Starting phenix.real_space_refine (version: dev) on Sun Sep 4 04:27:11 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/09_2022/7y45_33601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/09_2022/7y45_33601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/09_2022/7y45_33601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/09_2022/7y45_33601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/09_2022/7y45_33601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/09_2022/7y45_33601_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "O PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4709/modules/chem_data/mon_lib" Total number of atoms: 22638 Number of models: 1 Model: "" Number of chains: 22 Chain: "O" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7683 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain: "P" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "Q" 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: "R" Number of atoms: 7683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7683 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 43, 'TRANS': 949} Chain: "S" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "T" 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: "U" 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: 4 Unresolved non-hydrogen chiralities: 6 Chain: "V" 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: 3 Unresolved non-hydrogen chiralities: 6 Chain: "W" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "X" 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: "Y" 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: 4 Unresolved non-hydrogen chiralities: 6 Chain: "Z" 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: 3 Unresolved non-hydrogen chiralities: 6 Chain: "0" 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: 3 Unresolved non-hydrogen chiralities: 5 Chain: "1" 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: "O" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 557 Unusual residues: {' K': 3, 'CLR': 2, 'PCW': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "P" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 557 Unusual residues: {' K': 3, 'CLR': 2, 'PCW': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 96 Planarities with less than four sites: {'PCW:plan-2': 3, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 24 Chain: "S" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'PCW': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'PCW:plan-2': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" 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: 13.32, per 1000 atoms: 0.59 Number of scatterers: 22638 At special positions: 0 Unit cell: (183.996, 220.58, 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) K 6 19.00 S 118 16.00 P 26 15.00 O 4316 8.00 N 3516 7.00 C 14656 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS P 127 " - pdb=" SG CYS P 150 " distance=2.04 Simple disulfide: pdb=" SG CYS P 160 " - pdb=" SG CYS P 176 " distance=2.03 Simple disulfide: pdb=" SG CYS P 215 " - pdb=" SG CYS P 278 " distance=2.03 Simple disulfide: pdb=" SG CYS S 127 " - pdb=" SG CYS S 150 " distance=2.04 Simple disulfide: pdb=" SG CYS S 160 " - pdb=" SG CYS S 176 " distance=2.03 Simple disulfide: pdb=" SG CYS S 215 " - pdb=" SG CYS S 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 0 3 " - " MAN 0 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 6 " " BMA Y 3 " - " MAN Y 5 " " BMA Z 3 " - " MAN Z 6 " BETA1-2 " MAN V 4 " - " NAG V 5 " " MAN Z 4 " - " NAG Z 5 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " BETA1-6 " NAG 0 1 " - " FUC 0 5 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 6 " " NAG W 1 " - " FUC W 5 " " NAG Y 1 " - " FUC Y 6 " NAG-ASN " NAG 0 1 " - " ASN S 194 " " NAG 1 1 " - " ASN S 267 " " NAG U 1 " - " ASN P 114 " " NAG V 1 " - " ASN P 159 " " NAG W 1 " - " ASN P 194 " " NAG X 1 " - " ASN P 267 " " NAG Y 1 " - " ASN S 114 " " NAG Z 1 " - " ASN S 159 " Time building additional restraints: 9.88 Conformation dependent library (CDL) restraints added in 3.4 seconds 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4912 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 22 sheets defined 43.4% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.05 