Starting phenix.real_space_refine on Thu Apr 11 10:59:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/04_2024/8jfz_36220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/04_2024/8jfz_36220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/04_2024/8jfz_36220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/04_2024/8jfz_36220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/04_2024/8jfz_36220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/04_2024/8jfz_36220_updated.pdb" } resolution = 3.5 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 20 5.49 5 Mg 4 5.21 5 S 118 5.16 5 C 14458 2.51 5 N 3496 2.21 5 O 4244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 22340 Number of models: 1 Model: "" Number of chains: 22 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': 4, 'PTRANS': 11, 'TRANS': 278} Chain: "C" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7633 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 943} 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: "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': 4, 'PTRANS': 11, 'TRANS': 278} Chain: "A" Number of atoms: 7633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7633 Classifications: {'peptide': 987} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 943} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 452 Unusual residues: {' MG': 2, 'CLR': 1, 'PCW': 9} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CLR': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "A" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 508 Unusual residues: {' MG': 2, 'CLR': 3, 'PCW': 9} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'PCW:plan-2': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 82 Unusual residues: {'CLR': 1, 'PCW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 12.50, per 1000 atoms: 0.56 Number of scatterers: 22340 At special positions: 0 Unit cell: (200.136, 179.692, 100.068, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 20 15.00 Mg 4 11.99 O 4244 8.00 N 3496 7.00 C 14458 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 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 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 215 " - pdb=" SG CYS B 278 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 D 114 " " NAG H 1 " - " ASN D 159 " " NAG I 1 " - " ASN D 194 " " NAG J 1 " - " ASN D 267 " " NAG K 1 " - " ASN B 114 " " NAG L 1 " - " ASN B 159 " " NAG M 1 " - " ASN B 194 " " NAG N 1 " - " ASN B 267 " Time building additional restraints: 9.49 Conformation dependent library (CDL) restraints added in 4.0 seconds 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4888 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 18 sheets defined 43.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'D' and resid 30 through 61 removed outlier: 3.722A pdb=" N LEU D 58 " --> pdb=" O THR D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.721A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.287A 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 'C' and resid 48 through 55 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 101 through 120 removed outlier: 3.646A pdb=" N ALA C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 162 removed outlier: 3.646A pdb=" N THR C 138 " --> pdb=" O VAL C 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C 162 " --> pdb=" O MET C 158 " (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 274 removed outlier: 3.972A pdb=" N ILE C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU C 273 " --> pdb=" O ARG C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 312 Processing helix chain 'C' and resid 317 through 331 removed outlier: 3.512A pdb=" N VAL C 321 " --> pdb=" O TRP C 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 353 Processing helix chain 'C' and resid 361 through 369 removed outlier: 3.900A pdb=" N GLU C 365 " --> pdb=" O LEU C 361 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.606A pdb=" N ALA C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 467 through 473 Processing helix chain 'C' and resid 511 through 517 Processing helix chain 'C' and resid 532 through 547 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 621 through 631 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 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 695 through 708 removed outlier: 3.585A pdb=" N GLN C 708 " --> pdb=" O CYS C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 727 Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 756 through 796 removed outlier: 3.550A pdb=" N LEU C 767 " --> pdb=" O GLU C 763 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 768 " --> pdb=" O GLU C 764 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 781 " --> pdb=" O ALA C 777 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 4.690A 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 815 through 822 removed outlier: 3.630A pdb=" N ILE C 820 " --> pdb=" O MET C 816 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU C 822 " --> pdb=" O PRO C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'C' and resid 847 through 853 Processing helix chain 'C' and resid 858 through 876 Processing helix chain 'C' and resid 881 through 883 No H-bonds generated for 'chain 'C' and resid 881 through 883' Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 909 through 938 removed outlier: 3.595A pdb=" N VAL C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C 938 " --> pdb=" O LEU C 934 " (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 