Starting phenix.real_space_refine on Sun Feb 18 18:50:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyv_32895/02_2024/7wyv_32895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyv_32895/02_2024/7wyv_32895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyv_32895/02_2024/7wyv_32895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyv_32895/02_2024/7wyv_32895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyv_32895/02_2024/7wyv_32895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wyv_32895/02_2024/7wyv_32895_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 32 5.49 5 Mg 4 5.21 5 S 118 5.16 5 Na 2 4.78 5 C 14652 2.51 5 N 3524 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 538": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22668 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': 2, ' NA': 1, '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': 2, ' NA': 1, '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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 11.82, per 1000 atoms: 0.52 Number of scatterers: 22668 At special positions: 0 Unit cell: (216.276, 179.692, 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 4 11.99 Na 2 11.00 O 4336 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: 8.86 Conformation dependent library (CDL) restraints added in 3.8 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 43.5% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 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 90 through 96 removed outlier: 3.769A pdb=" N GLN A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 128 through 161 removed outlier: 4.527A 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 312 Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.663A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.947A pdb=" N ARG A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.921A 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: 3.522A 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: 3.801A 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: 4.133A 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: 4.156A 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 756 through 796 removed outlier: 3.756A pdb=" N ARG A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ASN A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Proline residue: A 785 - end of helix Proline residue: A 789 - end of helix 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: 4.288A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 removed outlier: 3.646A 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: 4.041A 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: 3.585A 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: 3.534A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.450A 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: 3.745A pdb=" N PHE B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.548A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.278A 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 90 through 96 removed outlier: 3.768A pdb=" N GLN C 95 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 121 Processing helix chain 'C' and resid 128 through 161 removed outlier: 4.526A 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 312 Processing helix chain 'C' and resid 317 through 331 removed outlier: 3.663A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.948A pdb=" N ARG C 350 " --> pdb=" O LEU C 346 " (cutoff:3.500A) removed outlier: 3.922A 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: 3.521A 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: 4.134A 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: 4.156A 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 756 through 796 removed outlier: 3.756A pdb=" N ARG C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C 784 " --> pdb=" O LEU C 780 " (cutoff:3.500A) Proline residue: C 785 - end of helix Proline residue: C 789 - end of helix 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: 4.289A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 removed outlier: 3.647A 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: 4.040A 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: 3.585A 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: 3.534A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.450A 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: 3.745A pdb=" N PHE D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.760A 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: 3.548A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.279A 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: 11.769A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.375A 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: 3.643A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.921A 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: 