Creating SS restraints... Processing helix chain 'O' and resid 34 through 37 No H-bonds generated for 'chain 'O' and resid 34 through 37' Processing helix chain 'O' and resid 48 through 55 removed outlier: 3.624A pdb=" N HIS O 52 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN O 53 " --> pdb=" O ASP O 49 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS O 54 " --> pdb=" O GLU O 50 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 75 Processing helix chain 'O' and resid 88 through 95 Processing helix chain 'O' and resid 100 through 121 Processing helix chain 'O' and resid 128 through 150 removed outlier: 3.603A pdb=" N CYS O 145 " --> pdb=" O ILE O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 162 Processing helix chain 'O' and resid 182 through 184 No H-bonds generated for 'chain 'O' and resid 182 through 184' Processing helix chain 'O' and resid 216 through 219 No H-bonds generated for 'chain 'O' and resid 216 through 219' Processing helix chain 'O' and resid 262 through 264 No H-bonds generated for 'chain 'O' and resid 262 through 264' Processing helix chain 'O' and resid 266 through 276 Processing helix chain 'O' and resid 283 through 312 removed outlier: 3.567A pdb=" N PHE O 291 " --> pdb=" O GLU O 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER O 305 " --> pdb=" O PHE O 301 " (cutoff:3.500A) Processing helix chain 'O' and resid 317 through 331 removed outlier: 3.972A pdb=" N ILE O 322 " --> pdb=" O LEU O 318 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 353 Processing helix chain 'O' and resid 361 through 366 Processing helix chain 'O' and resid 416 through 427 Processing helix chain 'O' and resid 451 through 463 Processing helix chain 'O' and resid 467 through 472 Processing helix chain 'O' and resid 511 through 517 Processing helix chain 'O' and resid 532 through 547 Processing helix chain 'O' and resid 599 through 609 Processing helix chain 'O' and resid 621 through 631 removed outlier: 4.014A pdb=" N ALA O 626 " --> pdb=" O ILE O 622 " (cutoff:3.500A) Processing helix chain 'O' and resid 641 through 647 Processing helix chain 'O' and resid 657 through 659 No H-bonds generated for 'chain 'O' and resid 657 through 659' Processing helix chain 'O' and resid 667 through 671 Processing helix chain 'O' and resid 675 through 684 Processing helix chain 'O' and resid 695 through 707 removed outlier: 4.347A pdb=" N LEU O 699 " --> pdb=" O PRO O 695 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE O 700 " --> pdb=" O GLN O 696 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG O 707 " --> pdb=" O GLU O 703 " (cutoff:3.500A) Processing helix chain 'O' and resid 722 through 727 removed outlier: 3.687A pdb=" N LYS O 727 " --> pdb=" O PRO O 723 " (cutoff:3.500A) Processing helix chain 'O' and resid 740 through 745 Processing helix chain 'O' and resid 756 through 795 removed outlier: 3.751A pdb=" N PHE O 769 " --> pdb=" O GLY O 765 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN O 771 " --> pdb=" O LEU O 767 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU O 772 " --> pdb=" O ILE O 768 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER O 782 " --> pdb=" O TYR O 778 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN O 783 " --> pdb=" O THR O 779 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE O 784 " --> pdb=" O LEU O 780 " (cutoff:3.500A) Proline residue: O 785 - end of helix Proline residue: O 789 - end of helix Processing helix chain 'O' and resid 804 through 811 Processing helix chain 'O' and resid 814 through 824 Proline residue: O 818 - end of helix removed outlier: 4.312A pdb=" N ALA O 823 " --> pdb=" O ALA O 819 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR O 824 " --> pdb=" O ILE O 820 " (cutoff:3.500A) Processing helix chain 'O' and resid 847 through 853 Processing helix chain 'O' and resid 857 through 876 Processing helix chain 'O' and resid 880 through 883 No H-bonds generated for 'chain 'O' and resid 880 through 883' Processing helix chain 'O' and resid 887 through 890 No H-bonds generated for 'chain 'O' and resid 887 through 890' Processing helix chain 'O' and resid 908 through 938 removed outlier: 4.046A pdb=" N ALA O 932 " --> pdb=" O VAL O 928 " (cutoff:3.500A) Processing helix chain 