Starting phenix.real_space_refine on Sat Nov 18 08:31:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/11_2023/8jfz_36220_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/11_2023/8jfz_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_36220/11_2023/8jfz_36220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/11_2023/8jfz_36220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/11_2023/8jfz_36220_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jfz_36220/11_2023/8jfz_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-1.21rc1-5144/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 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 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 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 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 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 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 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 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: 11.11, per 1000 atoms: 0.50 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: 9.97 Conformation dependent library (CDL) restraints added in 4.8 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: 5.62 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: 7.44 Time building geometry restraints manager: 10.62 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: 12582 30.66 - 61.31: 694 61.31 - 91.97: 46 91.97 - 122.62: 22 122.62 - 153.28: 8 Dihedral angle restraints: 13352 sinusoidal: 5732 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 13349 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: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.320 Check model and map are aligned: 0.330 Set scattering table: 0.190 Process input model: 61.200 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.120 ------------------------------------------------------------------------------- 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 : 17.923 153.281 8446 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 *********************** 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 : 2.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 169 outliers final: 22 residues processed: 573 average time/residue: 0.4277 time to fit residues: 354.2458 Evaluate side-chains 202 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 180 time to evaluate : 2.400 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 2 residues processed: 22 average time/residue: 0.2858 time to fit residues: 13.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 221 optimal weight: 4.9990 chunk 198 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 67 optimal weight: 20.0000 chunk 133 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 79 optimal weight: 8.9990 chunk 124 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 744 GLN C 783 ASN C 861 GLN C 904 GLN C 905 GLN C 910 GLN C 919 HIS B 107 HIS B 243 GLN B 258 GLN A 53 ASN ** 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 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 904 GLN A 905 GLN A 910 GLN A 919 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22768 Z= 0.264 Angle : 0.679 9.313 30730 Z= 0.340 Chirality : 0.046 0.415 3492 Planarity : 0.007 0.073 3774 Dihedral : 14.692 148.274 3516 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.84 % Allowed : 13.94 % Favored : 83.21 % 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: -0.28 (0.16), residues: 2630 helix: 1.20 (0.15), residues: 1124 sheet: -1.12 (0.28), residues: 266 loop : -1.29 (0.16), residues: 1240 *********************** 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 252 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 188 time to evaluate : 2.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 30 residues processed: 239 average time/residue: 0.3646 time to fit residues: 135.6540 Evaluate side-chains 175 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 145 time to evaluate : 2.368 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 2 residues processed: 30 average time/residue: 0.2432 time to fit residues: 15.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 132 optimal weight: 7.9990 chunk 73 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 chunk 162 optimal weight: 40.0000 chunk 65 optimal weight: 7.9990 chunk 238 optimal weight: 0.9990 chunk 257 optimal weight: 0.0050 chunk 212 optimal weight: 1.9990 chunk 236 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- 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 620 HIS ** C 744 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22768 Z= 0.255 Angle : 0.607 9.156 30730 Z= 0.303 Chirality : 0.044 0.377 3492 Planarity : 0.006 0.057 3774 Dihedral : 13.238 151.462 3516 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.49 % Allowed : 14.25 % Favored : 83.26 % 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: 0.32 (0.16), residues: 2630 helix: 1.58 (0.15), residues: 1142 sheet: -0.67 (0.28), residues: 274 loop : -0.90 (0.17), residues: 1214 *********************** 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 221 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 21 residues processed: 209 average time/residue: 0.4014 time to fit residues: 125.9559 Evaluate side-chains 172 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 151 time to evaluate : 2.413 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.2857 time to fit residues: 13.0192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 235 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 123 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 239 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 chunk 68 optimal weight: 50.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 483 ASN A 486 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22768 Z= 0.258 Angle : 0.579 9.035 30730 Z= 0.286 Chirality : 0.043 0.383 3492 Planarity : 0.005 0.051 3774 Dihedral : 12.591 152.797 3516 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.82 % Allowed : 14.70 % Favored : 83.48 % 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: 0.56 (0.16), residues: 2630 helix: 1.65 (0.15), residues: 1140 sheet: -0.23 (0.28), residues: 294 loop : -0.70 (0.17), residues: 1196 *********************** 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 213 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 2.550 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 outliers start: 41 outliers final: 18 residues processed: 204 average time/residue: 0.3898 time to fit residues: 122.6035 Evaluate side-chains 169 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 2.652 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 2 residues processed: 18 average time/residue: 0.2211 time to fit residues: 10.5803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 210 optimal weight: 20.0000 chunk 143 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 104 optimal weight: 0.0980 chunk 216 optimal weight: 5.9990 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: 9.9990 overall best weight: 3.3984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 22768 Z= 0.319 Angle : 0.611 8.569 30730 Z= 0.303 Chirality : 0.044 0.375 3492 Planarity : 0.005 0.047 3774 Dihedral : 12.491 155.229 3516 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.22 % Allowed : 14.74 % Favored : 83.04 % 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: 0.47 (0.16), residues: 2630 helix: 1.50 (0.15), residues: 1138 sheet: -0.24 (0.29), residues: 294 loop : -0.68 (0.17), residues: 1198 *********************** 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 222 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 172 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 212 average time/residue: 0.3799 time to fit residues: 