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 985 through 1011 removed outlier: 4.570A pdb=" N PHE C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N CYS C 990 " --> pdb=" O SER C 986 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA C 991 " --> pdb=" O TRP C 987 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 992 " --> pdb=" O TRP C 988 " (cutoff:3.500A) Proline residue: C 993 - end of helix Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'E' and resid 9 through 12 Processing helix chain 'E' and resid 16 through 39 Processing helix chain 'B' and resid 30 through 61 removed outlier: 3.721A pdb=" N LEU B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 98 No H-bonds generated for 'chain 'B' and resid 96 through 98' Processing helix chain 'B' and resid 100 through 112 removed outlier: 3.721A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.287A 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 'A' and resid 48 through 55 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 101 through 120 removed outlier: 3.646A pdb=" N ALA A 120 " --> pdb=" O GLY A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 162 removed outlier: 3.646A pdb=" N THR A 138 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS A 162 " --> pdb=" O MET A 158 " (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 274 removed outlier: 3.971A pdb=" N ILE A 270 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 312 Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.512A pdb=" N VAL A 321 " --> pdb=" O TRP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 361 through 369 removed outlier: 3.899A pdb=" N GLU A 365 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N SER A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 427 removed outlier: 3.606A pdb=" N ALA A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 511 through 517 Processing helix chain 'A' and resid 532 through 547 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 621 through 631 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 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 695 through 708 removed outlier: 3.585A pdb=" N GLN A 708 " --> pdb=" O CYS A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 756 through 796 removed outlier: 3.549A pdb=" N LEU A 767 " --> pdb=" O GLU A 763 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE A 768 " --> pdb=" O GLU A 764 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR A 781 " --> pdb=" O ALA A 777 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASN A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 4.689A 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 815 through 822 removed outlier: 3.630A pdb=" N ILE A 820 " --> pdb=" O MET A 816 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 822 " --> pdb=" O PRO A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 858 through 876 Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 909 through 938 removed outlier: 3.595A pdb=" N VAL A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS A 938 " --> pdb=" O LEU A 934 " (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 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 985 through 1011 removed outlier: 4.570A pdb=" N PHE A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS A 990 " --> pdb=" O SER A 986 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA A 991 " --> pdb=" O TRP A 987 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N PHE A 992 " --> pdb=" O TRP A 988 " (cutoff:3.500A) Proline residue: A 993 - end of helix Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'G' and resid 9 through 12 Processing helix chain 'G' and resid 16 through 39 Processing sheet with id= A, first strand: chain 'D' and resid 78 through 81 Processing sheet with id= B, first strand: chain 'D' and resid 88 through 92 removed outlier: 7.906A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU D 302 " --> pdb=" O PHE D 91 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 210 through 212 Processing sheet with id= D, first strand: chain 'C' and resid 176 through 181 removed outlier: 12.531A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 224 through 227 removed outlier: 4.344A pdb=" N CYS C 211 " --> pdb=" O ARG C 227 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ASP C 214 " --> pdb=" O CYS C 249 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS C 249 " --> pdb=" O ASP C 214 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 356 through 358 removed outlier: 6.492A pdb=" N THR C 372 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR C 715 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N CYS C 374 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LYS C 612 " --> pdb=" O ILE C 373 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER C 375 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE C 614 " --> pdb=" O SER C 375 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE C 688 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET C 615 " --> pdb=" O ILE C 688 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 396 through 399 removed outlier: 6.883A pdb=" N ALA C 590 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET C 391 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 588 " --> pdb=" O MET C 391 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE C 393 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL C 586 " --> pdb=" O PHE C 393 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 526 through 529 removed outlier: 6.968A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 