'O' and resid 944 through 947 No H-bonds generated for 'chain 'O' and resid 944 through 947' Processing helix chain 'O' and resid 952 through 970 removed outlier: 3.587A pdb=" N ALA O 965 " --> pdb=" O GLU O 961 " (cutoff:3.500A) Processing helix chain 'O' and resid 974 through 977 No H-bonds generated for 'chain 'O' and resid 974 through 977' Processing helix chain 'O' and resid 987 through 989 No H-bonds generated for 'chain 'O' and resid 987 through 989' Processing helix chain 'O' and resid 992 through 1011 removed outlier: 3.557A pdb=" N PHE O1007 " --> pdb=" O GLU O1003 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE O1008 " --> pdb=" O MET O1004 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE O1009 " --> pdb=" O ARG O1005 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ARG O1010 " --> pdb=" O ARG O1006 " (cutoff:3.500A) Processing helix chain 'O' and resid 1016 through 1021 Processing helix chain 'P' and resid 15 through 17 No H-bonds generated for 'chain 'P' and resid 15 through 17' Processing helix chain 'P' and resid 30 through 60 removed outlier: 3.750A pdb=" N LEU P 58 " --> pdb=" O THR P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 98 No H-bonds generated for 'chain 'P' and resid 96 through 98' Processing helix chain 'P' and resid 100 through 112 removed outlier: 3.761A pdb=" N SER P 105 " --> pdb=" O SER P 101 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU P 112 " --> pdb=" O LYS P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 201 through 203 No H-bonds generated for 'chain 'P' and resid 201 through 203' Processing helix chain 'P' and resid 221 through 225 Processing helix chain 'P' and resid 234 through 236 No H-bonds generated for 'chain 'P' and resid 234 through 236' Processing helix chain 'P' and resid 242 through 244 No H-bonds generated for 'chain 'P' and resid 242 through 244' Processing helix chain 'P' and resid 249 through 252 No H-bonds generated for 'chain 'P' and resid 249 through 252' Processing helix chain 'Q' and resid 8 through 12 Processing helix chain 'Q' and resid 16 through 39 Processing helix chain 'R' and resid 34 through 37 No H-bonds generated for 'chain 'R' and resid 34 through 37' Processing helix chain 'R' and resid 48 through 55 removed outlier: 3.626A pdb=" N HIS R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN R 53 " --> pdb=" O ASP R 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS R 54 " --> pdb=" O GLU R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 75 Processing helix chain 'R' and resid 88 through 95 Processing helix chain 'R' and resid 100 through 121 Processing helix chain 'R' and resid 128 through 150 removed outlier: 3.602A pdb=" N CYS R 145 " --> pdb=" O ILE R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 162 Processing helix chain 'R' and resid 182 through 184 No H-bonds generated for 'chain 'R' and resid 182 through 184' Processing helix chain 'R' and resid 216 through 219 No H-bonds generated for 'chain 'R' and resid 216 through 219' Processing helix chain 'R' and resid 262 through 264 No H-bonds generated for 'chain 'R' and resid 262 through 264' Processing helix chain 'R' and resid 266 through 276 Processing helix chain 'R' and resid 283 through 312 removed outlier: 3.568A pdb=" N PHE R 291 " --> pdb=" O GLU R 287 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE R 292 " --> pdb=" O ILE R 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 331 removed outlier: 3.972A pdb=" N ILE R 322 " --> pdb=" O LEU R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 353 Processing helix chain 'R' and resid 361 through 366 Processing helix chain 'R' and resid 416 through 427 Processing helix chain 'R' and resid 451 through 463 Processing helix chain 'R' and resid 467 through 472 Processing helix chain 'R' and resid 511 through 517 Processing helix chain 'R' and resid 532 through 547 Processing helix chain 'R' and resid 599 through 609 Processing helix chain 'R' and resid 621 through 631 removed outlier: 4.012A pdb=" N ALA R 626 " --> pdb=" O ILE R 622 " (cutoff:3.500A) Processing helix chain 'R' and resid 641 through 647 Processing helix chain 'R' and resid 657 through 659 No H-bonds generated for 'chain 'R' and resid 657 through 659' Processing helix chain 'R' and resid 