Starting phenix.real_space_refine on Sun Sep 29 21:31:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/09_2024/7wyx_32897.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/09_2024/7wyx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/09_2024/7wyx_32897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/09_2024/7wyx_32897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/09_2024/7wyx_32897.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyx_32897/09_2024/7wyx_32897.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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): 0.61s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: "E" 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: "E" 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, K, N, L, G, D, M Time building chain proxies: 28.87, per 1000 atoms: 1.27 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=3, 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 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: 7.30 Conformation dependent library (CDL) restraints added in 3.0 seconds 5272 Ramachandran restraints generated. 2636 Oldfield, 0 Emsley, 2636 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 20 sheets defined 49.8% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 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: 9.00 Time building geometry restraints manager: 8.21 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: 14199 35.90 - 71.81: 798 71.81 - 107.71: 84 107.71 - 143.61: 40 143.61 - 179.51: 2 Dihedral angle restraints: 15123 sinusoidal: 7467 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 15120 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: 105 2.49 - 3.10: 15866 3.10 - 3.70: 31119 3.70 - 4.30: 47965 4.30 - 4.90: 77914 Nonbonded interactions: 172969 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 172964 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and resid 1 through 4) selection = (chain 'H' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.230 Process input model: 69.410 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.810 ------------------------------------------------------------------------------- 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 23148 Z= 0.666 Angle : 1.353 11.630 31252 Z= 0.651 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 : 10.48 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.002 TRP A 894 HIS 0.009 0.002 HIS C 493 PHE 0.024 0.002 PHE D 297 TYR 0.030 0.002 TYR B 40 ARG 0.011 0.001 ARG C 596 *********************** 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 fitting. rotamer outliers: 236 poor density : 446 time to evaluate : 2.500 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: 0.5246 (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: 0.7114 (p0) REVERT: A 267 MET cc_start: 0.8414 (ppp) cc_final: 0.7749 (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: 0.7236 (mtt180) REVERT: A 460 ILE cc_start: 0.8305 (mm) cc_final: 0.8000 (mt) REVERT: A 484 SER cc_start: 0.7136 (OUTLIER) cc_final: 0.6635 (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: 0.5956 (m110) REVERT: C 267 MET cc_start: 0.8412 (ppp) cc_final: 0.7797 (ttt) REVERT: C 308 ILE cc_start: 0.8593 (mp) cc_final: 0.8333 (mm) REVERT: C 350 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7332 (mtt180) REVERT: C 460 ILE cc_start: 0.8405 (mm) cc_final: 0.8092 (mt) REVERT: C 484 SER cc_start: 0.7419 (OUTLIER) cc_final: 0.6897 (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: 0.3957 time to fit residues: 357.9489 Evaluate side-chains 282 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 210 time to evaluate : 2.539 ------------------------------------------------------------------------------- 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 222 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 474 ASN A 620 HIS A 683 HIS A 904 GLN B 203 GLN B 258 GLN B 271 ASN C 52 HIS C 225 GLN C 474 ASN C 566 ASN C 620 HIS C 904 GLN D 203 GLN D 258 GLN D 271 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23148 Z= 0.375 Angle : 0.768 9.497 31252 Z= 0.377 Chirality : 0.051 0.449 3532 Planarity : 0.006 0.071 3812 Dihedral : 17.359 170.556 5392 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.47 % Allowed : 12.