Starting phenix.real_space_refine on Thu Mar 5 15:42:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wyx_32897/03_2026/7wyx_32897.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wyx_32897/03_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_32897/03_2026/7wyx_32897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wyx_32897/03_2026/7wyx_32897.map" model { file = "/net/cci-nas-00/data/ceres_data/7wyx_32897/03_2026/7wyx_32897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wyx_32897/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 18 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 dihedrals: 18 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 dihedrals: 15 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 dihedrals: 6 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: 9.85, per 1000 atoms: 0.43 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: 1.55 Conformation dependent library (CDL) restraints added in 966.7 milliseconds 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: 0.83 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: 4.24 Time building geometry restraints manager: 2.00 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: 14206 35.90 - 71.81: 800 71.81 - 107.71: 84 107.71 - 143.61: 40 143.61 - 179.51: 2 Dihedral angle restraints: 15132 sinusoidal: 7476 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 15129 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 24.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 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 : 20.164 179.514 10202 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 covalent geometry : bond 0.01117 (23148) covalent geometry : angle 1.35287 (31252) SS BOND : bond 0.00285 ( 6) SS BOND : angle 1.88477 ( 12) hydrogen bonds : bond 0.16816 ( 1006) hydrogen bonds : angle 7.20162 ( 2916) link_ALPHA1-3 : bond 0.00761 ( 6) link_ALPHA1-3 : angle 3.10940 ( 18) link_ALPHA1-6 : bond 0.00662 ( 4) link_ALPHA1-6 : angle 1.33610 ( 12) link_BETA1-2 : bond 0.00827 ( 2) link_BETA1-2 : angle 5.40621 ( 6) link_BETA1-4 : bond 0.00894 ( 14) link_BETA1-4 : angle 5.98292 ( 42) link_BETA1-6 : bond 0.00247 ( 4) link_BETA1-6 : angle 1.09944 ( 12) link_NAG-ASN : bond 0.01434 ( 8) link_NAG-ASN : angle 3.54590 ( 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 : 0.709 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: 0.1827 time to fit residues: 166.1725 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 : 0.631 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3884 r_free = 0.3884 target = 0.133712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.094946 restraints weight = 37860.347| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.66 r_work: 0.3062 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23192 Z= 0.158 Angle : 0.702 11.226 31378 Z= 0.335 Chirality : 0.047 0.438 3532 Planarity : 0.006 0.071 3812 Dihedral : 17.317 176.328 5392 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.71 % Allowed : 13.09 % 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: -1.38 (0.15), residues: 2636 helix: 0.27 (0.15), residues: 1212 sheet: -1.94 (0.27), residues: 256 loop : -1.95 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 517 TYR 0.019 0.001 TYR B 40 PHE 0.017 0.002 PHE C 793 TRP 0.020 0.002 TRP A 392 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00341 (23148) covalent geometry : angle 0.67382 (31252) SS BOND : bond 0.00083 ( 6) SS BOND : angle 0.96856 ( 12) hydrogen bonds : bond 0.06076 ( 1006) hydrogen bonds : angle 5.08458 ( 2916) link_ALPHA1-3 : bond 0.01110 ( 6) link_ALPHA1-3 : angle 3.98570 ( 18) link_ALPHA1-6 : bond 0.00591 ( 4) link_ALPHA1-6 : angle 2.30196 ( 12) link_BETA1-2 : bond 0.00813 ( 2) link_BETA1-2 : angle 4.68973 ( 6) link_BETA1-4 : bond 0.00979 ( 14) link_BETA1-4 : angle 3.90069 ( 42) link_BETA1-6 : bond 0.01023 ( 4) link_BETA1-6 : angle 1.54855 ( 12) link_NAG-ASN : bond 0.00704 ( 8) link_NAG-ASN : angle 2.10464 ( 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 319 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 235 time to evaluate : 0.823 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: 0.7382 (OUTLIER) cc_final: 0.6790 (m-80) REVERT: A 217 SER cc_start: 0.8934 (t) cc_final: 0.8592 (p) REVERT: A 267 MET cc_start: 0.8429 (ppp) cc_final: 0.8034 (ttt) REVERT: A 308 ILE cc_start: 0.8803 (mp) cc_final: 0.8535 (mp) REVERT: A 350 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7444 (mtt180) REVERT: A 392 TRP cc_start: 0.7666 (t60) cc_final: 0.7281 (t60) REVERT: A 470 MET cc_start: 0.8342 (mmm) cc_final: 0.7239 (mpp) REVERT: A 488 TYR cc_start: 0.7842 (OUTLIER) cc_final: 0.7235 (p90) REVERT: A 833 LYS cc_start: 0.8891 (mptt) cc_final: 0.8546 (mptt) REVERT: A 1007 