667 through 671 Processing helix chain 'R' and resid 675 through 684 Processing helix chain 'R' and resid 695 through 707 removed outlier: 4.346A pdb=" N LEU R 699 " --> pdb=" O PRO R 695 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE R 700 " --> pdb=" O GLN R 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG R 707 " --> pdb=" O GLU R 703 " (cutoff:3.500A) Processing helix chain 'R' and resid 722 through 727 removed outlier: 3.687A pdb=" N LYS R 727 " --> pdb=" O PRO R 723 " (cutoff:3.500A) Processing helix chain 'R' and resid 740 through 745 Processing helix chain 'R' and resid 756 through 795 removed outlier: 3.752A pdb=" N PHE R 769 " --> pdb=" O GLY R 765 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN R 771 " --> pdb=" O LEU R 767 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU R 772 " --> pdb=" O ILE R 768 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER R 782 " --> pdb=" O TYR R 778 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN R 783 " --> pdb=" O THR R 779 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE R 784 " --> pdb=" O LEU R 780 " (cutoff:3.500A) Proline residue: R 785 - end of helix Proline residue: R 789 - end of helix Processing helix chain 'R' and resid 804 through 811 Processing helix chain 'R' and resid 814 through 824 Proline residue: R 818 - end of helix removed outlier: 4.312A pdb=" N ALA R 823 " --> pdb=" O ALA R 819 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR R 824 " --> pdb=" O ILE R 820 " (cutoff:3.500A) Processing helix chain 'R' and resid 847 through 853 Processing helix chain 'R' and resid 857 through 876 Processing helix chain 'R' and resid 880 through 883 No H-bonds generated for 'chain 'R' and resid 880 through 883' Processing helix chain 'R' and resid 887 through 890 No H-bonds generated for 'chain 'R' and resid 887 through 890' Processing helix chain 'R' and resid 908 through 938 removed outlier: 4.046A pdb=" N ALA R 932 " --> pdb=" O VAL R 928 " (cutoff:3.500A) Processing helix chain 'R' and resid 944 through 947 No H-bonds generated for 'chain 'R' and resid 944 through 947' Processing helix chain 'R' and resid 952 through 970 removed outlier: 3.587A pdb=" N ALA R 965 " --> pdb=" O GLU R 961 " (cutoff:3.500A) Processing helix chain 'R' and resid 974 through 977 No H-bonds generated for 'chain 'R' and resid 974 through 977' Processing helix chain 'R' and resid 987 through 989 No H-bonds generated for 'chain 'R' and resid 987 through 989' Processing helix chain 'R' and resid 992 through 1011 removed outlier: 3.557A pdb=" N PHE R1007 " --> pdb=" O GLU R1003 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE R1008 " --> pdb=" O MET R1004 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE R1009 " --> pdb=" O ARG R1005 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARG R1010 " --> pdb=" O ARG R1006 " (cutoff:3.500A) Processing helix chain 'R' and resid 1016 through 1021 Processing helix chain 'S' and resid 15 through 17 No H-bonds generated for 'chain 'S' and resid 15 through 17' Processing helix chain 'S' and resid 30 through 60 removed outlier: 3.750A pdb=" N LEU S 58 " --> pdb=" O THR S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 98 No H-bonds generated for 'chain 'S' and resid 96 through 98' Processing helix chain 'S' and resid 100 through 112 removed outlier: 3.761A pdb=" N SER S 105 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU S 112 " --> pdb=" O LYS S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 201 through 203 No H-bonds generated for 'chain 'S' and resid 201 through 203' Processing helix chain 'S' and resid 221 through 225 Processing helix chain 'S' and resid 234 through 236 No H-bonds generated for 'chain 'S' and resid 234 through 236' Processing helix chain 'S' and resid 242 through 244 No H-bonds generated for 'chain 'S' and resid 242 through 244' Processing helix chain 'S' and resid 249 through 252 No H-bonds generated for 'chain 'S' and resid 249 through 252' Processing helix chain 'T' and resid 8 through 12 Processing helix chain 'T' and resid 16 through 39 Processing sheet with id= A, first strand: chain 'O' and resid 176 through 181 removed outlier: 12.081A pdb=" N GLN O 168 " --> pdb=" O LYS O 194 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N