202 through 205 removed outlier: 3.584A pdb=" N ASP C 202 " --> pdb=" O TYR C 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 260 " --> pdb=" O ASP C 202 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N VAL C 258 " --> pdb=" O ARG C 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 78 through 81 Processing sheet with id= K, first strand: chain 'B' and resid 88 through 92 removed outlier: 7.907A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU B 302 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 210 through 212 Processing sheet with id= M, first strand: chain 'A' and resid 176 through 181 removed outlier: 12.531A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 224 through 227 removed outlier: 4.343A pdb=" N CYS A 211 " --> pdb=" O ARG A 227 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A 214 " --> pdb=" O CYS A 249 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N CYS A 249 " --> pdb=" O ASP A 214 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'A' and resid 356 through 358 removed outlier: 6.493A pdb=" N THR A 372 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 715 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N CYS A 374 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS A 612 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N SER A 375 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ILE A 614 " --> pdb=" O SER A 375 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 688 " --> pdb=" O VAL A 613 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N MET A 615 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 396 through 399 removed outlier: 6.883A pdb=" N ALA A 590 " --> pdb=" O ALA A 389 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N MET A 391 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU A 588 " --> pdb=" O MET A 391 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE A 393 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 9.759A pdb=" N VAL A 586 " --> pdb=" O PHE A 393 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 526 through 529 removed outlier: 6.967A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 202 through 205 removed outlier: 3.584A pdb=" N ASP A 202 " --> pdb=" O TYR A 260 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 260 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 872 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.79 Time building geometry restraints manager: 10.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6670 1.34 - 1.46: 4950 1.46 - 1.58: 10925 1.58 - 1.71: 51 1.71 - 1.83: 172 Bond restraints: 22768 Sorted by residual: bond pdb=" C39 PCW A1111 " pdb=" C40 PCW A1111 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C39 PCW C1109 " pdb=" C40 PCW C1109 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C39 PCW C1106 " pdb=" C40 PCW C1106 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C39 PCW A1108 " pdb=" C40 PCW A1108 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C39 PCW C1107 " pdb=" C40 PCW C1107 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 22763 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.71: 627 105.71 - 112.80: 12106 112.80 - 119.89: 8359 119.89 - 126.97: 9450 126.97 - 134.06: 188 Bond angle restraints: 30730 Sorted by residual: angle pdb=" N LYS D 158 " pdb=" CA LYS D 158 " pdb=" C LYS D 158 " ideal model delta sigma weight residual 111.03 121.59 -10.56 1.11e+00 8.12e-01 9.05e+01 angle pdb=" N LYS B 158 " pdb=" CA LYS B 158 " pdb=" C LYS B 158 " ideal model delta sigma weight residual 111.03 121.51 -10.48 1.11e+00 8.12e-01 8.91e+01 angle pdb=" N TYR A 970 " pdb=" CA TYR A 970 " pdb=" C TYR A 970 " ideal model delta sigma weight residual 112.23 120.57 -8.34 1.26e+00 6.30e-01 4.38e+01 angle pdb=" N TYR C 970 " pdb=" CA TYR C 970 " pdb=" C TYR C 970 " ideal model delta sigma weight residual 112.23 120.57 -8.34 1.26e+00 6.30e-01 4.38e+01 angle pdb=" N THR A1021 " pdb=" CA THR A1021 " pdb=" C THR A1021 " ideal model delta sigma weight residual 112.23 120.52 -8.29 1.26e+00 6.30e-01 4.33e+01 ... (remaining 30725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.66: 13806 30.66 - 61.31: 806 61.31 - 91.97: 84 91.97 - 122.62: 46 122.62 - 153.28: 8 Dihedral angle restraints: 14750 sinusoidal: 7130 harmonic: 7620 Sorted by residual: dihedral pdb=" C33 PCW A1110 " pdb=" C31 PCW A1110 " pdb=" C32 PCW A1110 " pdb=" O2 PCW A1110 " ideal model delta sinusoidal sigma weight residual 191.83 38.55 153.28 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C33 PCW C1108 " pdb=" C31 PCW C1108 " pdb=" C32 PCW C1108 " pdb=" O2 PCW C1108 " ideal model delta sinusoidal sigma weight residual 191.83 38.57 153.26 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" N PCW G1302 " pdb=" C4 PCW G1302 " pdb=" C5 PCW G1302 " pdb=" O4P PCW G1302 " ideal model delta sinusoidal sigma weight residual 293.34 150.31 143.03 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 14747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2734 0.078 - 0.156: 601 0.156 - 0.234: 99 0.234 - 0.312: 43 0.312 - 0.389: 15 Chirality restraints: 3492 Sorted by residual: chirality pdb=" C1 FUC I 5 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 5 " pdb=" O5 FUC I 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.40e+01 chirality pdb=" C1 FUC M 5 " pdb=" O6 NAG M 1 " pdb=" C2 FUC M 5 " pdb=" O5 FUC M 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.37e+01 chirality pdb=" C1 FUC K 6 " pdb=" O6 NAG K 1 " pdb=" C2 FUC K 6 " pdb=" O5 FUC K 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.32 -0.08 2.00e-02 2.50e+03 1.54e+01 ... (remaining 3489 not shown) Planarity restraints: 3782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 282 " -0.082 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO A 283 " 0.219 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 282 " 0.082 5.00e-02 4.00e+02 1.27e-01 2.57e+01 pdb=" N PRO C 283 " -0.219 5.00e-02 4.00e+02 pdb=" CA PRO C 283 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO C 283 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR C 917 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C THR C 917 " -0.077 2.00e-02 2.50e+03 pdb=" O THR C 917 " 0.029 2.00e-02 2.50e+03 pdb=" N CYS C 918 " 0.026 2.00e-02 2.50e+03 ... (remaining 3779 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 491 2.65 - 3.22: 20888 3.22 - 3.78: 32342 3.78 - 4.34: 46002 4.34 - 4.90: 74174 Nonbonded interactions: 173897 Sorted by model distance: nonbonded pdb=" OD1 ASP A 811 " pdb="MG MG A1113 " model vdw 2.092 2.170 nonbonded pdb=" OD1 ASP C 811 " pdb="MG MG C1111 " model vdw 2.093 2.170 nonbonded pdb=" OG SER C 782 " pdb="MG MG C1111 " model vdw 2.093 2.170 nonbonded pdb=" OG SER A 782 " pdb="MG MG A1113 " model vdw 2.093 2.170 nonbonded pdb="MG MG A1114 " pdb=" O HOH A2102 " model vdw 2.247 2.170 ... (remaining 173892 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' and (resid 37 through 1023 or resid 1101 or resid 1104 through 1110)) \ selection = (chain 'C' and (resid 37 through 1023 or resid 1101 or (resid 1104 through 1105 \ and (name N or name C1 or name C11 or name C12 or name C2 or name C3 or name C31 \ or name C32 or name C4 or name C5 or name C6 or name C7 or name C8 or name O11 \ or name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4 \ P or name P )) or resid 1106 through 1110)) } 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: 0.010 Normalize map: mean=0, sd=1: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.290 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 60.850 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 0.207 22768 Z= 0.661 Angle : 1.554 12.160 30730 Z= 0.824 Chirality : 0.075 0.389 3492 Planarity : 0.013 0.127 3774 Dihedral : 18.974 153.281 9844 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.86 % Favored : 93.99 % Rotamer: Outliers : 7.50 % Allowed : 9.19 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: -1.79 (0.15), residues: 2630 helix: -0.05 (0.15), residues: 1130 sheet: -1.65 (0.25), residues: 326 loop : -2.18 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP D 156 HIS 0.010 0.003 HIS A 557 PHE 0.036 0.004 PHE C 100 TYR 0.028 0.003 TYR A 970 ARG 0.017 0.002 ARG C 893 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 444 time to evaluate : 2.617 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: D 17 LEU cc_start: 0.7965 (tp) cc_final: 0.7618 (tt) REVERT: C 168 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: C 534 MET cc_start: 0.5596 (mmp) cc_final: 0.5362 (mmm) REVERT: C 794 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8687 (mp) REVERT: C 849 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8642 (tt) REVERT: C 949 MET cc_start: 0.9004 (tpt) cc_final: 0.8751 (mmt) REVERT: B 20 SER cc_start: 0.6838 (OUTLIER) cc_final: 0.6513 (m) REVERT: B 56 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7980 (mm-40) REVERT: B 156 TRP cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (m-10) REVERT: B 207 ASN cc_start: 0.8447 (t0) cc_final: 0.8195 (t0) REVERT: A 155 SER cc_start: 0.8062 (m) cc_final: 0.7744 (p) REVERT: A 199 ILE cc_start: 0.7917 (mm) cc_final: 0.7671 (mm) REVERT: A 224 PRO cc_start: 0.6319 (Cg_exo) cc_final: 0.5995 (Cg_endo) REVERT: A 357 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8370 (tp) REVERT: A 534 MET cc_start: 0.4846 (mmp) cc_final: 0.4376 (mmm) REVERT: A 543 LEU cc_start: 0.7226 (mt) cc_final: 0.6951 (tp) REVERT: A 734 MET cc_start: 0.8825 (mmp) cc_final: 0.8596 (mmm) REVERT: A 794 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8460 (mp) REVERT: A 849 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8493 (tt) REVERT: A 1023 TYR cc_start: 0.8608 (p90) cc_final: 0.8268 (p90) outliers start: 169 outliers final: 22 residues processed: 573 average time/residue: 0.4318 time to fit residues: 355.2061 Evaluate side-chains 214 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 183 time to evaluate : 2.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 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 160 CYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 168 GLN Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain B residue 20 SER Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1006 ARG Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 8.9990 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 67 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 205 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 107 HIS D 258 GLN ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 129 ASN C 235 ASN C 248 ASN C 396 GLN C 434 GLN C 439 ASN C 483 ASN C 489 GLN ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 GLN C 577 ASN ** C 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 654 GLN C 656 ASN C 666 HIS C 708 GLN C 744 GLN C 783 ASN C 861 GLN C 904 GLN C 905 GLN C 910 GLN C 919 HIS C 930 GLN B 56 GLN B 107 HIS B 258 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 167 GLN A 215 ASN A 235 ASN A 248 ASN A 396 GLN A 405 ASN A 434 GLN A 439 ASN A 483 ASN A 539 GLN A 654 GLN A 656 ASN A 666 HIS A 783 ASN A 861 GLN A 905 GLN A 