6.733A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS A 612 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N SER A 375 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE A 614 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.733A 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: 7.197A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N GLY A 587 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 490 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.562A 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: 6.404A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.937A 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: 7.951A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.753A 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: 11.769A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.921A 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: 6.733A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS C 612 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N SER C 375 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE C 614 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.734A 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: 7.197A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 11.319A pdb=" N GLY C 587 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C 490 " --> pdb=" O ILE C 480 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 6.563A 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: 6.404A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.936A 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 92 removed outlier: 7.951A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.752A 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 212 846 hydrogen bonds defined for protein. 2472 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: 8.21 Time building geometry restraints manager: 9.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6867 1.35 - 1.47: 5220 1.47 - 1.59: 10763 1.59 - 1.71: 68 1.71 - 1.83: 172 Bond restraints: 23090 Sorted by residual: bond pdb=" OD1 PHD C 376 " pdb=" P PHD C 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" OD1 PHD A 376 " pdb=" P PHD A 376 " ideal model delta sigma weight residual 1.816 1.508 0.308 2.00e-02 2.50e+03 2.37e+02 bond pdb=" C39 PCW A1114 " pdb=" C40 PCW A1114 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C39 PCW C1114 " pdb=" C40 PCW C1114 " ideal model delta sigma weight residual 1.333 1.541 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C19 PCW A1110 " pdb=" C20 PCW A1110 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 ... (remaining 23085 not shown) Histogram of bond angle deviations from ideal: 99.37 - 107.47: 1071 107.47 - 115.58: 14453 115.58 - 123.68: 14891 123.68 - 131.78: 709 131.78 - 139.89: 38 Bond angle restraints: 31162 Sorted by residual: angle pdb=" N PHE A 92 " pdb=" CA PHE A 92 " pdb=" C PHE A 92 " ideal model delta sigma weight residual 113.12 106.65 6.47 1.25e+00 6.40e-01 2.68e+01 angle pdb=" N PHE C 92 " pdb=" CA PHE C 92 " pdb=" C PHE C 92 " ideal model delta sigma weight residual 113.12 106.71 6.41 1.25e+00 6.40e-01 2.63e+01 angle pdb=" N LEU B 157 " pdb=" CA LEU B 157 " pdb=" C LEU B 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.46e+01 angle pdb=" N LEU D 157 " pdb=" CA LEU D 157 " pdb=" C LEU D 157 " ideal model delta sigma weight residual 108.67 100.99 7.68 1.55e+00 4.16e-01 2.45e+01 angle pdb=" C SER D 122 " pdb=" N PRO D 123 " pdb=" CA PRO D 123 " ideal model delta sigma weight residual 127.00 115.44 11.56 2.40e+00 1.74e-01 2.32e+01 ... (remaining 31157 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 14080 35.94 - 71.89: 796 71.89 - 107.83: 86 107.83 - 143.78: 40 143.78 - 179.72: 2 Dihedral angle restraints: 15004 sinusoidal: 7348 harmonic: 7656 Sorted by residual: 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 -168.17 11.55 -179.72 1 3.00e+01 1.11e-03 2.13e+01 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 -168.17 11.52 -179.69 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 -29.69 -138.48 1 3.00e+01 1.11e-03 1.87e+01 ... (remaining 15001 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2920 0.074 - 0.148: 497 0.148 - 0.222: 59 0.222 - 0.296: 24 0.296 - 0.370: 20 Chirality restraints: 3520 Sorted by residual: chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.91e+01 chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.69e+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 -2.33 -0.07 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3517 not shown) Planarity restraints: 3814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO C 283 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " -0.068 5.00e-02 4.00e+02 1.05e-01 1.75e+01 pdb=" N PRO A 283 " 0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 594 " -0.056 5.00e-02 4.00e+02 8.51e-02 1.16e+01 pdb=" N PRO A 595 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " -0.046 