LYS O 194 " --> pdb=" O GLN O 168 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU O 170 " --> pdb=" O GLU O 192 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU O 190 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR O 253 " --> pdb=" O HIS O 209 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER O 207 " --> pdb=" O ARG O 255 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'O' and resid 212 through 214 Processing sheet with id= C, first strand: chain 'O' and resid 356 through 358 Processing sheet with id= D, first strand: chain 'O' and resid 612 through 616 removed outlier: 3.596A pdb=" N SER O 375 " --> pdb=" O ILE O 614 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP O 376 " --> pdb=" O THR O 715 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE O 730 " --> pdb=" O VAL O 714 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLY O 716 " --> pdb=" O ILE O 730 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL O 732 " --> pdb=" O GLY O 716 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'O' and resid 390 through 392 Processing sheet with id= F, first strand: chain 'O' and resid 526 through 529 removed outlier: 7.177A pdb=" N LEU O 583 " --> pdb=" O SER O 519 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE O 521 " --> pdb=" O LEU O 583 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE O 585 " --> pdb=" O ILE O 521 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU O 523 " --> pdb=" O PHE O 585 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N GLY O 587 " --> pdb=" O LEU O 523 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE O 555 " --> pdb=" O VAL O 586 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU O 588 " --> pdb=" O LEU O 553 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU O 553 " --> pdb=" O LEU O 588 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA O 590 " --> pdb=" O ARG O 551 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG O 551 " --> pdb=" O ALA O 590 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR O 503 " --> pdb=" O LEU O 560 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU O 494 " --> pdb=" O LYS O 476 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS O 476 " --> pdb=" O GLU O 494 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'O' and resid 662 through 666 removed outlier: 6.713A pdb=" N GLU O 687 " --> pdb=" O CYS O 663 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL O 665 " --> pdb=" O GLU O 687 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL O 689 " --> pdb=" O VAL O 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'O' and resid 202 through 205 removed outlier: 6.523A pdb=" N ARG O 204 " --> pdb=" O VAL O 258 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL O 258 " --> pdb=" O ARG O 204 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'P' and resid 78 through 80 removed outlier: 3.514A pdb=" N THR P 266 " --> pdb=" O SER P 228 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 88 through 91 removed outlier: 7.939A pdb=" N ILE P 89 " --> pdb=" O GLU P 298 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS P 300 " --> pdb=" O ILE P 89 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE P 91 " --> pdb=" O LYS P 300 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU P 302 " --> pdb=" O PHE P 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'P' and resid 210 through 212 Processing sheet with id= L, first strand: chain 'R' and resid 176 through 181 removed outlier: 12.081A pdb=" N GLN R 168 " --> pdb=" O LYS R 194 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N LYS R 194 " --> pdb=" O GLN R 168 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU R 170 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU R 190 " --> pdb=" O ILE R 172 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR R 253 " --> pdb=" O HIS R 209 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER R 207 " --> pdb=" O ARG R 255 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 212 through 214 Processing sheet with id= N, first strand: chain 'R' and resid 356 through 358 Processing sheet with id= O, first strand: chain 'R' and resid 612 through 616 removed outlier: 3.595A pdb=" N SER R 375 " --> pdb=" O ILE R 614 