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8067 (t80) REVERT: B 26 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8498 (mm) REVERT: B 32 SER cc_start: 0.8050 (OUTLIER) cc_final: 0.7630 (t) REVERT: B 73 VAL cc_start: 0.8268 (OUTLIER) cc_final: 0.7809 (p) REVERT: B 156 TRP cc_start: 0.8861 (OUTLIER) cc_final: 0.7802 (m-10) REVERT: C 58 ASP cc_start: 0.7290 (t0) cc_final: 0.6905 (m-30) REVERT: C 100 PHE cc_start: 0.7444 (OUTLIER) cc_final: 0.6778 (m-80) REVERT: C 127 ASN cc_start: 0.6209 (OUTLIER) cc_final: 0.6006 (m-40) REVERT: C 181 ASN cc_start: 0.7087 (OUTLIER) cc_final: 0.6377 (t0) REVERT: C 267 MET cc_start: 0.8524 (ppp) cc_final: 0.8233 (ttt) REVERT: C 308 ILE cc_start: 0.8913 (mp) cc_final: 0.8624 (mp) REVERT: C 350 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7447 (mtt180) REVERT: C 470 MET cc_start: 0.8378 (mmm) cc_final: 0.7172 (mpp) REVERT: C 488 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.7341 (p90) REVERT: C 900 ASP cc_start: 0.8978 (p0) cc_final: 0.8568 (p0) REVERT: C 1007 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8016 (t80) REVERT: D 26 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8511 (mt) REVERT: D 32 SER cc_start: 0.8148 (OUTLIER) cc_final: 0.7697 (t) REVERT: D 73 VAL cc_start: 0.8304 (OUTLIER) cc_final: 0.7946 (p) REVERT: D 223 ARG cc_start: 0.7723 (ttm110) cc_final: 0.7328 (mtt180) REVERT: D 255 LYS cc_start: 0.8750 (mttt) cc_final: 0.8296 (mmtm) outliers start: 84 outliers final: 47 residues processed: 308 average time/residue: 0.1744 time to fit residues: 81.8819 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 : 0.779 ------------------------------------------------------------------------------- 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 127 ASN 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 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: 2.9990 chunk 164 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 49 optimal weight: 0.6980 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: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3758 r_free = 0.3758 target = 0.124983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.084514 restraints weight = 37515.128| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.76 r_work: 0.2878 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23192 Z= 0.254 Angle : 0.754 12.510 31378 Z= 0.365 Chirality : 0.049 0.471 3532 Planarity : 0.005 0.061 3812 Dihedral : 16.328 166.154 5311 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.24 % Allowed : 13.26 % Favored : 82.49 % 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: -0.71 (0.16), residues: 2636 helix: 0.59 (0.14), residues: 1212 sheet: -1.24 (0.29), residues: 282 loop : -1.39 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 61 TYR 0.032 0.002 TYR B 44 PHE 0.029 0.003 PHE A 793 TRP 0.023 0.002 TRP C 392 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00619 (23148) covalent geometry : angle 0.73095 (31252) SS BOND : bond 0.00311 ( 6) SS BOND : angle 1.31288 ( 12) hydrogen bonds : bond 0.07492 ( 1006) hydrogen bonds : angle 4.83611 ( 2916) link_ALPHA1-3 : bond 0.01398 ( 6) link_ALPHA1-3 : angle 3.81577 ( 18) link_ALPHA1-6 : bond 0.00462 ( 4) link_ALPHA1-6 : angle 2.04954 ( 12) link_BETA1-2 : bond 0.00283 ( 2) link_BETA1-2 : angle 4.59578 ( 6) link_BETA1-4 : bond 0.00629 ( 14) link_BETA1-4 : angle 3.64254 ( 42) link_BETA1-6 : bond 0.00798 ( 4) link_BETA1-6 : angle 1.80706 ( 12) link_NAG-ASN : bond 0.00468 ( 8) link_NAG-ASN : angle 1.91872 ( 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 277 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 181 time to evaluate : 0.821 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: 0.7048 (t0) cc_final: 0.6595 (m-30) REVERT: A 248 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7202 (p0) REVERT: A 470 MET cc_start: 0.8155 (mmm) cc_final: 0.7405 (mpp) REVERT: A 678 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7753 (tt) REVERT: B 55 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7797 (tp) REVERT: B 73 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8508 (m) REVERT: B 156 TRP cc_start: 0.8972 (OUTLIER) cc_final: 0.7739 (m-90) REVERT: C 58 ASP cc_start: 0.7297 (t0) cc_final: 0.6494 (m-30) REVERT: C 127 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6326 (m-40) REVERT: C 308 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8726 (mp) REVERT: C 392 TRP cc_start: 0.7865 (t60) cc_final: 0.7295 (t60) REVERT: C 470 MET cc_start: 0.8390 (mmm) cc_final: 0.7337 (mpp) REVERT: C 488 TYR cc_start: 0.7925 (p90) cc_final: 0.7715 (p90) REVERT: C 678 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8085 (tt) REVERT: D 55 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.7811 (tp) REVERT: D 73 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8203 (p) outliers start: 96 outliers final: 53 residues processed: 261 average time/residue: 0.1556 time to fit residues: 63.5882 Evaluate side-chains 216 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 153 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 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 127 ASN Chi-restraints excluded: chain C residue 138 THR 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 308 ILE Chi-restraints excluded: chain C residue 381 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 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 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 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: 0.9980 chunk 215 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 180 optimal weight: 0.5980 chunk 245 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 152 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 557 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 = 0.3794 r_free = 0.3794 target = 0.127509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089450 restraints weight = 38344.395| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.83 r_work: 0.2934 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23192 Z= 0.117 Angle : 0.585 10.223 31378 Z= 0.274 Chirality : 0.044 0.483 3532 Planarity : 0.004 0.046 3812 Dihedral : 15.045 162.822 5285 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.21 % Allowed : 14.99 % Favored : 82.80 % 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: -0.03 (0.16), residues: 2636 helix: 1.25 (0.15), residues: 1222 sheet: -0.64 (0.30), residues: 282 loop : -1.27 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 473 TYR 0.015 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 covalent geometry : bond 0.00251 (23148) covalent geometry : angle 0.55702 (31252) SS BOND : bond 0.00081 ( 6) SS BOND : angle 1.10892 ( 12) hydrogen bonds : bond 0.05182 ( 1006) hydrogen bonds : angle 4.32225 ( 2916) link_ALPHA1-3 : bond 0.01208 ( 6) link_ALPHA1-3 : angle 3.95919 ( 18) link_ALPHA1-6 : bond 0.00568 ( 4) link_ALPHA1-6 : angle 2.05321 ( 12) link_BETA1-2 : bond 0.00387 ( 2) link_BETA1-2 : angle 4.69129 ( 6) link_BETA1-4 : bond 0.00614 ( 14) link_BETA1-4 : angle 3.34612 ( 42) link_BETA1-6 : bond 0.00239 ( 4) link_BETA1-6 : angle 1.64171 ( 12) link_NAG-ASN : bond 0.00567 ( 8) link_NAG-ASN : angle 1.58084 ( 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 214 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.7101 (t0) cc_final: 0.6613 (m-30) REVERT: A 100 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.7033 (m-80) REVERT: A 470 MET cc_start: 0.8201 (mmm) cc_final: 0.7451 (mpp) REVERT: A 678 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7702 (tt) REVERT: A 1007 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7993 (t80) REVERT: B 73 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.7945 (p) REVERT: B 180 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8133 (ttpt) REVERT: B 302 GLU cc_start: 0.8220 (tt0) cc_final: 0.7961 (mm-30) REVERT: C 58 ASP cc_start: 0.7267 (t0) cc_final: 0.6503 (m-30) REVERT: C 100 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: C 127 ASN cc_start: 0.6261 (OUTLIER) cc_final: 0.6044 (m-40) REVERT: C 158 MET cc_start: 0.6861 (tpp) cc_final: 0.6573 (tmm) REVERT: C 392 TRP cc_start: 0.7767 (t60) cc_final: 0.7054 (t60) REVERT: C 470 MET cc_start: 0.8377 (mmm) cc_final: 0.7315 (mpp) REVERT: C 488 TYR cc_start: 0.7770 (p90) cc_final: 0.7470 (p90) REVERT: C 678 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7986 (tt) REVERT: C 1007 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.8100 (t80) REVERT: D 37 PHE cc_start: 0.8233 (t80) cc_final: 0.7931 (t80) REVERT: D 73 VAL cc_start: 0.8434 (OUTLIER) cc_final: 0.7992 (p) REVERT: D 156 TRP cc_start: 0.8940 (OUTLIER) cc_final: 0.8008 (m-10) REVERT: D 180 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8063 (ttpt) REVERT: D 255 LYS cc_start: 0.8641 (mttt) cc_final: 0.8107 (mmtm) outliers start: 50 outliers final: 31 residues processed: 207 average time/residue: 0.1567 time to fit residues: 51.1666 Evaluate side-chains 196 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 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 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 130 THR 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 100 PHE Chi-restraints excluded: chain C residue 127 ASN 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 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 116 SER Chi-restraints excluded: chain D residue 156 TRP 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: 0.8980 chunk 163 optimal weight: 0.8980 chunk 240 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 231 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 2.