 (t60) cc_final: 0.7437 (t60) REVERT: C 470 MET cc_start: 0.8285 (mmm) cc_final: 0.7260 (mpp) REVERT: C 534 MET cc_start: 0.7732 (mmm) cc_final: 0.7501 (mmm) REVERT: D 37 PHE cc_start: 0.8517 (t80) cc_final: 0.8247 (t80) REVERT: D 55 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7763 (tp) REVERT: D 73 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8517 (m) outliers start: 70 outliers final: 54 residues processed: 219 average time/residue: 0.1503 time to fit residues: 53.8589 Evaluate side-chains 214 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 155 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 197 ASP Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 36 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 148 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 136 optimal weight: 20.0000 chunk 187 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.124035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.083214 restraints weight = 37029.709| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.52 r_work: 0.2878 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 23192 Z= 0.241 Angle : 0.660 10.209 31378 Z= 0.318 Chirality : 0.046 0.413 3532 Planarity : 0.004 0.045 3812 Dihedral : 13.438 128.780 3676 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.61 % Allowed : 16.27 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2636 helix: 1.19 (0.15), residues: 1228 sheet: -0.46 (0.32), residues: 266 loop : -1.32 (0.16), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 423 TYR 0.019 0.002 TYR D 40 PHE 0.030 0.002 PHE A 967 TRP 0.021 0.002 TRP A 392 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.24 (23148) covalent geometry : angle 0.64445 / 0.31 (31252) SS BOND : bond 0.00168 / 0.08 ( 6) SS BOND : angle 0.82213 / 0.39 ( 12) hydrogen bonds : bond 0.06585 / 4.36 ( 1006) hydrogen bonds : angle 4.49427 / 3.13 ( 2916) link_ALPHA1-3 : bond 0.00739 / 0.40 ( 6) link_ALPHA1-3 : angle 2.63454 / 1.60 ( 18) link_ALPHA1-6 : bond 0.00214 / 0.10 ( 4) link_ALPHA1-6 : angle 1.68332 / 0.96 ( 12) link_BETA1-2 : bond 0.00599 / 0.30 ( 2) link_BETA1-2 : angle 3.95559 / 1.95 ( 6) link_BETA1-4 : bond 0.00530 / 0.32 ( 14) link_BETA1-4 : angle 2.81612 / 1.53 ( 42) link_BETA1-6 : bond 0.00383 / 0.19 ( 4) link_BETA1-6 : angle 1.86886 / 1.05 ( 12) link_NAG-ASN : bond 0.00477 / 0.21 ( 8) link_NAG-ASN : angle 1.66031 / 0.92 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 158 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7365 (mp) cc_final: 0.7109 (mt) REVERT: A 158 MET cc_start: 0.7348 (tpp) cc_final: 0.6827 (tmm) REVERT: A 488 TYR cc_start: 0.8005 (p90) cc_final: 0.7589 (p90) REVERT: A 534 MET cc_start: 0.7556 (mmm) cc_final: 0.7266 (mmm) REVERT: A 1011 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.8121 (mmm160) REVERT: B 55 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.7627 (tp) REVERT: B 283 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8437 (tt0) REVERT: C 117 ILE cc_start: 0.8520 (mm) cc_final: 0.8290 (mt) REVERT: C 158 MET cc_start: 0.7457 (tpp) cc_final: 0.7089 (tmm) REVERT: C 392 TRP cc_start: 0.7871 (t60) cc_final: 0.7428 (t60) REVERT: C 470 MET cc_start: 0.8281 (mmm) cc_final: 0.7341 (mpp) REVERT: D 55 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7625 (tp) outliers start: 59 outliers final: 50 residues processed: 208 average time/residue: 0.1484 time to fit residues: 50.4348 Evaluate side-chains 197 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 492 ILE Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 97 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 248 optimal weight: 3.9990 chunk 236 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 20.