910 GLN A 919 HIS A 930 GLN A 942 ASN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22768 Z= 0.220 Angle : 0.658 9.347 30730 Z= 0.328 Chirality : 0.046 0.419 3492 Planarity : 0.007 0.072 3774 Dihedral : 16.439 147.553 4973 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.89 % Allowed : 14.21 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: -0.23 (0.16), residues: 2630 helix: 1.28 (0.15), residues: 1122 sheet: -1.11 (0.28), residues: 276 loop : -1.29 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 156 HIS 0.011 0.001 HIS A 398 PHE 0.018 0.002 PHE D 25 TYR 0.014 0.001 TYR B 206 ARG 0.007 0.001 ARG C 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 194 time to evaluate : 2.369 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: D 180 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7796 (ttpp) REVERT: C 41 MET cc_start: 0.1978 (pmm) cc_final: 0.1266 (tmm) REVERT: C 52 HIS cc_start: 0.3114 (t70) cc_final: 0.2824 (t70) REVERT: C 395 ASN cc_start: 0.5491 (t0) cc_final: 0.5210 (t0) REVERT: C 434 GLN cc_start: 0.6909 (mt0) cc_final: 0.6689 (mp10) REVERT: E 10 GLU cc_start: 0.7242 (tp30) cc_final: 0.6995 (tp30) REVERT: E 13 THR cc_start: 0.8342 (m) cc_final: 0.8100 (p) REVERT: B 156 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8359 (m-10) REVERT: B 159 ASN cc_start: 0.9014 (OUTLIER) cc_final: 0.8646 (t0) REVERT: A 55 TYR cc_start: 0.4076 (m-80) cc_final: 0.3876 (m-80) REVERT: A 164 MET cc_start: 0.7623 (mtt) cc_final: 0.7416 (ttm) REVERT: A 199 ILE cc_start: 0.8242 (mm) cc_final: 0.7974 (mm) REVERT: A 206 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6378 (pt) REVERT: A 534 MET cc_start: 0.4911 (mmp) cc_final: 0.4284 (mmm) REVERT: A 734 MET cc_start: 0.8783 (mmp) cc_final: 0.8470 (mmm) REVERT: A 911 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7445 (ptt180) outliers start: 65 outliers final: 31 residues processed: 248 average time/residue: 0.3567 time to fit residues: 138.0413 Evaluate side-chains 191 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 180 LYS Chi-restraints excluded: chain D residue 271 ASN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 123 ASP Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain A residue 897 ASP Chi-restraints excluded: chain A residue 911 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 198 optimal weight: 5.9990 chunk 162 optimal weight: 40.0000 chunk 65 optimal weight: 6.9990 chunk 238 optimal weight: 0.5980 chunk 257 optimal weight: 4.9990 chunk 212 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 557 HIS C 620 HIS C 861 GLN C 930 GLN A 861 GLN A 930 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22768 Z= 0.414 Angle : 0.698 9.085 30730 Z= 0.350 Chirality : 0.049 0.388 3492 Planarity : 0.006 0.060 3774 Dihedral : 15.373 152.753 4939 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.46 % Allowed : 14.52 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.04 (0.16), residues: 2630 helix: 1.34 (0.15), residues: 1132 sheet: -0.86 (0.27), residues: 278 loop : -1.00 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 894 HIS 0.015 0.002 HIS C 209 PHE 0.025 0.002 PHE D 25 TYR 0.028 0.002 TYR D 248 ARG 0.013 0.001 ARG A 173 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 164 time to evaluate : 2.579 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: C 41 MET cc_start: 0.2219 (pmm) cc_final: 0.1439 (tmm) REVERT: C 52 HIS cc_start: 0.3225 (t70) cc_final: 0.2950 (t70) REVERT: C 255 ARG cc_start: 0.5522 (OUTLIER) cc_final: 0.4704 (mmm-85) REVERT: C 337 LEU cc_start: 0.7308 (tm) cc_final: 0.7027 (tp) REVERT: C 346 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8741 (tp) REVERT: C 391 MET cc_start: 0.5731 (mpp) cc_final: 0.5485 (mpp) REVERT: C 395 ASN cc_start: 0.5589 (t0) cc_final: 0.5369 (t0) REVERT: C 794 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8822 (mp) REVERT: C 911 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8221 (ptt-90) REVERT: A 128 ASP cc_start: 0.6838 (OUTLIER) cc_final: 0.6443 (m-30) REVERT: A 199 ILE cc_start: 0.8510 (mm) cc_final: 0.8244 (mm) REVERT: A 395 ASN cc_start: 0.5039 (t0) cc_final: 0.4795 (t0) REVERT: A 534 MET cc_start: 0.4864 (mmp) cc_final: 0.4294 (mmm) REVERT: A 734 MET cc_start: 0.8789 (mmp) cc_final: 0.8588 (mmm) REVERT: A 780 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8936 (mp) REVERT: A 911 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.8256 (ptt-90) outliers start: 78 outliers final: 46 residues processed: 232 average time/residue: 0.3725 time to fit residues: 133.2622 Evaluate side-chains 202 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 149 time to evaluate : 2.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 196 THR Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 841 THR Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 163 ASN Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 640 THR Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 841 THR Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 0.2980 chunk 179 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 239 optimal weight: 10.0000 chunk 253 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 0.9990 chunk 68 optimal weight: 50.