Starting phenix.real_space_refine on Tue Mar 19 00:53:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyu_32894/03_2024/7wyu_32894_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyu_32894/03_2024/7wyu_32894.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/7wyu_32894/03_2024/7wyu_32894.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyu_32894/03_2024/7wyu_32894.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyu_32894/03_2024/7wyu_32894_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyu_32894/03_2024/7wyu_32894_updated.pdb" } 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= 0.001 sd= 0.005 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 4 4.78 5 C 14652 2.51 5 N 3524 2.21 5 O 4330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22662 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 7687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7687 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'PHD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "C" 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: "D" 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: "K" 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: "L" 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: "M" 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: "N" 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 562 Unusual residues: {' MG': 1, ' NA': 2, 'ATP': 1, 'CLR': 3, 'PCW': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 562 Unusual residues: {' MG': 1, ' NA': 2, 'ATP': 1, 'CLR': 3, 'PCW': 10} Classifications: {'undetermined': 17} Link IDs: {None: 16} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 12.26, per 1000 atoms: 0.54 Number of scatterers: 22662 At special positions: 0 Unit cell: (216.276, 178.616, 103.296, 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 4 11.00 O 4330 8.00 N 3524 7.00 C 14652 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 160 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 215 " - pdb=" SG CYS D 278 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " 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: 9.37 Conformation dependent library (CDL) restraints added in 4.0 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... running ksdssp... Secondary structure from input PDB file: 104 helices and 16 sheets defined 43.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.46 Creating SS restraints... Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 129 through 161 removed outlier: 4.544A pdb=" N PHE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 283 through 313 Processing helix chain 'A' and resid 317 through 330 removed outlier: 3.551A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.714A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET A 351 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 366 through 369 No H-bonds generated for 'chain 'A' and resid 366 through 369' Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 511 through 517 removed outlier: 3.519A pdb=" N ARG A 517 " --> pdb=" O ARG A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 547 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 621 through 631 removed outlier: 3.802A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 667 through 672 removed outlier: 4.141A pdb=" N ASP A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 719 through 727 Proline residue: A 723 - end of helix removed outlier: 4.126A pdb=" N LYS A 726 " --> pdb=" O PRO A 723 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A 727 " --> pdb=" O ALA A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 755 through 796 removed outlier: 3.831A pdb=" N GLY A 765 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE A 768 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 771 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A 782 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 784 " --> pdb=" O THR A 781 " (cutoff:3.500A) Proline residue: A 785 - end of helix removed outlier: 5.492A pdb=" N THR A 788 " --> pdb=" O PRO A 785 " (cutoff:3.500A) Proline residue: A 789 - end of helix removed outlier: 3.690A pdb=" N ILE A 795 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY A 796 " --> pdb=" O PHE A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 814 through 824 Proline residue: A 818 - end of helix removed outlier: 4.270A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.658A pdb=" N MET A 852 " --> pdb=" O ARG A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 875 Processing helix chain 'A' and resid 880 through 883 No H-bonds generated for 'chain 'A' and resid 880 through 883' Processing helix chain 'A' and resid 887 through 891 Processing helix chain 'A' and resid 908 through 938 removed outlier: 4.028A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 947 No H-bonds