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 2636 helix: 0.07 (0.14), residues: 1214 sheet: -1.73 (0.28), residues: 256 loop : -1.89 (0.16), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 392 HIS 0.005 0.002 HIS C 52 PHE 0.024 0.003 PHE C 793 TYR 0.025 0.002 TYR B 40 ARG 0.007 0.001 ARG D 137 *********************** 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 335 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 234 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.6930 (t0) cc_final: 0.6252 (m-30) REVERT: A 100 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: A 127 ASN cc_start: 0.5990 (OUTLIER) cc_final: 0.5716 (m-40) REVERT: A 217 SER cc_start: 0.9079 (t) cc_final: 0.8814 (p) REVERT: A 267 MET cc_start: 0.8279 (ppp) cc_final: 0.8025 (ttt) REVERT: A 350 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7792 (mtm180) REVERT: A 470 MET cc_start: 0.8598 (mmm) cc_final: 0.7628 (mpp) REVERT: A 473 ARG cc_start: 0.7324 (mtm-85) cc_final: 0.7092 (mmm-85) REVERT: B 26 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8822 (mm) REVERT: B 55 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7487 (tp) REVERT: B 73 VAL cc_start: 0.7965 (OUTLIER) cc_final: 0.7737 (m) REVERT: B 156 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.7810 (m-10) REVERT: C 58 ASP cc_start: 0.7094 (t0) cc_final: 0.6611 (m-30) REVERT: C 127 ASN cc_start: 0.6043 (OUTLIER) cc_final: 0.5773 (m-40) REVERT: C 181 ASN cc_start: 0.6556 (OUTLIER) cc_final: 0.5550 (t0) REVERT: C 217 SER cc_start: 0.8919 (t) cc_final: 0.8600 (p) REVERT: C 267 MET cc_start: 0.8257 (ppp) cc_final: 0.8047 (ttt) REVERT: C 308 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8725 (mp) REVERT: C 350 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7845 (mtm180) REVERT: C 488 TYR cc_start: 0.7432 (OUTLIER) cc_final: 0.7157 (p90) REVERT: C 859 MET cc_start: 0.8127 (mmt) cc_final: 0.7922 (mmt) REVERT: C 1007 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7826 (t80) REVERT: D 26 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8920 (mt) REVERT: D 55 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7518 (tp) REVERT: D 73 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7613 (p) REVERT: D 223 ARG cc_start: 0.7680 (ttm110) cc_final: 0.7459 (mtp180) outliers start: 101 outliers final: 58 residues processed: 319 average time/residue: 0.3967 time to fit residues: 193.4029 Evaluate side-chains 242 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 168 time to evaluate : 2.430 ------------------------------------------------------------------------------- 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 127 ASN 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 350 ARG Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 464 CYS 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 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 895 ILE Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU 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 104 LYS Chi-restraints excluded: chain B residue 130 THR 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 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 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 181 ASN Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 350 ARG Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 26 LEU 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 159 ASN 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 133 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 192 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23148 Z= 0.233 Angle : 0.605 13.333 31252 Z= 0.294 Chirality : 0.045 0.453 3532 Planarity : 0.005 0.057 3812 Dihedral : 16.109 168.896 5307 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.45 % Allowed : 13.57 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2636 helix: 0.89 (0.15), residues: 1218 sheet: -1.16 (0.30), residues: 248 loop : -1.44 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 392 HIS 0.004 0.001 HIS A 493 PHE 0.030 0.002 PHE C 184 TYR 0.020 0.001 TYR C 488 ARG 0.008 0.000 ARG C 517 *********************** 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 255 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 177 time to evaluate : 2.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ASP cc_start: 0.6845 (t0) cc_final: 0.6280 (m-30) REVERT: A 100 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: A 127 ASN cc_start: 0.5973 (OUTLIER) cc_final: 0.5625 (m-40) REVERT: A 217 SER cc_start: 0.9139 (t) cc_final: 0.8907 (p) REVERT: A 350 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7807 (mtm180) REVERT: A 470 MET cc_start: 0.8385 (mmm) cc_final: 0.7665 (mpp) REVERT: A 678 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.8061 (tt) REVERT: A 1007 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7855 (t80) REVERT: B 26 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8881 (mt) REVERT: B 73 VAL cc_start: 0.7909 (OUTLIER) cc_final: 0.7502 (p) REVERT: B 156 TRP cc_start: 0.8841 (OUTLIER) cc_final: 0.7886 (m-10) REVERT: C 58 ASP cc_start: 0.7093 (t0) cc_final: 0.6594 (m-30) REVERT: C 100 PHE cc_start: 0.7347 (OUTLIER) cc_final: 0.6906 (m-80) REVERT: C 127 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5660 (m-40) REVERT: C 217 SER cc_start: 0.8999 (t) cc_final: 0.8732 (p) REVERT: C 350 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7864 (mtm180) REVERT: C 365 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7341 (tm-30) REVERT: C 392 TRP cc_start: 0.7646 (t60) cc_final: 0.7176 (t60) REVERT: C 470 MET cc_start: 0.8596 (mmm) cc_final: 0.7658 (mpp) REVERT: C 678 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7946 (tt) REVERT: C 1007 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7705 (t80) REVERT: D 26 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9074 (mt) REVERT: D 73 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.7556 (p) REVERT: D 255 LYS cc_start: 0.8322 (mttt) cc_final: 0.7939 (mmtm) outliers start: 78 outliers final: 45 residues processed: 243 average time/residue: 0.3742 time to fit residues: 139.4173 Evaluate side-chains 216 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 156 time to evaluate : 2.