5.00e-02 4.00e+02 ... (remaining 3811 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 144 2.54 - 3.13: 17113 3.13 - 3.72: 32001 3.72 - 4.31: 47189 4.31 - 4.90: 77008 Nonbonded interactions: 173455 Sorted by model distance: nonbonded pdb=" OP3 PHD C 376 " pdb="MG MG C1101 " model vdw 1.954 2.170 nonbonded pdb=" OP3 PHD A 376 " pdb="MG MG A1101 " model vdw 1.954 2.170 nonbonded pdb="MG MG A1101 " pdb=" O HOH A1202 " model vdw 1.994 2.170 nonbonded pdb="MG MG C1101 " pdb=" O HOH C1202 " model vdw 2.003 2.170 nonbonded pdb=" O THR C 378 " pdb="MG MG C1101 " model vdw 2.020 2.170 ... (remaining 173450 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.370 Check model and map are aligned: 0.300 Set scattering table: 0.210 Process input model: 59.010 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.308 23090 Z= 0.599 Angle : 1.297 11.673 31162 Z= 0.614 Chirality : 0.063 0.370 3520 Planarity : 0.008 0.105 3806 Dihedral : 20.330 179.724 10074 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.97 % Favored : 91.58 % Rotamer: Outliers : 10.52 % Allowed : 8.36 % 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: -3.15 (0.14), residues: 2636 helix: -1.48 (0.13), residues: 1192 sheet: -2.36 (0.28), residues: 266 loop : -2.61 (0.16), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 894 HIS 0.009 0.001 HIS A 493 PHE 0.023 0.002 PHE D 297 TYR 0.035 0.002 TYR D 40 ARG 0.009 0.001 ARG B 137 *********************** 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 717 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 479 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4443 (tp) REVERT: A 64 THR cc_start: 0.4283 (OUTLIER) cc_final: 0.3833 (p) REVERT: A 127 ASN cc_start: 0.3716 (OUTLIER) cc_final: 0.3475 (t0) REVERT: A 180 ILE cc_start: 0.6921 (pt) cc_final: 0.6662 (tp) REVERT: A 240 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7797 (mtt180) REVERT: A 241 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7800 (p0) REVERT: A 260 TYR cc_start: 0.7321 (m-80) cc_final: 0.6735 (m-80) REVERT: A 493 HIS cc_start: 0.4723 (OUTLIER) cc_final: 0.3433 (m-70) REVERT: A 515 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7260 (pp) REVERT: A 524 ASN cc_start: 0.8008 (t0) cc_final: 0.7593 (t0) REVERT: A 753 ASP cc_start: 0.7234 (m-30) cc_final: 0.6948 (m-30) REVERT: A 837 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.7022 (ptt-90) REVERT: A 923 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.8267 (t80) REVERT: B 32 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7158 (t) REVERT: B 73 VAL cc_start: 0.7844 (OUTLIER) cc_final: 0.7464 (p) REVERT: B 94 SER cc_start: 0.6956 (OUTLIER) cc_final: 0.6538 (p) REVERT: B 284 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7449 (p0) REVERT: C 63 LEU cc_start: 0.4999 (OUTLIER) cc_final: 0.4689 (tp) REVERT: C 174 ASP cc_start: 0.7076 (t0) cc_final: 0.6305 (m-30) REVERT: C 180 ILE cc_start: 0.7228 (pt) cc_final: 0.6787 (tp) REVERT: C 240 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7807 (mtt180) REVERT: C 272 THR cc_start: 0.7851 (m) cc_final: 0.7620 (p) REVERT: C 381 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8553 (mt) REVERT: C 489 GLN cc_start: 0.7815 (tt0) cc_final: 0.7028 (tt0) REVERT: C 493 HIS cc_start: 0.4326 (OUTLIER) cc_final: 0.2965 (m-70) REVERT: C 515 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7261 (pp) REVERT: C 524 ASN cc_start: 0.7894 (t0) cc_final: 0.7437 (p0) REVERT: C 692 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6252 (tpt170) REVERT: C 837 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7248 (ptt-90) REVERT: C 923 PHE cc_start: 0.8504 (OUTLIER) cc_final: 0.8233 (t80) REVERT: D 32 SER cc_start: 0.7504 (OUTLIER) cc_final: 0.7238 (t) REVERT: D 73 VAL cc_start: 0.7808 (OUTLIER) cc_final: 0.7435 (p) REVERT: D 94 SER cc_start: 0.7062 (OUTLIER) cc_final: 0.6663 (p) REVERT: D 284 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7410 (p0) outliers start: 238 outliers final: 28 residues processed: 654 average time/residue: 0.4117 time to fit residues: 393.1444 Evaluate side-chains 272 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 219 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 240 ARG Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 484 SER Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 837 ARG 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 B residue 32 SER Chi-restraints excluded: chain B residue 37 PHE 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 160 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 287 TYR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 240 ARG Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 484 SER Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 923 PHE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 68 optimal weight: 2.9990 chunk 134 optimal weight: 10.0000 chunk 106 optimal weight: 0.0470 chunk 206 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 154 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 overall best weight: 3.