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN B 243 GLN B 271 ASN A 405 ASN A 483 ASN A 486 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22768 Z= 0.171 Angle : 0.548 8.801 30730 Z= 0.269 Chirality : 0.043 0.395 3492 Planarity : 0.005 0.052 3774 Dihedral : 14.224 152.715 4933 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.35 % Allowed : 15.19 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.51 (0.16), residues: 2630 helix: 1.71 (0.15), residues: 1140 sheet: -0.36 (0.29), residues: 268 loop : -0.81 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 894 HIS 0.005 0.001 HIS C 398 PHE 0.012 0.001 PHE A 433 TYR 0.013 0.001 TYR C 869 ARG 0.007 0.001 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 157 time to evaluate : 2.416 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: D 159 ASN cc_start: 0.9111 (OUTLIER) cc_final: 0.8683 (t0) REVERT: C 41 MET cc_start: 0.2444 (pmm) cc_final: 0.1676 (tmm) REVERT: C 52 HIS cc_start: 0.3223 (t70) cc_final: 0.2913 (t70) REVERT: C 255 ARG cc_start: 0.5280 (OUTLIER) cc_final: 0.4423 (mmm-85) REVERT: C 337 LEU cc_start: 0.7150 (tm) cc_final: 0.6850 (tp) REVERT: C 911 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7844 (ptt-90) REVERT: B 159 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8749 (t0) REVERT: A 395 ASN cc_start: 0.5156 (t0) cc_final: 0.4891 (t0) REVERT: A 534 MET cc_start: 0.4817 (mmp) cc_final: 0.4155 (mmm) REVERT: A 911 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7634 (ptp90) outliers start: 53 outliers final: 30 residues processed: 201 average time/residue: 0.3908 time to fit residues: 120.3217 Evaluate side-chains 181 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 911 ARG Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 10.0000 chunk 143 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 188 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 216 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 227 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 942 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22768 Z= 0.295 Angle : 0.604 8.729 30730 Z= 0.298 Chirality : 0.045 0.427 3492 Planarity : 0.005 0.051 3774 Dihedral : 13.777 157.447 4931 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.29 % Allowed : 14.65 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.48 (0.16), residues: 2630 helix: 1.55 (0.15), residues: 1140 sheet: -0.28 (0.29), residues: 268 loop : -0.71 (0.17), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 894 HIS 0.004 0.001 HIS C 685 PHE 0.016 0.002 PHE A 793 TYR 0.024 0.002 TYR D 248 ARG 0.011 0.001 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 161 time to evaluate : 2.288 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: D 159 ASN cc_start: 0.9137 (OUTLIER) cc_final: 0.8761 (t0) REVERT: D 200 GLU cc_start: 0.7933 (tp30) cc_final: 0.7657 (mm-30) REVERT: C 41 MET cc_start: 0.2474 (pmm) cc_final: 0.1343 (tmm) REVERT: C 52 HIS cc_start: 0.3446 (t70) cc_final: 0.3011 (t70) REVERT: C 90 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6607 (mt) REVERT: C 255 ARG cc_start: 0.5446 (OUTLIER) cc_final: 0.4805 (mmm-85) REVERT: C 309 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8955 (tt) REVERT: C 346 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8787 (tp) REVERT: C 535 LYS cc_start: 0.6157 (mttt) cc_final: 0.5428 (ttpp) REVERT: C 780 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8702 (mp) REVERT: C 911 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.8113 (ptt-90) REVERT: B 159 ASN cc_start: 0.9053 (OUTLIER) cc_final: 0.8810 (t0) REVERT: A 55 TYR cc_start: 0.5254 (m-80) cc_final: 0.4839 (m-80) REVERT: A 309 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.8895 (tt) REVERT: A 395 ASN cc_start: 0.5327 (t0) cc_final: 0.5081 (t0) REVERT: A 534 MET cc_start: 0.4831 (mmp) cc_final: 0.4091 (mmm) REVERT: A 780 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8753 (mp) outliers start: 74 outliers final: 46 residues processed: 227 average time/residue: 0.3615 time to fit residues: 128.0701 Evaluate side-chains 199 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 143 time to evaluate : 2.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 911 ARG Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 0.0670 chunk 228 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 148 optimal weight: 0.3980 chunk 62 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1019 GLN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.4997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22768 Z= 0.225 Angle : 0.545 8.889 30730 Z= 0.267 Chirality : 0.044 0.447 3492 Planarity : 0.004 0.051 3774 Dihedral : 13.194 159.613 4926 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.75 % Allowed : 15.81 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.67 (0.16), residues: 2630 helix: 1.65 (0.16), residues: 1148 sheet: -0.05 (0.31), residues: 258 loop : -0.59 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 894 HIS 0.019 0.001 HIS A 493 PHE 0.012 0.001 PHE D 297 TYR 0.017 0.001 TYR A 869 ARG 0.011 0.000 ARG C1006 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 154 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9130 (OUTLIER) cc_final: 0.8767 (t0) REVERT: D 200 GLU cc_start: 0.7869 (tp30) cc_final: 0.7550 (tp30) REVERT: C 41 MET cc_start: 0.2465 (pmm) cc_final: 0.1248 (tmm) REVERT: C 52 HIS cc_start: 0.3351 (t70) cc_final: 0.2932 (t70) REVERT: C 155 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7521 (p) REVERT: C 255 ARG cc_start: 0.5801 (OUTLIER) cc_final: 0.4924 (mmm-85) REVERT: C 346 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8763 (tp) REVERT: C 520 THR cc_start: 0.5349 (OUTLIER) cc_final: 0.5146 (p) REVERT: C 535 LYS cc_start: 0.6003 (mttt) cc_final: 0.5341 (ttpp) REVERT: C 589 MET cc_start: 0.5947 (mtt) cc_final: 0.5596 (mpp) REVERT: B 159 ASN cc_start: 0.9070 (OUTLIER) cc_final: 0.8810 (t0) REVERT: A 534 MET cc_start: 0.4830 (mmp) cc_final: 0.4049 (mmm) REVERT: A 615 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7227 (ttp) outliers start: 62 outliers final: 37 residues processed: 204 average time/residue: 0.3586 time to fit residues: 115.4029 Evaluate side-chains 190 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 2.