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 127 ASN 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 457 LEU Chi-restraints excluded: chain A residue 464 CYS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 656 ASN Chi-restraints excluded: chain A residue 678 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 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 161 SER 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 91 LYS 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 350 ARG Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 737 SER 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 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 161 SER 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 237 optimal weight: 1.9990 chunk 180 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 9.9990 chunk 255 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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** D 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 23148 Z= 0.153 Angle : 0.548 11.917 31252 Z= 0.262 Chirality : 0.043 0.470 3532 Planarity : 0.004 0.048 3812 Dihedral : 15.109 166.047 5301 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.92 % Allowed : 14.94 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.16), residues: 2636 helix: 1.35 (0.15), residues: 1226 sheet: -0.67 (0.30), residues: 282 loop : -1.31 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 392 HIS 0.005 0.001 HIS C 493 PHE 0.020 0.001 PHE A 967 TYR 0.018 0.001 TYR A 488 ARG 0.005 0.000 ARG C 473 *********************** 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 234 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 168 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6856 (m-80) REVERT: A 102 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8335 (mt) REVERT: A 127 ASN cc_start: 0.5869 (OUTLIER) cc_final: 0.5563 (m-40) REVERT: A 217 SER cc_start: 0.9135 (t) cc_final: 0.8898 (p) REVERT: A 350 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7845 (mtm180) REVERT: A 470 MET cc_start: 0.8433 (mmm) cc_final: 0.7854 (mpp) REVERT: A 678 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8059 (tt) REVERT: A 1007 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7832 (t80) REVERT: B 26 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8848 (mt) REVERT: B 73 VAL cc_start: 0.7840 (OUTLIER) cc_final: 0.7513 (p) REVERT: B 156 TRP cc_start: 0.8795 (OUTLIER) cc_final: 0.7822 (m-10) REVERT: C 58 ASP cc_start: 0.7128 (t0) cc_final: 0.6610 (m-30) REVERT: C 100 PHE cc_start: 0.7157 (OUTLIER) cc_final: 0.6904 (m-80) REVERT: C 102 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8337 (mt) REVERT: C 127 ASN cc_start: 0.5911 (OUTLIER) cc_final: 0.5620 (m-40) REVERT: C 217 SER cc_start: 0.9051 (t) cc_final: 0.8778 (p) REVERT: C 350 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7854 (mtm180) REVERT: C 365 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7330 (tm-30) REVERT: C 392 TRP cc_start: 0.7598 (t60) cc_final: 0.7058 (t60) REVERT: C 470 MET cc_start: 0.8531 (mmm) cc_final: 0.7670 (mpp) REVERT: C 678 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8002 (tt) REVERT: C 1007 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7785 (t80) REVERT: D 26 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9054 (mt) REVERT: D 73 VAL cc_start: 0.7800 (OUTLIER) cc_final: 0.7527 (p) REVERT: D 224 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7981 (mm-30) REVERT: D 255 LYS cc_start: 0.8262 (mttt) cc_final: 0.7931 (mmtm) outliers start: 66 outliers final: 40 residues processed: 227 average time/residue: 0.3510 time to fit residues: 123.9195 Evaluate side-chains 216 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 159 time to evaluate : 2.566 ------------------------------------------------------------------------------- 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 102 ILE Chi-restraints excluded: chain A residue 127 ASN 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 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 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 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 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain 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 102 ILE 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 350 ARG 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 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 26 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 104 LYS Chi-restraints