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 493 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 = 0.3776 r_free = 0.3776 target = 0.126556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.086636 restraints weight = 37048.211| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.53 r_work: 0.2888 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.5406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23192 Z= 0.131 Angle : 0.574 8.724 31378 Z= 0.273 Chirality : 0.042 0.401 3532 Planarity : 0.004 0.042 3812 Dihedral : 12.548 119.234 3674 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.03 % Allowed : 16.84 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.16), residues: 2636 helix: 1.56 (0.15), residues: 1236 sheet: -0.27 (0.32), residues: 266 loop : -1.25 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 423 TYR 0.015 0.001 TYR C 869 PHE 0.032 0.002 PHE C 967 TRP 0.027 0.002 TRP A 392 HIS 0.007 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (23148) covalent geometry : angle 0.55833 / 0.27 (31252) SS BOND : bond 0.00106 / 0.05 ( 6) SS BOND : angle 0.66942 / 0.33 ( 12) hydrogen bonds : bond 0.05268 / 3.50 ( 1006) hydrogen bonds : angle 4.17116 / 2.89 ( 2916) link_ALPHA1-3 : bond 0.00758 / 0.43 ( 6) link_ALPHA1-3 : angle 2.49622 / 1.49 ( 18) link_ALPHA1-6 : bond 0.00346 / 0.17 ( 4) link_ALPHA1-6 : angle 1.50696 / 0.89 ( 12) link_BETA1-2 : bond 0.00594 / 0.30 ( 2) link_BETA1-2 : angle 3.99063 / 1.95 ( 6) link_BETA1-4 : bond 0.00573 / 0.35 ( 14) link_BETA1-4 : angle 2.61944 / 1.43 ( 42) link_BETA1-6 : bond 0.00299 / 0.15 ( 4) link_BETA1-6 : angle 1.71737 / 0.99 ( 12) link_NAG-ASN : bond 0.00495 / 0.23 ( 8) link_NAG-ASN : angle 1.41870 / 0.78 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7307 (mp) cc_final: 0.7063 (mt) REVERT: A 158 MET cc_start: 0.7363 (tpp) cc_final: 0.6858 (tmm) REVERT: A 470 MET cc_start: 0.8148 (mmm) cc_final: 0.7353 (mpp) REVERT: A 473 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7654 (mmm160) REVERT: A 488 TYR cc_start: 0.7966 (p90) cc_final: 0.7571 (p90) REVERT: A 1011 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7977 (mmm160) REVERT: B 110 MET cc_start: 0.8675 (mmt) cc_final: 0.8286 (mmt) REVERT: B 283 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8326 (tt0) REVERT: C 392 TRP cc_start: 0.7761 (t60) cc_final: 0.7368 (t60) REVERT: C 470 MET cc_start: 0.8248 (mmm) cc_final: 0.7306 (mpp) REVERT: C 473 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7767 (mmm160) outliers start: 46 outliers final: 32 residues processed: 193 average time/residue: 0.1583 time to fit residues: 49.5509 Evaluate side-chains 179 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 146 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 259 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 226 optimal weight: 0.0770 chunk 36 optimal weight: 6.9990 chunk 137 optimal weight: 0.0970 chunk 35 optimal weight: 5.9990 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 493 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 = 0.3791 r_free = 0.3791 target = 0.127752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.088683 restraints weight = 37033.998| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.59 r_work: 0.2932 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23192 Z= 0.114 Angle : 0.571 16.148 31378 Z= 0.266 Chirality : 0.041 0.399 3532 Planarity : 0.004 0.042 3812 Dihedral : 11.539 103.811 3664 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.33 % Allowed : 17.90 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2636 helix: 1.76 (0.15), residues: 1244 sheet: -0.14 (0.32), residues: 266 loop : -1.16 (0.16), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 423 TYR 0.016 0.001 TYR A 869 PHE 0.034 0.001 PHE A 967 TRP 0.027 0.001 