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN B 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.124598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.084300 restraints weight = 37350.019| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.61 r_work: 0.2885 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23192 Z= 0.190 Angle : 0.640 9.801 31378 Z= 0.303 Chirality : 0.046 0.513 3532 Planarity : 0.004 0.045 3812 Dihedral : 14.558 151.427 5281 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.27 % Allowed : 14.77 % Favored : 81.96 % 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: 0.04 (0.16), residues: 2636 helix: 1.26 (0.15), residues: 1212 sheet: -0.71 (0.31), residues: 280 loop : -1.12 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 473 TYR 0.020 0.002 TYR B 40 PHE 0.026 0.002 PHE C 793 TRP 0.020 0.002 TRP A 392 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00459 (23148) covalent geometry : angle 0.61526 (31252) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.91564 ( 12) hydrogen bonds : bond 0.06239 ( 1006) hydrogen bonds : angle 4.40277 ( 2916) link_ALPHA1-3 : bond 0.01193 ( 6) link_ALPHA1-3 : angle 3.99699 ( 18) link_ALPHA1-6 : bond 0.00479 ( 4) link_ALPHA1-6 : angle 2.05851 ( 12) link_BETA1-2 : bond 0.00440 ( 2) link_BETA1-2 : angle 4.58387 ( 6) link_BETA1-4 : bond 0.00538 ( 14) link_BETA1-4 : angle 3.24715 ( 42) link_BETA1-6 : bond 0.00369 ( 4) link_BETA1-6 : angle 1.81256 ( 12) link_NAG-ASN : bond 0.00436 ( 8) link_NAG-ASN : angle 1.52096 ( 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 231 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 157 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8143 (ppp) cc_final: 0.7941 (ppp) REVERT: A 46 LEU cc_start: 0.7236 (mp) cc_final: 0.6933 (mt) REVERT: A 100 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: A 470 MET cc_start: 0.8242 (mmm) cc_final: 0.7529 (mpp) REVERT: A 473 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7069 (tpt90) REVERT: B 37 PHE cc_start: 0.8461 (t80) cc_final: 0.8161 (t80) REVERT: B 55 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7653 (tp) REVERT: B 73 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8149 (p) REVERT: G 4 GLU cc_start: 0.5946 (mt-10) cc_final: 0.5632 (pp20) REVERT: C 41 MET cc_start: 0.8117 (ppp) cc_final: 0.7909 (ppp) REVERT: C 46 LEU cc_start: 0.7135 (mp) cc_final: 0.6839 (mt) REVERT: C 100 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: C 117 ILE cc_start: 0.8652 (mm) cc_final: 0.8415 (mt) REVERT: C 127 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6542 (m-40) REVERT: C 158 MET cc_start: 0.7163 (tpp) cc_final: 0.6769 (tmm) REVERT: C 392 TRP cc_start: 0.7854 (t60) cc_final: 0.7410 (t60) REVERT: C 470 MET cc_start: 0.8377 (mmm) cc_final: 0.7341 (mpp) REVERT: C 488 TYR cc_start: 0.7846 (p90) cc_final: 0.7561 (p90) REVERT: C 615 MET cc_start: 0.8996 (tpp) cc_final: 0.8729 (ttt) REVERT: C 678 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8071 (tt) REVERT: D 37 PHE cc_start: 0.8472 (t80) cc_final: 0.8192 (t80) REVERT: D 55 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7643 (tp) REVERT: D 73 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8183 (p) REVERT: D 156 TRP cc_start: 0.8989 (OUTLIER) cc_final: 0.7875 (m-10) outliers start: 74 outliers final: 49 residues processed: 220 average time/residue: 0.1553 time to fit residues: 54.2193 Evaluate side-chains 209 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 151 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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 102 ILE 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 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 203 GLN Chi-restraints excluded: chain B residue 210 VAL 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 121 THR Chi-restraints excluded: chain C residue 127 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 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 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 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: 0.0870 chunk 190 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 195 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 75 optimal weight: 0.0030 chunk 24 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 overall best weight: 0.9572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 946 GLN B 284 ASN C 383 GLN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.088001 restraints weight = 37430.391| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.77 r_work: 0.2950 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23192 Z= 0.111 Angle : 0.558 9.594 31378 Z= 0.262 Chirality : 0.043 0.517 