excluded: chain D residue 130 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 5.9990 chunk 144 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 ASN ** C 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23148 Z= 0.271 Angle : 0.593 9.971 31252 Z= 0.286 Chirality : 0.046 0.505 3532 Planarity : 0.004 0.042 3812 Dihedral : 14.626 156.711 5300 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.40 % Allowed : 14.94 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2636 helix: 1.34 (0.15), residues: 1226 sheet: -0.76 (0.31), residues: 280 loop : -1.16 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 392 HIS 0.003 0.001 HIS C 493 PHE 0.025 0.002 PHE C 793 TYR 0.019 0.001 TYR B 40 ARG 0.003 0.000 ARG C 61 *********************** 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 241 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 164 time to evaluate : 2.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: A 470 MET cc_start: 0.8442 (mmm) cc_final: 0.7853 (mpp) REVERT: A 473 ARG cc_start: 0.7851 (mmm-85) cc_final: 0.7146 (tpt90) REVERT: A 615 MET cc_start: 0.8644 (tpp) cc_final: 0.8122 (ttt) REVERT: A 678 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8129 (tt) REVERT: A 1007 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7769 (t80) REVERT: B 26 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8998 (mt) REVERT: B 37 PHE cc_start: 0.8101 (t80) cc_final: 0.7806 (t80) REVERT: B 55 ILE cc_start: 0.8175 (OUTLIER) cc_final: 0.7530 (tp) REVERT: B 73 VAL cc_start: 0.8030 (OUTLIER) cc_final: 0.7594 (p) REVERT: C 100 PHE cc_start: 0.7326 (OUTLIER) cc_final: 0.7012 (m-80) REVERT: C 217 SER cc_start: 0.9092 (t) cc_final: 0.8882 (p) REVERT: C 392 TRP cc_start: 0.7682 (t60) cc_final: 0.7198 (t60) REVERT: C 470 MET cc_start: 0.8507 (mmm) cc_final: 0.7677 (mpp) REVERT: C 615 MET cc_start: 0.8655 (tpp) cc_final: 0.8320 (ttt) REVERT: C 678 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8048 (tt) REVERT: D 26 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9119 (mt) REVERT: D 37 PHE cc_start: 0.8117 (t80) cc_final: 0.7803 (t80) REVERT: D 55 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7517 (tp) REVERT: D 73 VAL cc_start: 0.8028 (OUTLIER) cc_final: 0.7641 (p) REVERT: D 156 TRP cc_start: 0.8869 (OUTLIER) cc_final: 0.7976 (m-10) REVERT: D 234 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8472 (tm) REVERT: D 255 LYS cc_start: 0.8352 (mttt) cc_final: 0.8015 (mmtm) outliers start: 77 outliers final: 51 residues processed: 229 average time/residue: 0.3625 time to fit residues: 129.4288 Evaluate side-chains 215 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 151 time to evaluate : 2.540 ------------------------------------------------------------------------------- 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 121 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 381 LEU 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 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 55 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER 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 100 PHE Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 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 656 ASN 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 26 LEU 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 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 Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 149 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 255 optimal weight: 0.9990 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** A 946 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23148 Z= 0.143 Angle : 0.534 8.938 31252 Z= 0.256 Chirality : 0.043 0.509 3532 Planarity : 0.004 0.040 3812 Dihedral : 13.807 154.388 5284 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.65 % Allowed : 15.61 % Favored : 81.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 2636 helix: 1.66 (0.15), residues: 1242 sheet: -0.58 (0.31), residues: 282 loop : -1.07 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 392 HIS 0.005 0.001 HIS C 493 PHE 0.022 0.001 PHE A 967 TYR 0.013 0.001 TYR A 869 ARG 0.005 0.000 ARG A 473 *********************** 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 218 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 158 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6865 (tpp) cc_final: 0.6665 (tpp) REVERT: A 470 MET cc_start: 0.8350 (mmm) cc_final: 0.7781 (mpp) REVERT: A 473 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7265 (tpt90) REVERT: A 534 MET cc_start: 0.7658 (mmm) cc_final: 0.7201 (mmm) REVERT: A 615 MET cc_start: 0.8606 (tpp) cc_final: 0.8391 (ttt) REVERT: A 678 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8186 (tt) REVERT: A 1007 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7838 (t80) REVERT: B 26 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8916 (mt) REVERT: B 73 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7609 (p) REVERT: B 255 LYS cc_start: 