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 209 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 213 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 252 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.5160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22768 Z= 0.210 Angle : 0.541 8.597 30730 Z= 0.265 Chirality : 0.043 0.454 3492 Planarity : 0.004 0.049 3774 Dihedral : 12.861 161.522 4922 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.53 % Allowed : 16.70 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.74 (0.16), residues: 2630 helix: 1.67 (0.16), residues: 1152 sheet: 0.06 (0.31), residues: 258 loop : -0.53 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 894 HIS 0.021 0.001 HIS A 209 PHE 0.012 0.001 PHE B 297 TYR 0.016 0.001 TYR A 869 ARG 0.008 0.000 ARG C1006 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 149 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8756 (t0) REVERT: D 200 GLU cc_start: 0.7857 (tp30) cc_final: 0.7486 (tp30) REVERT: C 52 HIS cc_start: 0.3426 (t70) cc_final: 0.3002 (t70) REVERT: C 155 SER cc_start: 0.8187 (OUTLIER) cc_final: 0.7499 (p) REVERT: C 255 ARG cc_start: 0.5832 (OUTLIER) cc_final: 0.5043 (mmm-85) REVERT: C 309 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9000 (tt) REVERT: C 346 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 535 LYS cc_start: 0.6126 (mttt) cc_final: 0.5437 (ttpp) REVERT: C 589 MET cc_start: 0.5962 (mtt) cc_final: 0.5296 (mpp) REVERT: B 159 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8860 (t0) REVERT: A 507 MET cc_start: 0.3689 (mmm) cc_final: 0.3368 (mmm) REVERT: A 534 MET cc_start: 0.4840 (mmp) cc_final: 0.4031 (mmm) outliers start: 57 outliers final: 40 residues processed: 196 average time/residue: 0.3526 time to fit residues: 108.5014 Evaluate side-chains 190 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 2.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 557 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22768 Z= 0.220 Angle : 0.541 9.381 30730 Z= 0.264 Chirality : 0.043 0.448 3492 Planarity : 0.004 0.049 3774 Dihedral : 12.435 164.893 4922 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.84 % Allowed : 16.12 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.77 (0.16), residues: 2630 helix: 1.74 (0.16), residues: 1148 sheet: 0.13 (0.31), residues: 258 loop : -0.57 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 156 HIS 0.007 0.001 HIS A 493 PHE 0.012 0.001 PHE B 297 TYR 0.016 0.001 TYR A 869 ARG 0.008 0.000 ARG C1006 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 157 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9133 (OUTLIER) cc_final: 0.8825 (t0) REVERT: D 200 GLU cc_start: 0.7823 (tp30) cc_final: 0.7475 (tp30) REVERT: D 270 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: C 52 HIS cc_start: 0.3426 (t70) cc_final: 0.2987 (t70) REVERT: C 155 SER cc_start: 0.8241 (OUTLIER) cc_final: 0.7559 (p) REVERT: C 255 ARG cc_start: 0.5930 (OUTLIER) cc_final: 0.5232 (mmm-85) REVERT: C 309 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9005 (tt) REVERT: C 346 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8760 (tp) REVERT: C 535 LYS cc_start: 0.6118 (mttt) cc_final: 0.5469 (ttpp) REVERT: C 589 MET cc_start: 0.5323 (mtt) cc_final: 0.4973 (mpp) REVERT: B 159 ASN cc_start: 0.9094 (OUTLIER) cc_final: 0.8871 (t0) REVERT: A 215 ASN cc_start: 0.6163 (m-40) cc_final: 0.5898 (p0) REVERT: A 309 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8930 (tt) REVERT: A 534 MET cc_start: 0.4714 (mmp) cc_final: 0.3887 (mmm) REVERT: A 615 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7201 (ttp) outliers start: 64 outliers final: 44 residues processed: 208 average time/residue: 0.3646 time to fit residues: 118.2362 Evaluate side-chains 201 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 148 time to evaluate : 2.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 7.9990 chunk 241 optimal weight: 4.9990 chunk 220 optimal weight: 20.0000 chunk 235 optimal weight: 1.9990 chunk 141 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 184 optimal weight: 0.0020 chunk 72 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 222 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 overall best weight: 2.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22768 Z= 0.217 Angle : 0.542 9.883 30730 Z= 0.264 Chirality : 0.042 0.431 3492 Planarity : 0.004 0.048 3774 Dihedral : 12.273 166.272 4922 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.66 % Allowed : 16.52 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.81 (0.16), residues: 2630 helix: 1.73 (0.16), residues: 1152 sheet: 0.20 (0.32), residues: 258 loop : -0.53 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 890 HIS 0.006 0.001 HIS A 493 PHE 0.012 0.001 PHE B 297 TYR 0.017 0.001 TYR A 869 ARG 0.013 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 152 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9127 (OUTLIER) cc_final: 0.8820 (t0) REVERT: D 200 GLU cc_start: 0.7841 (tp30) cc_final: 0.7453 (tp30) REVERT: C 52 HIS cc_start: 0.3368 (t70) cc_final: 0.2992 (t70) REVERT: C 255 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.5014 (mmm-85) REVERT: C 309 