3532 Planarity : 0.004 0.040 3812 Dihedral : 13.844 149.032 5280 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.43 % Allowed : 15.21 % Favored : 82.36 % 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: 0.38 (0.16), residues: 2636 helix: 1.58 (0.15), residues: 1242 sheet: -0.55 (0.30), residues: 294 loop : -1.08 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 385 TYR 0.021 0.001 TYR A 684 PHE 0.022 0.001 PHE A 967 TRP 0.018 0.001 TRP A 392 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00238 (23148) covalent geometry : angle 0.53237 (31252) SS BOND : bond 0.00067 ( 6) SS BOND : angle 0.86721 ( 12) hydrogen bonds : bond 0.04800 ( 1006) hydrogen bonds : angle 4.12754 ( 2916) link_ALPHA1-3 : bond 0.01130 ( 6) link_ALPHA1-3 : angle 3.98031 ( 18) link_ALPHA1-6 : bond 0.00605 ( 4) link_ALPHA1-6 : angle 1.86340 ( 12) link_BETA1-2 : bond 0.00485 ( 2) link_BETA1-2 : angle 4.70951 ( 6) link_BETA1-4 : bond 0.00573 ( 14) link_BETA1-4 : angle 3.03119 ( 42) link_BETA1-6 : bond 0.00252 ( 4) link_BETA1-6 : angle 1.62539 ( 12) link_NAG-ASN : bond 0.00542 ( 8) link_NAG-ASN : angle 1.25243 ( 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 213 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 158 time to evaluate : 0.833 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: A 41 MET cc_start: 0.8121 (ppp) cc_final: 0.7874 (ppp) REVERT: A 158 MET cc_start: 0.7123 (tpp) cc_final: 0.6763 (tmm) REVERT: A 470 MET cc_start: 0.8218 (mmm) cc_final: 0.7585 (mpp) REVERT: A 534 MET cc_start: 0.7626 (mmm) cc_final: 0.7224 (mmm) REVERT: A 852 MET cc_start: 0.8483 (tpp) cc_final: 0.8271 (mmm) REVERT: A 1007 PHE cc_start: 0.8435 (OUTLIER) cc_final: 0.8162 (t80) REVERT: B 73 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8167 (p) REVERT: B 180 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8188 (ttpt) REVERT: C 41 MET cc_start: 0.8127 (ppp) cc_final: 0.7894 (ppp) REVERT: C 46 LEU cc_start: 0.7119 (mp) cc_final: 0.6828 (mt) REVERT: C 127 ASN cc_start: 0.6815 (OUTLIER) cc_final: 0.6592 (m-40) REVERT: C 158 MET cc_start: 0.7244 (tpp) cc_final: 0.6912 (tmm) REVERT: C 392 TRP cc_start: 0.7859 (t60) cc_final: 0.7441 (t60) REVERT: C 470 MET cc_start: 0.8320 (mmm) cc_final: 0.7299 (mpp) REVERT: C 488 TYR cc_start: 0.7836 (p90) cc_final: 0.7559 (p90) REVERT: C 615 MET cc_start: 0.8934 (tpp) cc_final: 0.8708 (ttt) REVERT: C 678 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8121 (tt) REVERT: C 1007 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.8170 (t80) REVERT: D 73 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8083 (p) REVERT: D 156 TRP cc_start: 0.8966 (OUTLIER) cc_final: 0.7931 (m-10) REVERT: D 180 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8154 (ttpt) REVERT: D 255 LYS cc_start: 0.8710 (mttt) cc_final: 0.8195 (mmtm) outliers start: 55 outliers final: 34 residues processed: 207 average time/residue: 0.1503 time to fit residues: 49.8468 Evaluate side-chains 194 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU 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 130 THR Chi-restraints excluded: chain B residue 156 TRP 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 127 ASN 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 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 1007 PHE 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 130 THR Chi-restraints excluded: chain D residue 156 TRP 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: 0.9990 chunk 65 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 224 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 186 optimal weight: 7.9990 chunk 211 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 247 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.123686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.083275 restraints weight = 37403.769| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.37 r_work: 0.2887 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 23192 Z= 0.262 Angle : 0.692 10.293 31378 Z= 0.332 Chirality : 0.049 0.533 3532 Planarity : 0.004 0.068 3812 Dihedral : 14.159 142.173 5274 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.74 % Allowed : 15.56 % 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: 0.10 (0.16), residues: 2636 helix: 1.25 (0.15), residues: 1230 sheet: -0.52 (0.33), residues: 246 loop : -1.09 (0.17), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 423 TYR 0.025 0.002 TYR D 40 PHE 0.030 0.002 PHE C 793 TRP 0.016 0.002 TRP A 392 HIS 0.005 0.001 HIS C 290 Details of bonding type rmsd covalent geometry : bond 0.00648 (23148) covalent geometry : angle 0.66949 (31252) SS BOND : bond 0.00202 ( 6) SS BOND : angle 0.91362 ( 12) hydrogen bonds : bond 0.06726 ( 1006) hydrogen bonds : angle 4.46793 ( 2916) link_ALPHA1-3 : bond 0.01240 ( 6) link_ALPHA1-3 : angle 4.12331 ( 18) link_ALPHA1-6 : bond 0.00481 ( 4) link_ALPHA1-6 : angle 2.07427 ( 12) link_BETA1-2 : bond 0.00401 ( 2) link_BETA1-2 : angle 4.52181 ( 6) link_BETA1-4 : bond 0.00491 ( 14) link_BETA1-4 : angle 3.12654 ( 42) link_BETA1-6 : bond 0.00401 ( 4) link_BETA1-6 : angle 1.94207 ( 12) link_NAG-ASN : bond 0.00475 ( 8) link_NAG-ASN : angle 1.50695 ( 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 221 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 159 time to evaluate : 0.709 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 41 MET cc_start: 0.8205 (ppp) cc_final: 0.7942 (ppp) REVERT: A 46 LEU cc_start: 0.7256 (mp) cc_final: 0.6963 (mt) REVERT: A 158 MET cc_start: 0.7322 (tpp) cc_final: 0.6873 (tmm) REVERT: A 217 SER cc_start: 0.9291 (t) cc_final: 0.9088 (p) REVERT: A 470 MET cc_start: 0.8120 (mmm) cc_final: 0.7523 (mpp) REVERT: A 507 MET cc_start: 0.6165 (ttp) cc_final: 0.5809 (ppp) REVERT: B 37 PHE cc_start: 0.8488 (t80) cc_final: 0.8206 (t80) REVERT: B 55 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7694 (tp) REVERT: G 4 GLU cc_start: 0.6300 (mt-10) cc_final: 0.5879 (pp20) REVERT: C 46 LEU cc_start: 0.7231 (mp) cc_final: 0.6960 (mt) REVERT: C 58 ASP cc_start: 0.7445 (t0) cc_final: 0.6749 (m-30) REVERT: C 117 ILE cc_start: 0.8604 (mm) cc_final: 0.8373 (mt) REVERT: C 127 ASN cc_start: 0.6657 (OUTLIER) cc_final: 0.6370 (m-40) REVERT: C 158 MET cc_start: 0.7406 (tpp) cc_final: 0.7002 (tmm) REVERT: C 392 TRP cc_start: 0.7859 (t60) cc_final: 0.7421 (t60) REVERT: C 470 MET cc_start: 0.8305 (mmm) cc_final: 0.7287 (mpp) REVERT: C 488 TYR cc_start: 0.7936 (p90) cc_final: 0.7496 (p90) REVERT: C 615 MET cc_start: 0.9010 (tpp) cc_final: 0.8567 (ttt) REVERT: D 13 TRP cc_start: 0.5268 (t60) cc_final: 0.4910 (m100) REVERT: D 37 PHE cc_start: 0.8491 (t80) cc_final: 0.8231 (t80) REVERT: D 55 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7684 (tp) outliers start: 62 outliers final: 46 residues processed: 214 average time/residue: 0.1475 time to fit residues: 50.7995 Evaluate side-chains 202 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 153 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 116 SER 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 96 LEU Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 127 ASN 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 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 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 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 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 210 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 36 optimal weight: 6.9990 chunk 236 optimal weight: 0.2980 chunk 51 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 81 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.125406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.084994 restraints weight = 36945.628| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.42 r_work: 0.2910 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23192 Z= 0.176 Angle : 0.621 11.297 31378 Z= 0.294 Chirality : 0.045 0.536 3532 Planarity : 0.004 0.043 3812 Dihedral : 13.868 138.773 5270 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.30 % Allowed : 16.31 % Favored : 81.39 % 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: 0.21 (0.16), residues: 2636 helix: 1.42 (0.15), residues: 1230 sheet: -0.57 (0.31), residues: 280 loop : -1.13 (0.17), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 423 TYR 0.024 0.001 TYR A 684 PHE 0.028 0.002 PHE C 967 TRP 0.021 0.002 TRP A 392 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00425 (23148) covalent geometry : angle 0.59715 (31252) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.83083 ( 12) hydrogen bonds : bond 0.05837 ( 1006) hydrogen bonds : angle 4.30510 ( 2916) link_ALPHA1-3 : bond 0.01072 ( 6) link_ALPHA1-3 : angle 4.07636 ( 18) link_ALPHA1-6 : bond 0.00548 ( 4) link_ALPHA1-6 : angle 1.98172 ( 12) link_BETA1-2 : bond 0.00447 ( 2) link_BETA1-2 : angle 4.64440 ( 6) link_BETA1-4 : bond 0.00483 ( 14) link_BETA1-4 : angle 2.98862 ( 42) link_BETA1-6 : bond 0.00250 ( 4) link_BETA1-6 : angle 1.81534 ( 12) link_NAG-ASN : bond 0.00514 ( 8) link_NAG-ASN : angle 1.34523 ( 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 212 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 160 time to evaluate : 0.757 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 41 MET cc_start: 0.8228 (ppp) cc_final: 0.7952 (ppp) REVERT: A 46 LEU cc_start: 0.7285 (mp) cc_final: 0.7020 (mt) REVERT: A 158 MET cc_start: 0.7284 (tpp) cc_final: 0.6908 (tmm) REVERT: A 534 MET cc_start: 0.7589 (mmm) cc_final: 0.7229 (mmm) REVERT: B 37 PHE cc_start: 0.8488 (t80) cc_final: 0.8288 (t80) REVERT: B 55 