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 ASN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 ASN A 683 HIS A 754 ASN A 783 ASN A 826 GLN A 904 GLN A1019 GLN B 70 GLN B 258 GLN C 225 GLN C 406 GLN C 437 GLN C 683 HIS C 754 ASN C 783 ASN C 826 GLN C 904 GLN C1019 GLN D 70 GLN D 258 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 23090 Z= 0.349 Angle : 0.770 12.563 31162 Z= 0.372 Chirality : 0.050 0.454 3520 Planarity : 0.006 0.062 3806 Dihedral : 17.058 166.065 5216 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.55 % Allowed : 14.19 % Favored : 81.26 % 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: -1.27 (0.16), residues: 2636 helix: 0.17 (0.15), residues: 1174 sheet: -1.63 (0.30), residues: 242 loop : -1.67 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 392 HIS 0.008 0.002 HIS A 620 PHE 0.028 0.002 PHE C 571 TYR 0.021 0.002 TYR D 40 ARG 0.007 0.001 ARG C 889 *********************** 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: 103 poor density : 205 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6443 (ppp) cc_final: 0.5768 (ppp) REVERT: A 63 LEU cc_start: 0.5186 (OUTLIER) cc_final: 0.4976 (tp) REVERT: A 64 THR cc_start: 0.3741 (OUTLIER) cc_final: 0.2891 (t) REVERT: A 65 ASN cc_start: 0.5371 (OUTLIER) cc_final: 0.5054 (t0) REVERT: A 127 ASN cc_start: 0.4370 (OUTLIER) cc_final: 0.3783 (t0) REVERT: A 493 HIS cc_start: 0.4802 (OUTLIER) cc_final: 0.3816 (m-70) REVERT: A 494 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: A 524 ASN cc_start: 0.8177 (t0) cc_final: 0.7556 (p0) REVERT: B 284 ASN cc_start: 0.7763 (OUTLIER) cc_final: 0.7377 (p0) REVERT: C 64 THR cc_start: 0.4045 (OUTLIER) cc_final: 0.3288 (t) REVERT: C 65 ASN cc_start: 0.5803 (OUTLIER) cc_final: 0.5102 (t0) REVERT: C 69 LYS cc_start: 0.6776 (mmtm) cc_final: 0.6498 (tptp) REVERT: C 230 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6724 (pm20) REVERT: C 493 HIS cc_start: 0.4535 (OUTLIER) cc_final: 0.3498 (m-70) REVERT: C 495 ASN cc_start: 0.5858 (t0) cc_final: 0.5632 (t0) REVERT: C 524 ASN cc_start: 0.7947 (t0) cc_final: 0.7348 (p0) REVERT: C 530 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5976 (tt) REVERT: C 692 ARG cc_start: 0.7704 (OUTLIER) cc_final: 0.7137 (tpm170) REVERT: C 816 MET cc_start: 0.8003 (mmm) cc_final: 0.7671 (mmp) REVERT: C 837 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7690 (ptt-90) REVERT: D 284 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7351 (p0) outliers start: 103 outliers final: 56 residues processed: 303 average time/residue: 0.3477 time to fit residues: 163.7311 Evaluate side-chains 228 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 157 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 127 ASN Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 986 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 47 LEU 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 160 CYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 656 ASN Chi-restraints excluded: chain C residue 692 ARG Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 826 GLN B 70 GLN B 146 GLN B 264 GLN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 331 ASN C 406 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23090 Z= 0.333 Angle : 0.654 8.776 31162 Z= 0.321 Chirality : 0.047 0.416 3520 Planarity : 0.005 0.056 3806 Dihedral : 15.950 128.424 5167 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.47 % Allowed : 15.34 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2636 helix: 0.87 (0.16), residues: 1126 sheet: -1.29 (0.31), residues: 256 loop : -1.21 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 418 HIS 0.007 0.002 HIS C 493 PHE 0.028 0.002 PHE C 231 TYR 0.014 0.002 TYR C 869 ARG 0.004 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 279 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 178 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6615 (ppp) cc_final: 0.6141 (ppp) REVERT: A 64 THR cc_start: 0.3601 (OUTLIER) cc_final: 0.2845 (t) REVERT: A 65 ASN cc_start: 0.5378 (OUTLIER) cc_final: 0.5082 (t0) REVERT: A 173 ARG cc_start: 0.5296 (OUTLIER) cc_final: 0.4980 (ptp90) REVERT: A 418 TRP cc_start: 0.7129 (t-100) cc_final: 0.6904 (t-100) REVERT: A 493 HIS cc_start: 0.4444 (OUTLIER) cc_final: 0.3363 (m-70) REVERT: A 494 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.4618 (pm20) REVERT: A 524 ASN cc_start: 0.8326 (t0) cc_final: 0.7813 (t0) REVERT: A 605 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7769 (mtpt) REVERT: A 783 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7916 (m-40) REVERT: C 38 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7561 (mt-10) REVERT: C 61 ARG cc_start: 0.7381 (tpp-160) cc_final: 0.6960 (ttm-80) REVERT: C 65 ASN cc_start: 0.5861 (OUTLIER) cc_final: 0.4861 (t0) REVERT: C 69 LYS cc_start: 0.6737 (mmtm) cc_final: 0.6409 (tmtt) REVERT: C 230 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6776 (pm20) REVERT: C 493 HIS cc_start: 0.4205 (OUTLIER) cc_final: 0.3159 (m-70) REVERT: C 495 ASN cc_start: 0.5845 (t0) cc_final: 0.5551 (t0) REVERT: C 524 ASN cc_start: 0.8150 (t0) cc_final: 0.7618 (t0) REVERT: C 605 LYS cc_start: 0.8008 (mmtp) cc_final: 0.7552 (mtmt) REVERT: C 837 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7666 (ptt-90) outliers start: 101 outliers final: 65 residues processed: 268 average time/residue: 0.3457 time to fit residues: 143.9384 Evaluate side-chains 225 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 150 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 781 THR Chi-restraints excluded: chain A residue 783 ASN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain D residue 47 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 167 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 266 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 4.9990 chunk 180 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 241 optimal weight: 7.9990 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 0.6980 chunk 68 optimal weight: 0.2980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 225 GLN A 384 ASN A 406 GLN A 434 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 384 ASN C 406 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23090 Z= 0.188 Angle : 0.546 8.204 31162 Z= 0.264 Chirality : 0.043 0.431 3520 Planarity : 0.004 0.048 3806 Dihedral : 14.706 115.753 5152 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.18 % Allowed : 16.62 % Favored : 80.19 % 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: -0.02 (0.16), residues: 2636 helix: 1.28 (0.16), residues: 1138 sheet: -0.90 (0.31), residues: 276 loop : -1.02 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 418 HIS 0.004 0.001 HIS C 493 PHE 0.030 0.001 PHE A 184 TYR 0.010 0.001 TYR D 40 ARG 0.005 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 237 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 165 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6552 (ppp) cc_final: 0.6167 (ppp) REVERT: A 64 THR cc_start: 0.3568 (OUTLIER) cc_final: 0.2886 (t) REVERT: A 65 ASN cc_start: 0.5258 (OUTLIER) cc_final: 0.4926 (t0) REVERT: A 96 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8895 (mp) REVERT: A 418 TRP cc_start: 0.7148 (t-100) cc_final: 0.6784 (t-100) REVERT: A 464 CYS cc_start: 0.7025 (t) cc_final: 0.6715 (m) REVERT: A 493 HIS cc_start: 0.4228 (OUTLIER) cc_final: 0.3433 (m-70) REVERT: A 495 ASN cc_start: 0.6266 (t0) cc_final: 0.6006 (t0) REVERT: A 524 ASN cc_start: 0.8375 (t0) cc_final: 0.7801 (t0) REVERT: A 605 LYS cc_start: 0.7925 (mmtp) cc_final: 0.7617 (mtmt) REVERT: C 61 ARG cc_start: 0.7385 (tpp-160) cc_final: 0.7172 (tpp-160) REVERT: C 64 THR cc_start: 0.3445 (OUTLIER) cc_final: 0.3155 (p) REVERT: C 65 ASN cc_start: 0.5738 (OUTLIER) cc_final: 0.4881 (t0) REVERT: C 69 LYS cc_start: 0.6797 (mmtm) cc_final: 0.6418 (tmtt) REVERT: C 96 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8902 (mp) REVERT: C 230 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: C 493 HIS cc_start: 0.3987 (OUTLIER) cc_final: 0.3290 (m-70) REVERT: C 495 ASN cc_start: 0.5859 (t0) cc_final: 0.5627 (t0) REVERT: C 524 ASN cc_start: 0.8158 (t0) cc_final: 0.7543 (t0) REVERT: C 530 LEU cc_start: 0.6204 (OUTLIER) cc_final: 0.5669 (tt) REVERT: C 534 MET cc_start: 0.6201 (mmt) cc_final: 0.5832 (mpp) REVERT: C 605 LYS cc_start: 0.7930 (mmtp) cc_final: 0.7554 (mtmt) REVERT: C 852 MET cc_start: 0.8838 (mmp) cc_final: 0.8591 (mmm) outliers start: 72 outliers final: 42 residues processed: 222 average time/residue: 0.3528 time to fit residues: 124.1044 Evaluate side-chains 202 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 150 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 415 SER Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 5.9990 chunk 144 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 229 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN C 406 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23090 Z= 0.291 Angle : 0.605 9.640 31162 Z= 0.293 Chirality : 0.046 0.479 3520 Planarity : 0.004 0.046 3806 Dihedral : 14.254 110.915 5134 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.76 % Allowed : 16.76 % Favored : 79.49 % 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: 0.03 (0.16), residues: 2636 helix: 1.22 (0.16), residues: 1134 sheet: -0.80 (0.32), residues: 276 loop : -0.90 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 156 HIS 0.005 0.001 HIS A 493 PHE 0.029 0.002 PHE A 184 TYR 0.014 0.002 TYR C 869 ARG 0.004 0.000 ARG C 240 *********************** 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 244 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 159 time to evaluate : 2.