generated for 'chain 'A' and resid 944 through 947' Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.559A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 977 No H-bonds generated for 'chain 'A' and resid 974 through 977' Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 992 through 1011 removed outlier: 3.565A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'B' and resid 30 through 61 removed outlier: 3.661A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 112 removed outlier: 3.500A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'G' and resid 10 through 12 No H-bonds generated for 'chain 'G' and resid 10 through 12' Processing helix chain 'G' and resid 16 through 39 Processing helix chain 'C' and resid 34 through 37 No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 100 through 121 Processing helix chain 'C' and resid 129 through 161 removed outlier: 4.544A pdb=" N PHE C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 266 through 275 Processing helix chain 'C' and resid 283 through 313 Processing helix chain 'C' and resid 317 through 330 removed outlier: 3.550A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.714A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N MET C 351 " --> pdb=" O THR C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 364 No H-bonds generated for 'chain 'C' and resid 362 through 364' Processing helix chain 'C' and resid 366 through 369 No H-bonds generated for 'chain 'C' and resid 366 through 369' Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 511 through 517 removed outlier: 3.520A pdb=" N ARG C 517 " --> pdb=" O ARG C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 547 Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 621 through 631 removed outlier: 3.802A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 648 Processing helix chain 'C' and resid 657 through 659 No H-bonds generated for 'chain 'C' and resid 657 through 659' Processing helix chain 'C' and resid 667 through 672 removed outlier: 4.141A pdb=" N ASP C 672 " --> pdb=" O SER C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 695 through 706 Processing helix chain 'C' and resid 719 through 727 Proline residue: C 723 - end of helix removed outlier: 4.125A pdb=" N LYS C 726 " --> pdb=" O PRO C 723 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS C 727 " --> pdb=" O ALA C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 755 through 796 removed outlier: 3.831A pdb=" N GLY C 765 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 768 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN C 771 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 782 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE C 784 " --> pdb=" O THR C 781 " (cutoff:3.500A) Proline residue: C 785 - end of helix removed outlier: 5.491A pdb=" N THR C 788 " --> pdb=" O PRO C 785 " (cutoff:3.500A) Proline residue: C 789 - end of helix removed outlier: 3.690A pdb=" N ILE C 795 " --> pdb=" O VAL C 792 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY C 796 " --> pdb=" O PHE C 793 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 814 through 824 Proline residue: C 818 - end of helix removed outlier: 4.269A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.657A pdb=" N MET C 852 " --> pdb=" O ARG C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 875 Processing helix chain 'C' and resid 880 through 883 No H-bonds generated for 'chain 'C' and resid 880 through 883' Processing helix chain 'C' and resid 887 through 891 Processing helix chain 'C' and resid 908 through 938 removed outlier: 4.029A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 947 No H-bonds generated for 'chain 'C' and resid 944 through 947' Processing helix chain 'C' and resid 952 through 970 removed outlier: 3.560A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 977 No H-bonds generated for 'chain 'C' and resid 974 through 977' Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 992 through 1011 removed outlier: 3.565A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'D' and resid 30 through 61 removed outlier: 3.660A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 100 through 112 removed outlier: 4.296A pdb=" N LEU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 249 through 252 No H-bonds generated for 'chain 'D' and resid 249 through 252' Processing helix chain 'E' and resid 10 through 12 No H-bonds generated for 'chain 'E' and resid 10 through 12' Processing helix chain 'E' and resid 16 through 39 Processing sheet with id= A, first strand: chain 'A' and resid 176 through 181 removed outlier: 11.764A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 207 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.720A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS A 612 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER A 375 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE A 614 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ILE A 688 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 390 through 392 Processing sheet with id= D, first strand: chain 'A' and resid 526 through 529 removed outlier: 7.221A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N GLY A 587 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.394A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 78 through 80 Processing sheet with id= G, first strand: chain 'B' and resid 88 through 91 removed outlier: 7.958A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLU B 302 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 210 through 212 Processing sheet with id= I, first strand: chain 'C' and resid 176 through 181 removed outlier: 11.764A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER C 207 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.720A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS C 612 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER C 375 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 614 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE C 688 " --> pdb=" O VAL C 613 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 390 through 392 Processing sheet with id= L, first strand: chain 'C' and resid 526 through 529 removed outlier: 7.221A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 11.316A pdb=" N GLY C 587 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.394A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N VAL C 258 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 78 through 80 Processing sheet with id= O, first strand: chain 'D' and resid 88 through 91 removed outlier: 7.959A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLU D 302 " --> pdb=" O PHE D 91 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 210 through 212 849 hydrogen bonds defined for protein. 2331 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: 7.94 Time building geometry restraints manager: 10.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6876 1.34 - 1.46: 5156 1.46 - 1.58: 10794 1.58 - 1.70: 92 1.70 - 1.82: 172 Bond restraints: 23090 Sorted by residual: bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.505 0.311 2.00e-02 2.50e+03 2.42e+02 bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.506 0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C19 PCW A1110 " pdb=" C20 PCW A1110 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C39 PCW A1114 " pdb=" C40 PCW A1114 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 bond pdb=" C19 PCW C1110 " pdb=" C20 PCW C1110 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 98.66 - 106.91: 884 106.91 - 115.15: 14380 115.15 - 123.40: 14996 123.40 - 131.64: 864 131.64 - 139.89: 38 Bond angle restraints: 31162 Sorted by residual: angle pdb=" C SER B 122 " pdb=" N PRO B 123 " pdb=" CA PRO B 123 " ideal model delta sigma weight residual 127.00 114.18 12.82 2.40e+00 1.74e-01 2.85e+01 angle pdb=" C SER D 122 " pdb=" N PRO D 123 " pdb=" CA PRO D 123 " ideal model delta sigma weight residual 127.00 114.20 12.80 2.40e+00 1.74e-01 2.84e+01 angle pdb=" N GLY C 855 " pdb=" CA GLY C 855 " pdb=" C GLY C 855 " ideal model delta sigma weight residual 113.18 124.66 -11.48 2.37e+00 1.78e-01 2.35e+01 angle pdb=" N GLY A 314 " pdb=" CA GLY A 314 " pdb=" C GLY A 314 " ideal model delta sigma weight residual 114.37 120.46 -6.09 1.26e+00 6.30e-01 2.33e+01 angle pdb=" N GLY A 855 " pdb=" CA GLY A 855 " pdb=" C GLY A 855 " ideal model delta sigma weight residual 113.18 124.61 -11.43 2.37e+00 1.78e-01 2.32e+01 ... (remaining 31157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 14105 35.98 - 71.95: 773 71.95 - 107.93: 84 107.93 - 143.91: 40 143.91 - 179.88: 2 Dihedral angle restraints: 15004 sinusoidal: 7348 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW G 102 " pdb=" C31 PCW G 102 " pdb=" C32 PCW G 102 " pdb=" O2 PCW G 102 " ideal model delta sinusoidal sigma weight residual 191.83 11.95 179.88 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW E 102 " pdb=" C31 PCW E 102 " pdb=" C32 PCW E 102 " pdb=" O2 PCW E 102 " ideal model delta sinusoidal sigma weight residual 191.83 11.97 179.86 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A1113 " pdb=" C31 PCW A1113 " pdb=" C32 PCW A1113 " pdb=" O2 PCW A1113 " ideal model delta sinusoidal sigma weight residual -168.17 -29.38 -138.79 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 2887 0.070 - 0.141: 512 0.141 - 0.211: 67 0.211 - 0.281: 29 0.281 - 0.352: 25 Chirality restraints: 3520 Sorted by residual: 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 -2.27 -0.13 2.00e-02 2.50e+03 4.47e+01 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 -2.27 -0.13 2.00e-02 2.50e+03 4.45e+01 chirality pdb=" C1 FUC F 6 " pdb=" O6 