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7603 (tp) REVERT: B 110 MET cc_start: 0.8721 (mmt) cc_final: 0.8320 (mmt) REVERT: G 4 GLU cc_start: 0.6261 (mt-10) cc_final: 0.5896 (pp20) REVERT: C 46 LEU cc_start: 0.7272 (mp) cc_final: 0.7014 (mt) REVERT: C 117 ILE cc_start: 0.8587 (mm) cc_final: 0.8352 (mt) REVERT: C 158 MET cc_start: 0.7387 (tpp) cc_final: 0.7057 (tmm) REVERT: C 392 TRP cc_start: 0.7832 (t60) cc_final: 0.7382 (t60) REVERT: C 470 MET cc_start: 0.8301 (mmm) cc_final: 0.7359 (mpp) REVERT: C 488 TYR cc_start: 0.7917 (p90) cc_final: 0.7529 (p90) REVERT: C 585 PHE cc_start: 0.7529 (t80) cc_final: 0.6803 (t80) REVERT: C 615 MET cc_start: 0.9002 (tpp) cc_final: 0.8564 (ttt) outliers start: 52 outliers final: 45 residues processed: 206 average time/residue: 0.1482 time to fit residues: 48.9333 Evaluate side-chains 196 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 150 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 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 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 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 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 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 116 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 159 ASN 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: 0.9980 chunk 26 optimal weight: 0.8980 chunk 138 optimal weight: 0.9980 chunk 48 optimal weight: 10.0000 chunk 240 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 248 optimal weight: 2.9990 chunk 236 optimal weight: 0.8980 chunk 186 optimal weight: 0.0970 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.128969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089478 restraints weight = 37038.917| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.35 r_work: 0.2962 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23192 Z= 0.104 Angle : 0.565 10.556 31378 Z= 0.264 Chirality : 0.043 0.522 3532 Planarity : 0.004 0.040 3812 Dihedral : 13.147 133.027 5268 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.33 % Allowed : 17.29 % Favored : 81.39 % 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: 0.51 (0.16), residues: 2636 helix: 1.69 (0.15), residues: 1266 sheet: -0.33 (0.31), residues: 292 loop : -1.13 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 385 TYR 0.025 0.001 TYR A 684 PHE 0.032 0.001 PHE C 967 TRP 0.029 0.002 TRP A 392 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00212 (23148) covalent geometry : angle 0.54181 (31252) SS BOND : bond 0.00088 ( 6) SS BOND : angle 0.66620 ( 12) hydrogen bonds : bond 0.04415 ( 1006) hydrogen bonds : angle 3.99448 ( 2916) link_ALPHA1-3 : bond 0.00943 ( 6) link_ALPHA1-3 : angle 3.85000 ( 18) link_ALPHA1-6 : bond 0.00669 ( 4) link_ALPHA1-6 : angle 1.83654 ( 12) link_BETA1-2 : bond 0.00476 ( 2) link_BETA1-2 : angle 4.76034 ( 6) link_BETA1-4 : bond 0.00556 ( 14) link_BETA1-4 : angle 2.76271 ( 42) link_BETA1-6 : bond 0.00213 ( 4) link_BETA1-6 : angle 1.62932 ( 12) link_NAG-ASN : bond 0.00542 ( 8) link_NAG-ASN : angle 1.09807 ( 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 191 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7363 (mp) cc_final: 0.7103 (mt) REVERT: A 470 MET cc_start: 0.8035 (mmm) cc_final: 0.7311 (mpp) REVERT: A 473 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7401 (tpt90) REVERT: A 534 MET cc_start: 0.7611 (mmm) cc_final: 0.7319 (mmm) REVERT: A 1007 PHE cc_start: 0.8385 (OUTLIER) cc_final: 0.8069 (t80) REVERT: B 110 MET cc_start: 0.8590 (mmt) cc_final: 0.8167 (mmt) REVERT: B 255 LYS cc_start: 0.8574 (mttt) cc_final: 0.8053 (mmtm) REVERT: C 46 LEU cc_start: 0.7400 (mp) cc_final: 0.7191 (mt) REVERT: C 392 TRP cc_start: 0.7793 (t60) cc_final: 0.7348 (t60) REVERT: C 470 MET cc_start: 0.8272 (mmm) cc_final: 0.7309 (mpp) REVERT: C 488 TYR cc_start: 0.7876 (p90) cc_final: 0.7452 (p90) REVERT: C 615 MET cc_start: 0.8928 (tpp) cc_final: 0.8384 (ttt) REVERT: D 255 LYS cc_start: 0.8633 (mttt) cc_final: 0.8094 (mmtm) outliers start: 30 outliers final: 22 residues processed: 187 average time/residue: 0.1500 time to fit residues: 44.9318 Evaluate side-chains 178 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 767 LEU Chi-restraints excluded: chain A residue 831 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 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 284 ASN 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 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 259 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 70 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 105 optimal weight: 0.1980 chunk 226 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 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 = 0.3767 r_free = 0.3767 