124.6182 Evaluate side-chains 174 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 2.333 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 2 residues processed: 24 average time/residue: 0.2619 time to fit residues: 14.1886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 85 optimal weight: 6.9990 chunk 228 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 148 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 253 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 117 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22768 Z= 0.229 Angle : 0.550 8.403 30730 Z= 0.273 Chirality : 0.042 0.375 3492 Planarity : 0.004 0.048 3774 Dihedral : 12.239 154.227 3516 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.02 % Allowed : 16.12 % Favored : 82.86 % 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: 0.62 (0.16), residues: 2630 helix: 1.58 (0.16), residues: 1152 sheet: -0.12 (0.29), residues: 294 loop : -0.58 (0.17), residues: 1184 *********************** 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 184 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 2.437 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 outliers start: 23 outliers final: 12 residues processed: 177 average time/residue: 0.3695 time to fit residues: 102.1652 Evaluate side-chains 161 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 149 time to evaluate : 2.361 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 12 average time/residue: 0.2044 time to fit residues: 7.7991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 244 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 213 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 252 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 153 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 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** C 474 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: 0.7909 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22768 Z= 0.212 Angle : 0.535 9.126 30730 Z= 0.265 Chirality : 0.042 0.373 3492 Planarity : 0.004 0.050 3774 Dihedral : 11.933 153.510 3516 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.98 % Allowed : 16.43 % Favored : 82.59 % 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: 1.72 (0.16), residues: 1142 sheet: -0.01 (0.30), residues: 294 loop : -0.56 (0.17), residues: 1194 *********************** 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 186 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 181 average time/residue: 0.3718 time to fit residues: 107.1800 Evaluate side-chains 164 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 2.504 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.1986 time to fit residues: 6.9068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 156 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 160 optimal weight: 0.0570 chunk 172 optimal weight: 0.0000 chunk 124 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.6108 ------------------------------------------------------------------------------- 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 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.5412 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= 0.185 Angle : 0.524 10.143 30730 Z= 0.257 Chirality : 0.041 0.375 3492 Planarity : 0.004 0.049 3774 Dihedral : 11.678 152.049 3516 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.40 % Allowed : 16.96 % Favored : 82.64 % 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: 0.82 (0.16), residues: 2630 helix: 1.80 (0.16), residues: 1140 sheet: 0.09 (0.30), residues: 294 loop : -0.55 (0.17), residues: 1196 *********************** 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 171 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 169 average time/residue: 0.3933 time to fit residues: 103.0832 Evaluate side-chains 161 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 155 time to evaluate : 2.295 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 6 average time/residue: 0.3170 time to fit residues: 6.6008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 229 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 212 optimal weight: 20.0000 chunk 222 optimal weight: 9.9990 chunk 234 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 215 ASN ** 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: 0.7920 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22768 Z= 0.220 Angle : 0.541 10.074 30730 Z= 0.268 Chirality : 0.042 0.372 3492 Planarity : 0.004 0.049 3774 Dihedral : 11.586 149.860 3516 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.44 % Allowed : 17.36 % Favored : 82.19 % 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: 0.80 (0.16), residues: 2630 helix: 1.75 (0.16), residues: 1140 sheet: 0.07 (0.30), residues: 294 loop : -0.52 (0.17), residues: 1196 *********************** 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 164 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 162 average time/residue: 0.3904 time to fit residues: 97.5444 Evaluate side-chains 153 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3524 time to fit residues: 5.2727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 154 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 172 optimal weight: 1.9990 chunk 261 optimal weight: 0.0770 chunk 240 optimal weight: 7.9990 chunk 207 optimal weight: 30.0000 chunk 21 optimal weight: 9.9990 chunk 160 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- 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 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 22768 Z= 0.155 Angle : 0.509 11.469 30730 Z= 0.250 Chirality : 0.040 0.373 3492 Planarity : 0.004 0.049 3774 Dihedral : 11.183 145.908 3516 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.27 % Allowed : 17.45 % Favored : 82.28 % 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: 0.95 (0.17), residues: 2630 helix: 1.90 (0.16), residues: 1140 sheet: 0.13 (0.31), residues: 290 loop : -0.46 (0.17), residues: 1200 ********************** 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 166 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 2.568 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 163 average time/residue: 0.4076 time to fit residues: 102.2418 Evaluate side-chains 144 residues out of total 2252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 143 time to evaluate : 2.414 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2653 time to fit residues: 3.7848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 262 random chunks: chunk 165 optimal weight: 6.9990 chunk 221 optimal weight: 0.0870 chunk 63 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 208 optimal weight: 20.0000 chunk 87 optimal weight: 9.9990 chunk 213 optimal weight: 30.0000 chunk 26 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- 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 248 ASN ** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.138398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.098414 restraints weight = 39390.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.093848 restraints weight = 44502.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.094540 restraints weight = 40646.381| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 22768 Z= 0.282 Angle : 0.570 10.830 30730 Z= 0.282 Chirality : 0.043 0.370 3492 Planarity : 0.004 0.049 3774 Dihedral : 11.445 145.579 3516 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.44 % Allowed : 17.67 % Favored : 81.88 % 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: 0.78 (0.16), residues: 2630 helix: 1.75 (0.16), residues: 1136 sheet: 0.00 (0.31), residues: 290 loop : -0.52 (0.17), residues: 1204 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3893.71 seconds wall clock time: 72 minutes 19.98 seconds (4339.98 seconds total)