0.8247 (mttt) cc_final: 0.7856 (mmtm) REVERT: C 385 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6942 (ttp80) REVERT: C 392 TRP cc_start: 0.7635 (t60) cc_final: 0.7237 (t60) REVERT: C 470 MET cc_start: 0.8491 (mmm) cc_final: 0.7671 (mpp) REVERT: C 615 MET cc_start: 0.8617 (tpp) cc_final: 0.8380 (ttt) REVERT: C 678 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8094 (tt) REVERT: C 1007 PHE cc_start: 0.8124 (t80) cc_final: 0.7799 (t80) REVERT: D 26 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.9052 (mt) REVERT: D 73 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7658 (p) REVERT: D 156 TRP cc_start: 0.8792 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: D 255 LYS cc_start: 0.8280 (mttt) cc_final: 0.7867 (mmtm) outliers start: 60 outliers final: 31 residues processed: 211 average time/residue: 0.3577 time to fit residues: 119.1992 Evaluate side-chains 192 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER 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 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 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 197 ASP Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 385 ARG 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 678 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 159 ASN 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 246 optimal weight: 0.0020 chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 0.0770 chunk 186 optimal weight: 0.9980 chunk 144 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 0.0470 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.6246 ------------------------------------------------------------------------------- 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 56 GLN C 946 GLN D 284 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23148 Z= 0.132 Angle : 0.518 9.754 31252 Z= 0.245 Chirality : 0.043 0.512 3532 Planarity : 0.004 0.039 3812 Dihedral : 12.915 148.691 5276 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.95 % Allowed : 16.53 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.16), residues: 2636 helix: 1.91 (0.15), residues: 1242 sheet: -0.47 (0.32), residues: 270 loop : -0.95 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 392 HIS 0.004 0.001 HIS A 493 PHE 0.025 0.001 PHE C 967 TYR 0.019 0.001 TYR A 488 ARG 0.004 0.000 ARG A 473 *********************** 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 207 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 TRP cc_start: 0.6709 (m100) cc_final: 0.6448 (m100) REVERT: A 470 MET cc_start: 0.8239 (mmm) cc_final: 0.7879 (mpp) REVERT: A 473 ARG cc_start: 0.7855 (mmm-85) cc_final: 0.7292 (tpt90) REVERT: A 615 MET cc_start: 0.8617 (tpp) cc_final: 0.8393 (ttt) REVERT: A 678 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8135 (tt) REVERT: A 1007 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 26 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8887 (mt) REVERT: B 180 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7871 (pttp) REVERT: B 255 LYS cc_start: 0.8238 (mttt) cc_final: 0.7844 (mmtm) REVERT: C 365 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 392 TRP cc_start: 0.7619 (t60) cc_final: 0.7307 (t60) REVERT: C 470 MET cc_start: 0.8461 (mmm) cc_final: 0.7713 (mpp) REVERT: C 615 MET cc_start: 0.8610 (tpp) cc_final: 0.8367 (ttt) REVERT: C 678 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8087 (tt) REVERT: C 1007 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7750 (t80) REVERT: D 26 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8933 (mt) REVERT: D 95 ASN cc_start: 0.8395 (t0) cc_final: 0.8092 (m-40) REVERT: D 156 TRP cc_start: 0.8703 (OUTLIER) cc_final: 0.7937 (m-10) REVERT: D 180 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7891 (pttp) REVERT: D 255 LYS cc_start: 0.8222 (mttt) cc_final: 0.7812 (mmtm) outliers start: 44 outliers final: 28 residues processed: 202 average time/residue: 0.3311 time to fit residues: 106.3979 Evaluate side-chains 192 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 155 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 986 SER 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 130 THR Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 457 LEU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 639 GLU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 26 LEU 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 Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 200 optimal weight: 0.9980 chunk 231 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN ** D 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23148 Z= 0.241 Angle : 0.569 10.662 31252 Z= 0.273 Chirality : 0.045 0.521 3532 Planarity : 0.004 0.043 3812 Dihedral : 12.898 144.081 5268 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.12 % Allowed : 16.40 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2636 helix: 1.79 (0.15), residues: 1244 sheet: -0.42 (0.31), residues: 280 loop : -1.03 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 