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP R 376 " --> pdb=" O THR R 715 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE R 730 " --> pdb=" O VAL R 714 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY R 716 " --> pdb=" O ILE R 730 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL R 732 " --> pdb=" O GLY R 716 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'R' and resid 390 through 392 Processing sheet with id= Q, first strand: chain 'R' and resid 526 through 529 removed outlier: 7.175A pdb=" N LEU R 583 " --> pdb=" O SER R 519 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE R 521 " --> pdb=" O LEU R 583 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE R 585 " --> pdb=" O ILE R 521 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU R 523 " --> pdb=" O PHE R 585 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N GLY R 587 " --> pdb=" O LEU R 523 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE R 555 " --> pdb=" O VAL R 586 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU R 588 " --> pdb=" O LEU R 553 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU R 553 " --> pdb=" O LEU R 588 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA R 590 " --> pdb=" O ARG R 551 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG R 551 " --> pdb=" O ALA R 590 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR R 503 " --> pdb=" O LEU R 560 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU R 494 " --> pdb=" O LYS R 476 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS R 476 " --> pdb=" O GLU R 494 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'R' and resid 662 through 666 removed outlier: 6.715A pdb=" N GLU R 687 " --> pdb=" O CYS R 663 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL R 665 " --> pdb=" O GLU R 687 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL R 689 " --> pdb=" O VAL R 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'R' and resid 202 through 205 removed outlier: 6.522A pdb=" N ARG R 204 " --> pdb=" O VAL R 258 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL R 258 " --> pdb=" O ARG R 204 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'S' and resid 78 through 80 removed outlier: 3.515A pdb=" N THR S 266 " --> pdb=" O SER S 228 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'S' and resid 88 through 92 removed outlier: 7.938A pdb=" N ILE S 89 " --> pdb=" O GLU S 298 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS S 300 " --> pdb=" O ILE S 89 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE S 91 " --> pdb=" O LYS S 300 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU S 302 " --> pdb=" O PHE S 91 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'S' and resid 210 through 212 817 hydrogen bonds defined for protein. 2373 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: 7.67 Time building geometry restraints manager: 10.44 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: 6804 1.34 - 1.46: 4994 1.46 - 1.58: 11012 1.58 - 1.71: 76 1.71 - 1.83: 172 Bond restraints: 23058 Sorted by residual: bond pdb=" C39 PCW Q 102 " pdb=" C40 PCW Q 102 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C39 PCW T 102 " pdb=" C40 PCW T 102 " ideal model delta sigma weight residual 1.333 1.542 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C19 PCW R1108 " pdb=" C20 PCW R1108 " ideal model delta sigma weight residual 1.333 1.540 -0.207 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C19 PCW O1108 " pdb=" C20 PCW O1108 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.07e+02 bond pdb=" C19 PCW O1111 " pdb=" C20 PCW O1111 " ideal model delta sigma weight residual 1.333 1.538 -0.205 2.00e-02 2.50e+03 1.05e+02 ... (remaining 23053 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.51: 642 105.51 - 112.65: 12088 112.65 - 119.78: 8352 119.78 - 126.92: 9788 126.92 - 134.06: 232 Bond angle restraints: 31102 Sorted by residual: angle pdb=" C PRO R 84 " pdb=" N THR R 85 " pdb=" CA THR R 85 " ideal model delta sigma weight residual 123.03 111.73 11.30 1.79e+00 3.12e-01 3.99e+01 angle pdb=" C PRO O 84 " pdb=" N THR O 85 " pdb=" CA THR O 85 " ideal model delta sigma weight residual 123.03 111.83 11.20 1.79e+00 3.12e-01 3.91e+01 angle pdb=" C SER R 310 " pdb=" N LEU