NAG F 1 " pdb=" C2 FUC F 6 " pdb=" O5 FUC F 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.31 -0.09 2.00e-02 2.50e+03 1.85e+01 ... (remaining 3517 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " -0.085 5.00e-02 4.00e+02 1.31e-01 2.76e+01 pdb=" N PRO B 123 " 0.227 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " 0.084 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO D 123 " -0.227 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 332 " 0.064 5.00e-02 4.00e+02 9.86e-02 1.55e+01 pdb=" N PRO C 333 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.053 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 100 2.51 - 3.11: 16293 3.11 - 3.70: 31527 3.70 - 4.30: 47664 4.30 - 4.90: 77779 Nonbonded interactions: 173363 Sorted by model distance: nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.911 2.170 nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.911 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C2001 " model vdw 1.947 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A2001 " model vdw 1.957 2.170 nonbonded pdb=" O THR A 378 " pdb="MG MG A1101 " model vdw 2.023 2.170 ... (remaining 173358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.730 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: 0.020 Extract box with map and model: 4.410 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 61.420 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.311 23090 Z= 0.663 Angle : 1.297 12.821 31162 Z= 0.600 Chirality : 0.063 0.352 3520 Planarity : 0.008 0.131 3806 Dihedral : 20.272 179.885 10074 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.55 % Favored : 92.15 % Rotamer: Outliers : 10.48 % Allowed : 8.36 % 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: -3.01 (0.15), residues: 2636 helix: -1.25 (0.14), residues: 1188 sheet: -2.35 (0.28), residues: 268 loop : -2.68 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 894 HIS 0.009 0.002 HIS A 493 PHE 0.025 0.002 PHE B 297 TYR 0.033 0.002 TYR A 131 ARG 0.009 0.001 ARG A 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 668 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 431 time to evaluate : 2.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 LEU cc_start: 0.8080 (tp) cc_final: 0.7627 (tt) REVERT: A 223 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6972 (pt0) REVERT: A 231 PHE cc_start: 0.6742 (OUTLIER) cc_final: 0.6365 (t80) REVERT: A 493 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7033 (m-70) REVERT: A 523 LEU cc_start: 0.8533 (tp) cc_final: 0.8317 (tp) REVERT: A 680 ASP cc_start: 0.7318 (m-30) cc_final: 0.6849 (m-30) REVERT: A 729 ASP cc_start: 0.7881 (m-30) cc_final: 0.7651 (m-30) REVERT: A 837 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.7818 (ptt-90) REVERT: A 846 ASN cc_start: 0.8567 (OUTLIER) cc_final: 0.8072 (p0) REVERT: A 923 PHE cc_start: 0.9334 (OUTLIER) cc_final: 0.9128 (t80) REVERT: B 73 VAL cc_start: 0.8008 (OUTLIER) cc_final: 0.7562 (p) REVERT: B 106 MET cc_start: 0.8734 (mmm) cc_final: 0.8502 (mmm) REVERT: B 142 ASP cc_start: 0.7796 (t0) cc_final: 0.7459 (t70) REVERT: B 219 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6764 (mtp180) REVERT: C 223 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: C 231 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6328 (t80) REVERT: C 493 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.7032 (m-70) REVERT: C 658 ARG cc_start: 0.6928 (mmt-90) cc_final: 0.6503 (mmp80) REVERT: C 680 ASP cc_start: 0.7434 (m-30) cc_final: 0.6901 (m-30) REVERT: C 846 ASN cc_start: 0.8535 (OUTLIER) cc_final: 0.8063 (p0) REVERT: C 967 PHE cc_start: 0.7487 (t80) cc_final: 0.7277 (t80) REVERT: D 106 MET cc_start: 0.8249 (mmm) cc_final: 0.7984 (mmm) REVERT: D 142 ASP cc_start: 0.7661 (t0) cc_final: 0.7429 (t70) outliers start: 237 outliers final: 33 residues processed: 600 average time/residue: 0.3858 time to fit residues: 335.5463 Evaluate side-chains 247 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 202 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 223 GLU Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain B residue 64 ASP 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 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 223 GLU Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 812 LEU 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 D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 156 TRP Chi-restraints excluded: chain D residue 160 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 80 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 239 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN A 486 ASN A 524 ASN A 557 HIS A 904 GLN B 70 GLN B 258 GLN B 284 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 474 ASN C 486 ASN C 524 ASN C 557 HIS C 904 GLN D 70 GLN D 258 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 