894 HIS 0.004 0.001 HIS C 209 PHE 0.027 0.002 PHE A 967 TYR 0.019 0.001 TYR A 684 ARG 0.007 0.000 ARG C 423 *********************** 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 204 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7266 (mp) cc_final: 0.7032 (mt) REVERT: A 473 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7242 (tpt90) REVERT: A 534 MET cc_start: 0.7676 (mmm) cc_final: 0.7281 (mmm) REVERT: A 678 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8155 (tt) REVERT: A 1007 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7807 (t80) REVERT: B 26 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8917 (mt) REVERT: B 37 PHE cc_start: 0.8081 (t80) cc_final: 0.7808 (t80) REVERT: B 180 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.7948 (pttp) REVERT: B 255 LYS cc_start: 0.8355 (mttt) cc_final: 0.7964 (mmtm) REVERT: C 385 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.6941 (ttp80) REVERT: C 392 TRP cc_start: 0.7662 (t60) cc_final: 0.7314 (t60) REVERT: C 470 MET cc_start: 0.8479 (mmm) cc_final: 0.7719 (mpp) REVERT: C 678 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8112 (tt) REVERT: C 1007 PHE cc_start: 0.8147 (t80) cc_final: 0.7876 (t80) REVERT: D 26 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8995 (mt) REVERT: D 156 TRP cc_start: 0.8768 (OUTLIER) cc_final: 0.7886 (m-10) REVERT: D 180 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.7923 (pttp) REVERT: D 255 LYS cc_start: 0.8327 (mttt) cc_final: 0.7979 (mttp) outliers start: 48 outliers final: 35 residues processed: 196 average time/residue: 0.3445 time to fit residues: 106.3433 Evaluate side-chains 194 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 2.218 ------------------------------------------------------------------------------- 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 185 VAL 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 678 LEU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER 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 116 SER Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 156 TRP 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 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 385 ARG 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 678 LEU 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 26 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 5.9990 chunk 222 optimal weight: 0.6980 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 186 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 214 optimal weight: 2.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 155 optimal weight: 9.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 D 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23148 Z= 0.198 Angle : 0.557 11.758 31252 Z= 0.265 Chirality : 0.044 0.521 3532 Planarity : 0.004 0.041 3812 Dihedral : 12.728 141.649 5265 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.43 % Allowed : 16.53 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.16), residues: 2636 helix: 1.83 (0.15), residues: 1246 sheet: -0.38 (0.31), residues: 280 loop : -1.00 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 392 HIS 0.004 0.001 HIS C 209 PHE 0.027 0.002 PHE A 967 TYR 0.014 0.001 TYR A 869 ARG 0.006 0.000 ARG C 423 *********************** 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 209 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 154 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7249 (mp) cc_final: 0.7048 (mt) REVERT: A 217 SER cc_start: 0.9272 (t) cc_final: 0.9037 (p) REVERT: A 470 MET cc_start: 0.8307 (mmm) cc_final: 0.7690 (mpp) REVERT: A 473 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7287 (tpt90) REVERT: A 534 MET cc_start: 0.7701 (mmm) cc_final: 0.7287 (mmm) REVERT: A 1007 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7769 (t80) REVERT: B 26 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8936 (mt) REVERT: B 55 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7445 (tp) REVERT: B 180 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.7882 (pttp) REVERT: B 255 LYS cc_start: 0.8302 (mttt) cc_final: 0.7897 (mmtm) REVERT: C 46 LEU cc_start: 0.7129 (mp) cc_final: 0.6840 (mt) REVERT: C 385 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6926 (ttp80) REVERT: C 392 TRP cc_start: 0.7646 (t60) cc_final: 0.7308 (t60) REVERT: C 470 MET cc_start: 0.8469 (mmm) cc_final: 0.7712 (mpp) REVERT: C 585 PHE cc_start: 0.7458 (t80) cc_final: 0.6783 (t80) REVERT: C 1007 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7823 (t80) REVERT: D 26 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8978 (mt) REVERT: D 156 TRP cc_start: 0.8749 (OUTLIER) cc_final: 0.7883 (m-10) REVERT: D 180 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.7919 (pttp) REVERT: D 255 LYS cc_start: 0.8277 (mttt) cc_final: 0.7902 (mttp) outliers start: 55 outliers final: 36 residues processed: 200 average time/residue: 0.3487 time to fit residues: 109.1734 Evaluate side-chains 197 