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6647 (ppp) cc_final: 0.6301 (ppp) REVERT: A 64 THR cc_start: 0.3234 (OUTLIER) cc_final: 0.2426 (t) REVERT: A 65 ASN cc_start: 0.5084 (OUTLIER) cc_final: 0.4696 (t0) REVERT: A 173 ARG cc_start: 0.5513 (OUTLIER) cc_final: 0.4930 (ptp90) REVERT: A 464 CYS cc_start: 0.7320 (t) cc_final: 0.6954 (m) REVERT: A 493 HIS cc_start: 0.4366 (OUTLIER) cc_final: 0.3505 (m-70) REVERT: A 524 ASN cc_start: 0.8362 (t0) cc_final: 0.7751 (t0) REVERT: A 530 LEU cc_start: 0.6181 (OUTLIER) cc_final: 0.5980 (tt) REVERT: A 605 LYS cc_start: 0.8114 (mmtp) cc_final: 0.7875 (mtmt) REVERT: C 61 ARG cc_start: 0.7567 (tpp-160) cc_final: 0.7240 (tpp-160) REVERT: C 65 ASN cc_start: 0.5712 (OUTLIER) cc_final: 0.4775 (t0) REVERT: C 69 LYS cc_start: 0.6725 (mmtm) cc_final: 0.6346 (tmtt) REVERT: C 230 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: C 464 CYS cc_start: 0.7107 (t) cc_final: 0.6701 (m) REVERT: C 493 HIS cc_start: 0.4206 (OUTLIER) cc_final: 0.3343 (m-70) REVERT: C 495 ASN cc_start: 0.5877 (t0) cc_final: 0.5636 (t0) REVERT: C 524 ASN cc_start: 0.8221 (t0) cc_final: 0.7540 (t0) REVERT: C 530 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5888 (tt) REVERT: C 534 MET cc_start: 0.6307 (mmt) cc_final: 0.5897 (mpp) REVERT: C 605 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7852 (mtmt) REVERT: C 837 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7764 (ptt-90) outliers start: 85 outliers final: 60 residues processed: 229 average time/residue: 0.3318 time to fit residues: 119.3068 Evaluate side-chains 221 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 151 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 641 ILE Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 961 GLU Chi-restraints excluded: chain A residue 1007 PHE Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 837 ARG Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 303 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.0670 chunk 229 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.0670 chunk 255 optimal weight: 0.2980 chunk 212 optimal weight: 7.9990 chunk 118 optimal weight: 0.2980 chunk 21 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 134 optimal weight: 20.0000 overall best weight: 0.2856 ------------------------------------------------------------------------------- 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 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN B 146 GLN C 406 GLN C 483 ASN C 577 ASN D 264 GLN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23090 Z= 0.132 Angle : 0.521 9.232 31162 Z= 0.250 Chirality : 0.042 0.454 3520 Planarity : 0.004 0.043 3806 Dihedral : 13.494 103.357 5134 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.39 % Allowed : 18.57 % Favored : 79.05 % 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: 0.39 (0.16), residues: 2636 helix: 1.58 (0.16), residues: 1142 sheet: -0.52 (0.32), residues: 276 loop : -0.81 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 156 HIS 0.003 0.001 HIS C 493 PHE 0.021 0.001 PHE A 184 TYR 0.010 0.001 TYR C 569 ARG 0.004 0.000 ARG B 154 *********************** 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 222 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 168 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6429 (ppp) cc_final: 0.6199 (ppp) REVERT: A 65 ASN cc_start: 0.5435 (OUTLIER) cc_final: 0.5032 (t0) REVERT: A 96 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8823 (mp) REVERT: A 173 ARG cc_start: 0.5254 (OUTLIER) cc_final: 0.4704 (ptp90) REVERT: A 464 CYS cc_start: 0.7291 (t) cc_final: 0.6922 (m) REVERT: A 493 HIS cc_start: 0.4212 (OUTLIER) cc_final: 0.3569 (m-70) REVERT: A 524 ASN cc_start: 0.8359 (t0) cc_final: 0.7712 (t0) REVERT: C 61 ARG cc_start: 0.7476 (tpp-160) cc_final: 0.7200 (tpp-160) REVERT: C 65 ASN cc_start: 0.5883 (OUTLIER) cc_final: 0.5032 (t0) REVERT: C 69 LYS cc_start: 0.6861 (mmtm) cc_final: 0.6418 (tmtt) REVERT: C 96 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8815 (mp) REVERT: C 172 ILE cc_start: 0.5793 (OUTLIER) cc_final: 0.5407 (tt) REVERT: C 230 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7008 (pm20) REVERT: C 464 CYS cc_start: 0.6983 (t) cc_final: 0.6635 (m) REVERT: C 493 HIS cc_start: 0.3994 (OUTLIER) cc_final: 0.3414 (m-70) REVERT: C 495 ASN cc_start: 0.5916 (t0) cc_final: 0.5702 (t0) REVERT: C 524 ASN cc_start: 0.8263 (t0) cc_final: 0.7603 (t0) REVERT: C 530 LEU cc_start: 0.6342 (OUTLIER) cc_final: 0.5749 (tt) REVERT: C 534 MET cc_start: 0.6282 (mmt) cc_final: 0.5895 (mpp) REVERT: C 605 LYS cc_start: 0.7855 (mmtp) cc_final: 0.7621 (mtmt) outliers start: 54 outliers final: 24 residues processed: 212 average time/residue: 0.3628 time to fit residues: 120.1020 Evaluate side-chains 176 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 142 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 261 THR Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.0980 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 186 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN B 146 GLN B 284 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 ASN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23090 Z= 0.163 Angle : 0.524 9.927 31162 Z= 0.250 Chirality : 0.043 0.467 3520 Planarity : 0.004 0.044 3806 Dihedral : 13.080 102.867 5125 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.30 % Allowed : 18.74 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.53 (0.16), residues: 2636 helix: 1.66 (0.16), residues: 1142 sheet: -0.34 (0.32), residues: 276 loop : -0.74 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 156 HIS 0.003 0.001 HIS A 493 PHE 0.031 0.001 PHE C 184 TYR 0.011 0.001 TYR A 869 ARG 0.005 0.000 ARG A 227 *********************** 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 203 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 151 time to evaluate : 2.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6465 (ppp) cc_final: 0.6236 (ppp) REVERT: A 64 THR cc_start: 0.3530 (OUTLIER) cc_final: 0.2790 (t) REVERT: A 65 ASN cc_start: 0.5352 (OUTLIER) cc_final: 0.4939 (t0) REVERT: A 173 ARG cc_start: 0.5428 (OUTLIER) cc_final: 0.4791 (ptp90) REVERT: A 464 CYS cc_start: 0.7263 (t) cc_final: 0.6888 (m) REVERT: A 493 HIS cc_start: 0.4238 (OUTLIER) cc_final: 0.3657 (m-70) REVERT: A 524 ASN cc_start: 0.8390 (t0) cc_final: 0.7771 (t0) REVERT: C 65 ASN cc_start: 0.5829 (OUTLIER) cc_final: 0.4930 (t0) REVERT: C 69 LYS cc_start: 0.6849 (mmtm) cc_final: 0.6358 (tmtt) REVERT: C 172 ILE cc_start: 0.5754 (OUTLIER) cc_final: 0.5423 (tp) REVERT: C 230 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: C 464 CYS cc_start: 0.7155 (t) cc_final: 0.6758 (m) REVERT: C 493 HIS cc_start: 0.4248 (OUTLIER) cc_final: 0.3595 (m-70) REVERT: C 495 ASN cc_start: 0.5931 (t0) cc_final: 0.5713 (t0) REVERT: C 524 ASN cc_start: 0.8275 (t0) cc_final: 0.7589 (t0) REVERT: C 530 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6115 (tt) REVERT: C 534 MET cc_start: 0.6350 (mmt) cc_final: 0.5874 (mpp) outliers start: 52 outliers final: 29 residues processed: 196 average time/residue: 0.3384 time to fit residues: 105.6442 Evaluate side-chains 178 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 140 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 891 ASP Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 231 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23090 Z= 0.205 Angle : 0.544 10.487 31162 Z= 0.261 Chirality : 0.043 0.474 3520 Planarity : 0.004 0.049 3806 Dihedral : 12.906 103.963 5125 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.21 % Allowed : 18.97 % Favored : 78.82 % 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: 0.56 (0.16), residues: 2636 helix: 1.71 (0.16), residues: 1136 sheet: -0.36 (0.32), residues: 276 loop : -0.73 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 317 HIS 0.003 0.001 HIS D 80 PHE 0.026 0.001 PHE C 184 TYR 0.010 0.001 TYR A 869 ARG 0.004 0.000 ARG A 517 *********************** 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 191 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 141 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.6452 (ppp) cc_final: 0.6250 (ppp) REVERT: A 64 THR cc_start: 0.3327 (OUTLIER) cc_final: 0.2494 (t) REVERT: A 65 ASN cc_start: 0.5353 (OUTLIER) cc_final: 0.4949 (t0) REVERT: A 96 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (mp) REVERT: A 173 ARG cc_start: 0.5415 (OUTLIER) cc_final: 0.4690 (ptp90) REVERT: A 464 CYS cc_start: 0.7526 (t) cc_final: 0.7120 (m) REVERT: A 493 HIS cc_start: 0.4348 (OUTLIER) cc_final: 0.3698 (m-70) REVERT: A 524 ASN cc_start: 0.8314 (t0) cc_final: 0.7777 (t0) REVERT: C 65 ASN cc_start: 0.5712 (OUTLIER) cc_final: 0.4854 (t0) REVERT: C 69 LYS cc_start: 0.6846 (mmtm) cc_final: 0.6353 (tmtt) REVERT: C 172 ILE cc_start: 0.5943 (OUTLIER) cc_final: 0.5661 (tp) REVERT: C 464 CYS cc_start: 0.7346 (t) cc_final: 0.6927 (m) REVERT: C 493 HIS cc_start: 0.4436 (OUTLIER) cc_final: 0.3842 (m-70) REVERT: C 524 ASN cc_start: 0.8271 (t0) cc_final: 0.7557 (t0) REVERT: C 530 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6139 (tt) REVERT: C 534 MET cc_start: 0.6303 (mmt) cc_final: 0.5894 (mpp) outliers start: 50 outliers final: 30 residues processed: 184 average time/residue: 0.3293 time to fit residues: 96.6967 Evaluate side-chains 176 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 137 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 MET Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 4.9990 chunk 222 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.5665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23090 Z= 0.180 Angle : 0.537 11.329 31162 Z= 0.254 Chirality : 0.043 0.470 3520 Planarity : 0.004 0.051 3806 Dihedral : 12.699 104.086 5125 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.99 % Allowed : 19.23 % Favored : 78.78 % 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: 0.65 (0.16), residues: 2636 helix: 1.76 (0.16), residues: 1136 sheet: -0.15 (0.31), residues: 300 loop : -0.70 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 156 HIS 0.003 0.001 HIS D 80 PHE 0.026 0.001 PHE C 184 TYR 0.009 0.001 TYR C 869 ARG 0.003 0.000 ARG A 350 *********************** 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 185 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 140 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.5170 (OUTLIER) cc_final: 0.4659 (t0) REVERT: A 96 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8883 (mp) REVERT: A 173 ARG cc_start: 0.5235 (OUTLIER) cc_final: 0.4503 (ptp90) REVERT: A 464 CYS cc_start: 0.7549 (t) cc_final: 0.7083 (m) REVERT: A 493 HIS cc_start: 0.4660 (OUTLIER) cc_final: 0.4139 (m-70) REVERT: C 65 ASN cc_start: 0.5498 (OUTLIER) cc_final: 0.4655 (t0) REVERT: C 69 LYS cc_start: 0.6841 (mmtm) cc_final: 0.6325 (tmtt) REVERT: C 172 ILE cc_start: 0.5840 (OUTLIER) cc_final: 0.5565 (tp) REVERT: C 464 CYS cc_start: 0.7379 (t) cc_final: 0.7003 (m) REVERT: C 494 GLU cc_start: 0.6396 (OUTLIER) cc_final: 0.6170 (mp0) REVERT: C 530 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6123 (tt) REVERT: C 534 MET cc_start: 0.6310 (mmt) cc_final: 0.5896 (mpp) outliers start: 45 outliers final: 30 residues processed: 179 average time/residue: 0.3423 time to fit residues: 97.4376 Evaluate side-chains 172 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 134 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 406 GLN Chi-restraints excluded: chain C residue 494 GLU Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 263 optimal weight: 10.0000 chunk 242 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 150 GLN A 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23090 Z= 0.270 Angle : 0.600 11.448 31162 Z= 0.288 Chirality : 0.044 0.479 3520 Planarity : 0.004 0.053 3806 Dihedral : 12.895 109.402 5123 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.86 % Allowed : 19.36 % Favored : 78.78 % 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: 0.40 (0.16), residues: 2636 helix: 1.46 (0.16), residues: 1150 sheet: -0.51 (0.32), residues: 276 loop : -0.68 (0.17), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 988 HIS 0.004 0.001 HIS C 493 PHE 0.024 0.002 PHE C 184 TYR 0.012 0.001 TYR D 40 ARG 0.004 0.000 ARG B 151 ********************** 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 179 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 2.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 ASN cc_start: 0.5307 (OUTLIER) cc_final: 0.4700 (t0) REVERT: A 96 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8896 (mp) REVERT: A 493 HIS cc_start: 0.5054 (OUTLIER) cc_final: 0.4521 (m-70) REVERT: A 832 MET cc_start: 0.8215 (mmt) cc_final: 0.7945 (mmm) REVERT: C 65 ASN cc_start: 0.5541 (OUTLIER) cc_final: 0.4799 (t0) REVERT: C 172 ILE cc_start: 0.5818 (OUTLIER) cc_final: 0.5549 (tp) REVERT: C 530 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6175 (tt) REVERT: C 534 MET cc_start: 0.6324 (mmt) cc_final: 0.5890 (mpp) outliers start: 42 outliers final: 30 residues processed: 172 average time/residue: 0.3857 time to fit residues: 104.6903 Evaluate side-chains 167 residues out of total 2262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 131 time to evaluate : 2.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 334 GLU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 831 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 172 ILE Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 334 GLU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 693 THR Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 847 GLU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 284 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 209 optimal weight: 0.3980 chunk 87 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- 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 406 GLN ** A 437 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.083180 restraints weight = 50043.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.083209 restraints weight = 33524.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.084071 restraints weight = 25203.040| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.5988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23090 Z= 0.221 Angle : 0.563 11.625 31162 Z= 0.269 Chirality : 0.043 0.469 3520 Planarity : 0.004 0.054 3806 Dihedral : 12.654 109.305 5123 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.81 % Allowed : 19.58 % Favored : 78.60 % 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: 0.50 (0.16), residues: 2636 helix: 1.55 (0.16), residues: 1146 sheet: -0.24 (0.31), residues: 298 loop : -0.69 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 156 HIS 0.003 0.001 HIS B 80 PHE 0.021 0.001 PHE C 184 TYR 0.010 0.001 TYR C 869 ARG 0.003 0.000 ARG D 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3895.06 seconds wall clock time: 72 minutes 30.72 seconds (4350.72 seconds total)