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8999 (tt) REVERT: C 535 LYS cc_start: 0.6285 (mttt) cc_final: 0.5519 (ttpp) REVERT: C 589 MET cc_start: 0.5794 (mtt) cc_final: 0.5327 (mpp) REVERT: B 159 ASN cc_start: 0.9054 (OUTLIER) cc_final: 0.8842 (t0) REVERT: A 215 ASN cc_start: 0.6323 (m-40) cc_final: 0.6000 (p0) REVERT: A 309 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.8908 (tt) REVERT: A 534 MET cc_start: 0.4720 (mmp) cc_final: 0.3816 (mmm) REVERT: A 615 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7142 (ttp) outliers start: 60 outliers final: 43 residues processed: 201 average time/residue: 0.3733 time to fit residues: 117.0436 Evaluate side-chains 196 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 147 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 311 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 203 GLN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 240 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 160 optimal weight: 0.0040 chunk 127 optimal weight: 7.9990 overall best weight: 1.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22768 Z= 0.168 Angle : 0.521 10.965 30730 Z= 0.254 Chirality : 0.042 0.417 3492 Planarity : 0.004 0.048 3774 Dihedral : 11.992 166.684 4922 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.31 % Allowed : 16.96 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.89 (0.16), residues: 2630 helix: 1.82 (0.16), residues: 1152 sheet: 0.25 (0.32), residues: 258 loop : -0.51 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 156 HIS 0.005 0.001 HIS A 493 PHE 0.018 0.001 PHE C 967 TYR 0.017 0.001 TYR A 869 ARG 0.008 0.000 ARG C1006 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5260 Ramachandran restraints generated. 2630 Oldfield, 0 Emsley, 2630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 155 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 ASN cc_start: 0.9118 (OUTLIER) cc_final: 0.8828 (t0) REVERT: D 200 GLU cc_start: 0.7816 (tp30) cc_final: 0.7427 (tp30) REVERT: D 270 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: C 52 HIS cc_start: 0.3348 (t70) cc_final: 0.2985 (t70) REVERT: C 255 ARG cc_start: 0.5911 (OUTLIER) cc_final: 0.5025 (mmm-85) REVERT: C 309 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9059 (tt) REVERT: C 535 LYS cc_start: 0.6337 (mttt) cc_final: 0.5563 (ttpp) REVERT: C 589 MET cc_start: 0.5609 (mtt) cc_final: 0.5326 (mpp) REVERT: B 159 ASN cc_start: 0.9034 (OUTLIER) cc_final: 0.8830 (t0) REVERT: A 215 ASN cc_start: 0.6330 (m-40) cc_final: 0.6033 (p0) REVERT: A 309 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8884 (tt) REVERT: A 507 MET cc_start: 0.3980 (mmm) cc_final: 0.3498 (mmm) REVERT: A 534 MET cc_start: 0.4698 (mmp) cc_final: 0.3743 (mmm) REVERT: A 615 MET cc_start: 0.7531 (OUTLIER) cc_final: 0.7079 (ttp) REVERT: A 837 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8037 (ptm160) outliers start: 52 outliers final: 39 residues processed: 195 average time/residue: 0.3749 time to fit residues: 112.3046 Evaluate side-chains 195 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 148 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 203 GLN Chi-restraints excluded: chain D residue 270 GLN Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 255 ARG Chi-restraints excluded: chain C residue 295 ILE Chi-restraints excluded: chain C residue 309 LEU Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 507 MET Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 721 ASP Chi-restraints excluded: chain C residue 768 ILE Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain C residue 808 LEU Chi-restraints excluded: chain C residue 844 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 895 ILE Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 159 ASN Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain A residue 63 LEU Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 391 MET Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 677 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 826 GLN Chi-restraints excluded: chain A residue 837 ARG Chi-restraints excluded: chain A residue 868 SER Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 940 ARG Chi-restraints excluded: chain A residue 1000 LEU Chi-restraints excluded: chain A residue 1007 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 2.9990 chunk 221 optimal weight: 0.0000 chunk 63 optimal weight: 0.0670 chunk 191 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 213 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.140145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.101838 restraints weight = 39177.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096822 restraints weight = 34071.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098365 restraints weight = 36611.604| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22768 Z= 0.171 Angle : 0.528 15.239 30730 Z= 0.255 Chirality : 0.042 0.404 3492 Planarity : 0.004 0.048 3774 Dihedral : 11.860 167.528 4922 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.26 % Allowed : 16.83 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.78 % 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: 0.91 (0.16), residues: 2630 helix: 1.81 (0.16), residues: 1154 sheet: 0.24 (0.32), residues: 256 loop : -0.47 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 156 HIS 0.005 0.001 HIS A 493 PHE 0.019 0.001 PHE A 967 TYR 0.017 0.001 TYR A 869 ARG 0.007 0.000 ARG A 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3983.76 seconds wall clock time: 74 minutes 30.14 seconds (4470.14 seconds total)