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 152 time to evaluate : 2.373 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER 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 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 180 LYS Chi-restraints excluded: chain B residue 284 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 295 ILE Chi-restraints excluded: chain C residue 385 ARG 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 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 767 LEU 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 116 SER Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 180 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** C 209 HIS D 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23148 Z= 0.237 Angle : 0.580 12.682 31252 Z= 0.276 Chirality : 0.045 0.526 3532 Planarity : 0.004 0.048 3812 Dihedral : 12.692 136.965 5262 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.25 % Allowed : 16.67 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2636 helix: 1.77 (0.15), residues: 1244 sheet: -0.38 (0.31), residues: 280 loop : -1.00 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 392 HIS 0.005 0.001 HIS C 209 PHE 0.030 0.002 PHE A 967 TYR 0.016 0.001 TYR A 684 ARG 0.006 0.000 ARG A 61 ********************** 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 203 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 152 time to evaluate : 3.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7263 (mp) cc_final: 0.7062 (mt) REVERT: A 217 SER cc_start: 0.9287 (t) cc_final: 0.9043 (p) REVERT: A 470 MET cc_start: 0.8306 (mmm) cc_final: 0.7698 (mpp) REVERT: A 473 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7294 (tpt90) REVERT: A 615 MET cc_start: 0.8640 (tpp) cc_final: 0.8354 (ttt) REVERT: A 1007 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7828 (t80) REVERT: B 26 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8971 (mt) REVERT: B 55 ILE cc_start: 0.8169 (OUTLIER) cc_final: 0.7484 (tp) REVERT: B 180 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.7944 (pttp) REVERT: B 255 LYS cc_start: 0.8366 (mttt) cc_final: 0.7979 (mmtt) REVERT: C 46 LEU cc_start: 0.7245 (mp) cc_final: 0.6955 (mt) REVERT: C 385 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.6939 (ttp80) REVERT: C 392 TRP cc_start: 0.7664 (t60) cc_final: 0.7286 (t60) REVERT: C 470 MET cc_start: 0.8453 (mmm) cc_final: 0.7761 (mpp) REVERT: C 615 MET cc_start: 0.8654 (tpp) cc_final: 0.8361 (ttt) REVERT: C 1007 PHE cc_start: 0.8144 (t80) cc_final: 0.7851 (t80) REVERT: D 26 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8978 (mt) REVERT: D 37 PHE cc_start: 0.8124 (t80) cc_final: 0.7882 (t80) REVERT: D 55 ILE cc_start: 0.8154 (OUTLIER) cc_final: 0.7458 (tp) REVERT: D 156 TRP cc_start: 0.8756 (OUTLIER) cc_final: 0.7921 (m-90) REVERT: D 180 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7911 (pttp) REVERT: D 255 LYS cc_start: 0.8331 (mttt) cc_final: 0.7981 (mttp) outliers start: 51 outliers final: 39 residues processed: 194 average time/residue: 0.3518 time to fit residues: 107.9826 Evaluate side-chains 197 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 149 time to evaluate : 2.478 ------------------------------------------------------------------------------- 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 185 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain A residue 1011 ARG Chi-restraints excluded: chain B residue 26 LEU 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 180 LYS Chi-restraints excluded: chain B residue 210 VAL 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 295 ILE Chi-restraints excluded: chain C residue 385 ARG 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 656 ASN Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 767 LEU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 26 LEU 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 156 TRP Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 193 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 87 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 D 284 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.126618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085479 restraints weight = 36973.210| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.44 r_work: 0.2920 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23148 Z= 0.221 Angle : 0.571 12.917 31252 Z= 0.272 Chirality : 0.044 0.525 3532 Planarity : 0.004 0.041 3812 Dihedral : 12.613 133.274 5262 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.25 % Allowed : 16.58 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2636 helix: 1.80 (0.15), residues: 1246 sheet: -0.36 (0.31), residues: 280 loop : -0.99 (0.17), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 392 HIS 0.004 0.001 HIS C 493 PHE 0.031 0.002 PHE A 967 TYR 0.024 0.001 TYR C 684 ARG 0.003 0.000 ARG A 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4818.42 seconds wall clock time: 87 minutes 20.10 seconds (5240.10 seconds total)