23090 Z= 0.353 Angle : 0.703 10.174 31162 Z= 0.349 Chirality : 0.048 0.424 3520 Planarity : 0.006 0.067 3806 Dihedral : 17.115 172.938 5206 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.16 % Allowed : 13.35 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.19 (0.16), residues: 2636 helix: 0.16 (0.15), residues: 1194 sheet: -1.39 (0.30), residues: 256 loop : -1.61 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 392 HIS 0.009 0.002 HIS D 80 PHE 0.020 0.002 PHE C 923 TYR 0.025 0.002 TYR C 869 ARG 0.006 0.001 ARG C1006 *********************** 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 308 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 214 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7839 (m-80) REVERT: A 442 ILE cc_start: 0.8536 (mm) cc_final: 0.8253 (tt) REVERT: A 493 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6998 (m-70) REVERT: A 558 PHE cc_start: 0.7380 (t80) cc_final: 0.7131 (t80) REVERT: A 658 ARG cc_start: 0.7277 (mmt-90) cc_final: 0.6769 (mmp80) REVERT: A 846 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8252 (p0) REVERT: B 106 MET cc_start: 0.8991 (mmm) cc_final: 0.8668 (mmm) REVERT: B 180 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8542 (ttpt) REVERT: G 11 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8130 (ttt180) REVERT: C 100 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: C 231 PHE cc_start: 0.7049 (OUTLIER) cc_final: 0.6389 (t80) REVERT: C 267 MET cc_start: 0.8374 (tmm) cc_final: 0.7985 (ttt) REVERT: C 561 PRO cc_start: 0.5426 (Cg_endo) cc_final: 0.5073 (Cg_exo) REVERT: C 846 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8416 (p0) REVERT: C 872 ILE cc_start: 0.9125 (OUTLIER) cc_final: 0.8898 (mt) REVERT: D 142 ASP cc_start: 0.7858 (t0) cc_final: 0.7528 (t70) REVERT: D 156 TRP cc_start: 0.8801 (m-10) cc_final: 0.8591 (m-10) REVERT: D 180 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8415 (ttpt) outliers start: 94 outliers final: 48 residues processed: 291 average time/residue: 0.3392 time to fit residues: 154.4095 Evaluate side-chains 223 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 165 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 812 LEU 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 975 ASP Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 283 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain G residue 11 ARG Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 740 ASP Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 812 LEU Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 240 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 HIS A 168 GLN A 383 GLN B 243 GLN B 284 ASN ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN D 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23090 Z= 0.214 Angle : 0.563 10.366 31162 Z= 0.278 Chirality : 0.043 0.393 3520 Planarity : 0.005 0.052 3806 Dihedral : 15.605 165.402 5159 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.36 % Allowed : 14.59 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.41 (0.16), residues: 2636 helix: 0.75 (0.16), residues: 1196 sheet: -1.03 (0.31), residues: 256 loop : -1.13 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 392 HIS 0.005 0.001 HIS C 493 PHE 0.016 0.001 PHE C 538 TYR 0.014 0.001 TYR C 869 ARG 0.006 0.000 ARG A 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 254 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 178 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: A 100 PHE cc_start: 0.8135 (OUTLIER) cc_final: 0.7787 (m-80) REVERT: A 493 HIS cc_start: 0.6990 (OUTLIER) cc_final: 0.6700 (m-70) REVERT: A 561 PRO cc_start: 0.5172 (Cg_endo) cc_final: 0.4807 (Cg_exo) REVERT: A 846 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8480 (p0) REVERT: B 106 MET cc_start: 0.8962 (mmm) cc_final: 0.8607 (mmm) REVERT: B 180 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8491 (ttpt) REVERT: C 100 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7836 (m-80) REVERT: C 231 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6466 (t80) REVERT: C 267 MET cc_start: 0.8355 (tmm) cc_final: 0.7926 (ttt) REVERT: C 561 PRO cc_start: 0.5141 (Cg_endo) cc_final: 0.4780 (Cg_exo) REVERT: C 658 ARG cc_start: 0.7132 (mmt-90) cc_final: 0.6697 (mmp80) REVERT: C 846 ASN cc_start: 0.8934 (OUTLIER) cc_final: 0.8598 (p0) REVERT: D 97 LYS cc_start: 0.8148 (tppt) cc_final: 0.7899 (tppt) REVERT: D 156 TRP cc_start: 0.8831 (m-10) cc_final: 0.8588 (m-10) REVERT: D 180 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8314 (ttpt) outliers start: 76 outliers final: 40 residues processed: 238 average time/residue: 0.3303 time to fit residues: 126.6330 Evaluate side-chains 204 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 156 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 584 CYS Chi-restraints excluded: chain C residue 671 LYS 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 D residue 41 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.0670 chunk 180 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 114 optimal weight: 0.4980 chunk 161 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 904 GLN B 56 GLN B 70 GLN C 52 HIS C 654 GLN D 56 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23090 Z= 0.134 Angle : 0.510 8.572 31162 Z= 0.246 Chirality : 0.042 0.418 3520 Planarity : 0.004 0.045 3806 Dihedral : 14.362 156.704 5143 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.74 % Allowed : 16.18 % 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: 0.12 (0.16), residues: 2636 helix: 1.22 (0.16), residues: 1186 sheet: -0.83 (0.30), residues: 276 loop : -0.85 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 392 HIS 0.004 0.001 HIS A 52 PHE 0.015 0.001 PHE C 558 TYR 0.015 0.001 TYR C 488 ARG 0.003 0.000 ARG C 517 *********************** 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: 62 poor density : 172 time to evaluate : 2.622 Fit side-chains revert: symmetry clash REVERT: A 493 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6673 (m-70) REVERT: A 822 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9259 (mt) REVERT: B 106 MET cc_start: 0.8934 (mmm) cc_final: 0.8608 (mmm) REVERT: B 180 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8488 (ttpt) REVERT: C 658 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.6747 (mmp80) REVERT: D 97 LYS cc_start: 0.8171 (tppt) cc_final: 0.7760 (tppt) REVERT: D 180 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8377 (ttpt) outliers start: 62 outliers final: 35 residues processed: 217 average time/residue: 0.3231 time to fit residues: 112.4508 Evaluate side-chains 193 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 154 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 3.9990 chunk 144 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 chunk 176 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 384 ASN B 146 GLN C 118 GLN C 384 ASN C 904 GLN D 70 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 23090 Z= 0.358 Angle : 0.623 9.328 31162 Z= 0.305 Chirality : 0.046 0.420 3520 Planarity : 0.004 0.051 3806 Dihedral : 14.071 136.965 5131 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.40 % Allowed : 15.47 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.16), residues: 2636 helix: 0.96 (0.15), residues: 1202 sheet: -0.69 (0.31), residues: 266 loop : -0.79 (0.17), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 392 HIS 0.005 0.001 HIS A 290 PHE 0.025 0.002 PHE C 923 TYR 0.025 0.002 TYR D 44 ARG 0.005 0.001 ARG A 74 *********************** 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 230 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 153 time to evaluate : 2.455 Fit side-chains revert: symmetry clash REVERT: A 846 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8888 (p0) REVERT: B 106 MET cc_start: 0.8950 (mmm) cc_final: 0.8580 (mmm) REVERT: C 583 LEU cc_start: 0.6539 (mm) cc_final: 0.6321 (mm) REVERT: D 18 TRP cc_start: 0.7939 (t-100) cc_final: 0.7654 (t60) REVERT: D 97 LYS cc_start: 0.8405 (tppt) cc_final: 0.8116 (tppt) REVERT: D 180 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8605 (ttpt) outliers start: 77 outliers final: 59 residues processed: 218 average time/residue: 0.3194 time to fit residues: 114.1908 Evaluate side-chains 206 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 145 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 402 THR Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 740 ASP Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 285 ILE Chi-restraints excluded: chain D residue 305 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.7980 chunk 229 optimal weight: 0.9980 chunk 50 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 255 optimal weight: 0.9990 chunk 212 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 ASN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 23090 Z= 0.138 Angle : 0.499 8.086 31162 Z= 0.241 Chirality : 0.042 0.437 3520 Planarity : 0.004 0.039 3806 Dihedral : 13.283 129.579 5126 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.17 % Allowed : 17.20 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.32 (0.16), residues: 2636 helix: 1.33 (0.16), residues: 1188 sheet: -0.58 (0.30), residues: 292 loop : -0.70 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 392 HIS 0.005 0.001 HIS A 493 PHE 0.015 0.001 PHE C 538 TYR 0.018 0.001 TYR C 488 ARG 0.004 0.000 ARG A 517 *********************** 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 206 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 157 time to evaluate : 2.763 Fit side-chains revert: symmetry clash REVERT: A 577 ASN cc_start: 0.6158 (m-40) cc_final: 0.5074 (t0) REVERT: A 583 