TRP A 392 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (23148) covalent geometry : angle 0.55580 / 0.26 (31252) SS BOND : bond 0.00083 / 0.04 ( 6) SS BOND : angle 0.57456 / 0.29 ( 12) hydrogen bonds : bond 0.04696 / 3.12 ( 1006) hydrogen bonds : angle 4.01970 / 2.79 ( 2916) link_ALPHA1-3 : bond 0.00712 / 0.39 ( 6) link_ALPHA1-3 : angle 2.46358 / 1.45 ( 18) link_ALPHA1-6 : bond 0.00402 / 0.20 ( 4) link_ALPHA1-6 : angle 1.46109 / 0.86 ( 12) link_BETA1-2 : bond 0.00638 / 0.32 ( 2) link_BETA1-2 : angle 3.90873 / 1.91 ( 6) link_BETA1-4 : bond 0.00591 / 0.36 ( 14) link_BETA1-4 : angle 2.52322 / 1.39 ( 42) link_BETA1-6 : bond 0.00263 / 0.13 ( 4) link_BETA1-6 : angle 1.61733 / 0.93 ( 12) link_NAG-ASN : bond 0.00493 / 0.22 ( 8) link_NAG-ASN : angle 1.23869 / 0.69 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7293 (mp) cc_final: 0.7069 (mt) REVERT: A 158 MET cc_start: 0.7367 (tpp) cc_final: 0.6873 (tmm) REVERT: A 470 MET cc_start: 0.8099 (mmm) cc_final: 0.7370 (mpp) REVERT: A 473 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7643 (mmm160) REVERT: A 488 TYR cc_start: 0.7935 (p90) cc_final: 0.7569 (p90) REVERT: A 1011 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7967 (mmm160) REVERT: B 110 MET cc_start: 0.8694 (mmt) cc_final: 0.8364 (mmt) REVERT: B 255 LYS cc_start: 0.8674 (mttt) cc_final: 0.8162 (mmtt) REVERT: B 283 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8522 (tt0) REVERT: C 392 TRP cc_start: 0.7779 (t60) cc_final: 0.7331 (t60) REVERT: C 470 MET cc_start: 0.8275 (mmm) cc_final: 0.7381 (mpp) REVERT: C 473 ARG cc_start: 0.8176 (mmm-85) cc_final: 0.7827 (mmm160) REVERT: D 255 LYS cc_start: 0.8684 (mttt) cc_final: 0.8173 (mmtt) outliers start: 30 outliers final: 26 residues processed: 179 average time/residue: 0.1414 time to fit residues: 41.1328 Evaluate side-chains 174 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 127 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 226 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 166 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 214 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.127936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088116 restraints weight = 37325.609| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.58 r_work: 0.2953 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23192 Z= 0.109 Angle : 0.559 17.016 31378 Z= 0.261 Chirality : 0.041 0.396 3532 Planarity : 0.004 0.042 3812 Dihedral : 11.040 89.590 3664 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.41 % Allowed : 17.95 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2636 helix: 1.86 (0.15), residues: 1244 sheet: -0.31 (0.30), residues: 292 loop : -1.10 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 423 TYR 0.016 0.001 TYR C 869 PHE 0.034 0.001 PHE A 967 TRP 0.025 0.001 TRP A 392 HIS 0.006 0.001 HIS C 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (23148) covalent geometry : angle 0.54469 / 0.26 (31252) SS BOND : bond 0.00083 / 0.04 ( 6) SS BOND : angle 0.52319 / 0.26 ( 12) hydrogen bonds : bond 0.04552 / 3.03 ( 1006) hydrogen bonds : angle 3.97870 / 2.76 ( 2916) link_ALPHA1-3 : bond 0.00748 / 0.43 ( 6) link_ALPHA1-3 : angle 2.43144 / 1.44 ( 18) link_ALPHA1-6 : bond 0.00432 / 0.21 ( 4) link_ALPHA1-6 : angle 1.45929 / 0.87 ( 12) link_BETA1-2 : bond 0.00607 / 0.31 ( 2) link_BETA1-2 : angle 3.89939 / 1.90 ( 6) link_BETA1-4 : bond 0.00575 / 0.35 ( 14) link_BETA1-4 : angle 2.44542 / 1.34 ( 42) link_BETA1-6 : bond 0.00275 / 0.14 ( 4) link_BETA1-6 : angle 1.58506 / 0.91 ( 12) link_NAG-ASN : bond 0.00459 / 0.21 ( 8) link_NAG-ASN : angle 1.15438 / 0.65 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6049.00 seconds wall clock time: 104 minutes 18.02 seconds (6258.02 seconds total)