target = 0.125704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085667 restraints weight = 37141.278| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.73 r_work: 0.2900 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23192 Z= 0.175 Angle : 0.638 16.609 31378 Z= 0.297 Chirality : 0.045 0.528 3532 Planarity : 0.004 0.045 3812 Dihedral : 13.113 128.365 5258 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.46 % Allowed : 17.55 % 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: 0.53 (0.16), residues: 2636 helix: 1.68 (0.15), residues: 1230 sheet: -0.09 (0.32), residues: 266 loop : -1.05 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 61 TYR 0.024 0.001 TYR A 684 PHE 0.034 0.002 PHE C 967 TRP 0.023 0.001 TRP A 392 HIS 0.005 0.001 HIS C 209 Details of bonding type rmsd covalent geometry : bond 0.00426 (23148) covalent geometry : angle 0.61671 (31252) SS BOND : bond 0.00122 ( 6) SS BOND : angle 0.65707 ( 12) hydrogen bonds : bond 0.05550 ( 1006) hydrogen bonds : angle 4.16444 ( 2916) link_ALPHA1-3 : bond 0.00965 ( 6) link_ALPHA1-3 : angle 3.92703 ( 18) link_ALPHA1-6 : bond 0.00580 ( 4) link_ALPHA1-6 : angle 1.95558 ( 12) link_BETA1-2 : bond 0.00429 ( 2) link_BETA1-2 : angle 4.57622 ( 6) link_BETA1-4 : bond 0.00500 ( 14) link_BETA1-4 : angle 2.80155 ( 42) link_BETA1-6 : bond 0.00296 ( 4) link_BETA1-6 : angle 1.70753 ( 12) link_NAG-ASN : bond 0.00527 ( 8) link_NAG-ASN : angle 1.40334 ( 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 186 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7403 (mp) cc_final: 0.7154 (mt) REVERT: A 470 MET cc_start: 0.8060 (mmm) cc_final: 0.7350 (mpp) REVERT: A 488 TYR cc_start: 0.8082 (p90) cc_final: 0.7484 (p90) REVERT: A 1011 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7991 (mmm160) REVERT: B 110 MET cc_start: 0.8731 (mmt) cc_final: 0.8385 (mmt) REVERT: B 255 LYS cc_start: 0.8767 (mttt) cc_final: 0.8283 (mmtt) REVERT: C 46 LEU cc_start: 0.7460 (mp) cc_final: 0.7238 (mt) REVERT: C 392 TRP cc_start: 0.7827 (t60) cc_final: 0.7351 (t60) REVERT: C 470 MET cc_start: 0.8275 (mmm) cc_final: 0.7360 (mpp) REVERT: C 488 TYR cc_start: 0.7920 (p90) cc_final: 0.7552 (p90) REVERT: C 585 PHE cc_start: 0.7529 (t80) cc_final: 0.6740 (t80) REVERT: C 615 MET cc_start: 0.9010 (tpp) cc_final: 0.8545 (ttt) REVERT: D 255 LYS cc_start: 0.8843 (mttt) cc_final: 0.8313 (mmtt) outliers start: 33 outliers final: 30 residues processed: 183 average time/residue: 0.1424 time to fit residues: 42.5703 Evaluate side-chains 181 residues out of total 2262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ILE 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 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1011 ARG 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 284 ASN Chi-restraints excluded: chain C residue 102 ILE 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 29 THR Chi-restraints excluded: chain D residue 116 SER 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: 3.9990 chunk 59 optimal weight: 7.9990 chunk 129 optimal weight: 1.9990 chunk 226 optimal weight: 0.0870 chunk 188 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.127195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088457 restraints weight = 37054.247| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.63 r_work: 0.2923 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5376 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= 0.119 Angle : 0.590 17.089 31378 Z= 0.273 Chirality : 0.044 0.522 3532 Planarity : 0.004 0.041 3812 Dihedral : 12.852 128.407 5258 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.37 % Allowed : 17.73 % Favored : 80.90 % 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: 0.60 (0.16), residues: 2636 helix: 1.81 (0.15), residues: 1242 sheet: -0.28 (0.30), residues: 292 loop : -1.07 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 385 TYR 0.026 0.001 TYR A 684 PHE 0.032 0.001 PHE C 967 TRP 0.025 0.001 TRP A 392 HIS 0.005 0.001 HIS C 493 Details of bonding type rmsd covalent geometry : bond 0.00267 (23148) covalent geometry : angle 0.56868 (31252) SS BOND : bond 0.00083 ( 6) SS BOND : angle 0.61793 ( 12) hydrogen bonds : bond 0.04909 ( 1006) hydrogen bonds : angle 4.04755 ( 2916) link_ALPHA1-3 : bond 0.00938 ( 6) link_ALPHA1-3 : angle 3.86055 ( 18) link_ALPHA1-6 : bond 0.00642 ( 4) link_ALPHA1-6 : angle 1.88398 ( 12) link_BETA1-2 : bond 0.00494 ( 2) link_BETA1-2 : angle 4.65609 ( 6) link_BETA1-4 : bond 0.00502 ( 14) link_BETA1-4 : angle 2.68617 ( 42) link_BETA1-6 : bond 0.00265 ( 4) link_BETA1-6 : angle 1.64318 ( 12) link_NAG-ASN : bond 0.00557 ( 8) link_NAG-ASN : angle 1.26658 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5896.19 seconds wall clock time: 101 minutes 19.02 seconds (6079.02 seconds total)