LEU cc_start: 0.6509 (mm) cc_final: 0.6299 (mm) REVERT: B 106 MET cc_start: 0.8941 (mmm) cc_final: 0.8546 (mmm) REVERT: D 18 TRP cc_start: 0.7912 (t-100) cc_final: 0.7632 (t60) REVERT: D 97 LYS cc_start: 0.8388 (tppt) cc_final: 0.8093 (tppt) REVERT: D 180 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8297 (ttpt) outliers start: 49 outliers final: 39 residues processed: 189 average time/residue: 0.3250 time to fit residues: 100.3512 Evaluate side-chains 184 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 684 TYR Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1004 MET Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 145 optimal weight: 20.0000 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN ** C 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 23090 Z= 0.219 Angle : 0.528 9.237 31162 Z= 0.255 Chirality : 0.043 0.450 3520 Planarity : 0.004 0.044 3806 Dihedral : 12.934 118.936 5126 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 17.55 % Favored : 79.97 % 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: 0.38 (0.16), residues: 2636 helix: 1.32 (0.16), residues: 1194 sheet: -0.44 (0.31), residues: 272 loop : -0.64 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 392 HIS 0.005 0.001 HIS A 493 PHE 0.022 0.001 PHE A 558 TYR 0.019 0.001 TYR C 488 ARG 0.002 0.000 ARG A1010 *********************** 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 210 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 154 time to evaluate : 2.806 Fit side-chains revert: symmetry clash REVERT: A 577 ASN cc_start: 0.6251 (m-40) cc_final: 0.5191 (t0) REVERT: A 583 LEU cc_start: 0.6630 (mm) cc_final: 0.6402 (mm) REVERT: B 23 LYS cc_start: 0.8293 (mttt) cc_final: 0.8050 (ptmt) REVERT: B 106 MET cc_start: 0.8957 (mmm) cc_final: 0.8502 (mmm) REVERT: C 164 MET cc_start: 0.6027 (mmm) cc_final: 0.5513 (pmm) REVERT: C 846 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8897 (p0) REVERT: D 18 TRP cc_start: 0.8188 (t-100) cc_final: 0.7677 (t60) REVERT: D 97 LYS cc_start: 0.8517 (tppt) cc_final: 0.8196 (tppt) REVERT: D 180 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8341 (ttpt) outliers start: 56 outliers final: 41 residues processed: 194 average time/residue: 0.3025 time to fit residues: 96.5422 Evaluate side-chains 191 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 148 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 64 ASP 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 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN ** C 654 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 23090 Z= 0.244 Angle : 0.534 8.789 31162 Z= 0.260 Chirality : 0.043 0.452 3520 Planarity : 0.004 0.041 3806 Dihedral : 12.630 114.934 5126 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.70 % Allowed : 17.02 % Favored : 80.28 % 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: 0.30 (0.16), residues: 2636 helix: 1.29 (0.16), residues: 1194 sheet: -0.71 (0.31), residues: 270 loop : -0.66 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 317 HIS 0.005 0.001 HIS A 493 PHE 0.021 0.002 PHE A 558 TYR 0.023 0.001 TYR A 488 ARG 0.003 0.000 ARG D 183 *********************** 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 221 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 160 time to evaluate : 2.516 Fit side-chains revert: symmetry clash REVERT: A 577 ASN cc_start: 0.6337 (m-40) cc_final: 0.5197 (t0) REVERT: B 23 LYS cc_start: 0.8397 (mttt) cc_final: 0.8048 (ptmt) REVERT: B 106 MET cc_start: 0.8949 (mmm) cc_final: 0.8525 (mmm) REVERT: C 164 MET cc_start: 0.6130 (mmm) cc_final: 0.5565 (pmm) REVERT: C 846 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8912 (p0) REVERT: D 18 TRP cc_start: 0.8408 (t-100) cc_final: 0.7889 (t60) REVERT: D 97 LYS cc_start: 0.8620 (tppt) cc_final: 0.8240 (tppt) REVERT: D 180 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8545 (ttpt) outliers start: 61 outliers final: 48 residues processed: 204 average time/residue: 0.3038 time to fit residues: 101.3967 Evaluate side-chains 199 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 149 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 64 ASP 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 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR 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: 6.9990 chunk 237 optimal weight: 0.4980 chunk 142 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 214 optimal weight: 0.8980 chunk 224 optimal weight: 0.8980 chunk 236 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 GLN C 638 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.4923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 23090 Z= 0.132 Angle : 0.490 8.882 31162 Z= 0.237 Chirality : 0.041 0.457 3520 Planarity : 0.004 0.039 3806 Dihedral : 12.045 110.987 5124 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.25 % Allowed : 17.82 % Favored : 79.93 % 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: 0.61 (0.16), residues: 2636 helix: 1.48 (0.16), residues: 1194 sheet: -0.42 (0.31), residues: 276 loop : -0.46 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 392 HIS 0.004 0.001 HIS A 493 PHE 0.041 0.001 PHE C 967 TYR 0.022 0.001 TYR A 488 ARG 0.002 0.000 ARG A1010 *********************** 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: 51 poor density : 158 time to evaluate : 2.397 Fit side-chains revert: symmetry clash REVERT: A 577 ASN cc_start: 0.6286 (m-40) cc_final: 0.5207 (t0) REVERT: B 23 LYS cc_start: 0.8380 (mttt) cc_final: 0.8069 (ptmt) REVERT: B 106 MET cc_start: 0.8909 (mmm) cc_final: 0.8460 (mmm) REVERT: C 164 MET cc_start: 0.6469 (mmm) cc_final: 0.5973 (pmm) REVERT: C 846 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8869 (p0) REVERT: D 18 TRP cc_start: 0.8419 (t-100) cc_final: 0.7905 (t60) REVERT: D 97 LYS cc_start: 0.8557 (tppt) cc_final: 0.8182 (tppt) REVERT: D 180 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8287 (ttpt) outliers start: 51 outliers final: 44 residues processed: 194 average time/residue: 0.3270 time to fit residues: 101.9892 Evaluate side-chains 198 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 197 ASP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 3.9990 chunk 153 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 242 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 23090 Z= 0.401 Angle : 0.617 8.723 31162 Z= 0.303 Chirality : 0.046 0.458 3520 Planarity : 0.004 0.049 3806 Dihedral : 12.604 116.107 5124 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.61 % Allowed : 17.55 % Favored : 79.84 % 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: 0.17 (0.16), residues: 2636 helix: 1.14 (0.15), residues: 1200 sheet: -0.78 (0.30), residues: 282 loop : -0.68 (0.17), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 317 HIS 0.007 0.001 HIS A 493 PHE 0.032 0.002 PHE C 967 TYR 0.023 0.002 TYR A 488 ARG 0.010 0.001 ARG C 423 ********************** 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 210 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 151 time to evaluate : 2.699 Fit side-chains revert: symmetry clash REVERT: A 583 LEU cc_start: 0.6712 (mm) cc_final: 0.6428 (mm) REVERT: B 23 LYS cc_start: 0.8496 (mttt) cc_final: 0.8105 (ptmt) REVERT: B 106 MET cc_start: 0.8976 (mmm) cc_final: 0.8582 (mmm) REVERT: C 164 MET cc_start: 0.6432 (mmm) cc_final: 0.5828 (pmm) REVERT: C 561 PRO cc_start: 0.5037 (Cg_endo) cc_final: 0.4820 (Cg_exo) REVERT: C 846 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8881 (p0) REVERT: D 18 TRP cc_start: 0.8631 (t-100) cc_final: 0.8006 (t60) REVERT: D 97 LYS cc_start: 0.8712 (tppt) cc_final: 0.8321 (tptt) REVERT: D 180 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8462 (ttpt) outliers start: 59 outliers final: 51 residues processed: 193 average time/residue: 0.3066 time to fit residues: 97.2419 Evaluate side-chains 202 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 149 time to evaluate : 2.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 671 LYS Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 886 LYS Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 924 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1004 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 195 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 231 PHE Chi-restraints excluded: chain C residue 248 ASN Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 552 VAL Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 591 MET Chi-restraints excluded: chain C residue 671 LYS Chi-restraints excluded: chain C residue 675 THR Chi-restraints excluded: chain C residue 758 ILE Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 197 ASP Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 266 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.116614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080701 restraints weight = 39528.606| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.31 r_work: 0.2836 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 23090 Z= 0.174 Angle : 0.512 9.113 31162 Z= 0.249 Chirality : 0.042 0.451 3520 Planarity : 0.004 0.039 3806 Dihedral : 12.141 112.754 5124 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.17 % Allowed : 18.17 % Favored : 79.66 % 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: 0.45 (0.16), residues: 2636 helix: 1.44 (0.16), residues: 1186 sheet: -0.69 (0.31), residues: 270 loop : -0.59 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 392 HIS 0.005 0.001 HIS A 493 PHE 0.033 0.001 PHE C 967 TYR 0.022 0.001 TYR A 488 ARG 0.003 0.000 ARG A1010 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4391.30 seconds wall clock time: 80 minutes 37.68 seconds (4837.68 seconds total)