R 311 " pdb=" CA LEU R 311 " ideal model delta sigma weight residual 122.06 111.39 10.67 1.86e+00 2.89e-01 3.29e+01 angle pdb=" C SER O 310 " pdb=" N LEU O 311 " pdb=" CA LEU O 311 " ideal model delta sigma weight residual 122.06 111.51 10.55 1.86e+00 2.89e-01 3.22e+01 angle pdb=" N ILE R 592 " pdb=" CA ILE R 592 " pdb=" C ILE R 592 " ideal model delta sigma weight residual 108.53 116.70 -8.17 1.45e+00 4.76e-01 3.18e+01 ... (remaining 31097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.85: 12681 27.85 - 55.71: 954 55.71 - 83.56: 131 83.56 - 111.42: 22 111.42 - 139.27: 24 Dihedral angle restraints: 13812 sinusoidal: 6156 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW R1113 " pdb=" C31 PCW R1113 " pdb=" C32 PCW R1113 " pdb=" O2 PCW R1113 " ideal model delta sinusoidal sigma weight residual 191.83 52.56 139.27 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C33 PCW O1113 " pdb=" C31 PCW O1113 " pdb=" C32 PCW O1113 " pdb=" O2 PCW O1113 " ideal model delta sinusoidal sigma weight residual 191.83 52.65 139.18 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C33 PCW O1111 " pdb=" C31 PCW O1111 " pdb=" C32 PCW O1111 " pdb=" O2 PCW O1111 " ideal model delta sinusoidal sigma weight residual -168.17 -29.88 -138.29 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 13809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2848 0.075 - 0.151: 559 0.151 - 0.226: 59 0.226 - 0.301: 31 0.301 - 0.377: 17 Chirality restraints: 3514 Sorted by residual: chirality pdb=" C1 FUC 0 5 " pdb=" O6 NAG 0 1 " pdb=" C2 FUC 0 5 " pdb=" O5 FUC 0 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 6.82e+01 chirality pdb=" C1 FUC W 5 " pdb=" O6 NAG W 1 " pdb=" C2 FUC W 5 " pdb=" O5 FUC W 5 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.79e+01 chirality pdb=" C1 FUC Y 6 " pdb=" O6 NAG Y 1 " pdb=" C2 FUC Y 6 " pdb=" O5 FUC Y 6 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.20e+01 ... (remaining 3511 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER S 122 " -0.090 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO S 123 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO S 123 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO S 123 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER P 122 " 0.090 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO P 123 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO P 123 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO P 123 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO R 594 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO R 595 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO R 595 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO R 595 " -0.055 5.00e-02 4.00e+02 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 7010 2.84 - 3.42: 22934 3.42 - 3.99: 40222 3.99 - 4.57: 55575 4.57 - 5.14: 83473 Nonbonded interactions: 209214 Sorted by model distance: nonbonded pdb=" N ASN O 127 " pdb=" OD1 ASN O 127 " model vdw 2.265 2.520 nonbonded pdb=" N ASN R 127 " pdb=" OD1 ASN R 127 " model vdw 2.266 2.520 nonbonded pdb=" O2 PCW R1112 " pdb=" O3 PCW R1112 " model vdw 2.291 2.432 nonbonded pdb=" O2 PCW O1112 " pdb=" O3 PCW O1112 " model vdw 2.292 2.432 nonbonded pdb=" O2 PCW R1111 " pdb=" O3 PCW R1111 " model vdw 2.297 2.432 ... (remaining 209209 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 '0' selection = chain 'W' } ncs_group { reference = chain '1' selection = chain 'X' } ncs_group { reference = chain 'O' selection = chain 'R' } ncs_group { reference = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'Q' selection = chain 'T' } ncs_group { reference = (chain 'U' and resid 1 through 4) selection = (chain 'V' and resid 1 through 4) selection = (chain 'Y' and resid 1 through 4) selection = (chain 'Z' and resid 1 through 4) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 6 8.98 5 P 26 5.49 5 S 118 5.16 5 C 14656 2.51 5 N 3516 2.21 5 O 4316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 4.990 Check model and map are aligned: 0.330 Convert atoms to be neutral: 0.200 Process input model: 59.620 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 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 0.209 23058 Z= 0.635 Angle : 1.447 12.479 31102 Z= 0.747 Chirality : 0.066 0.377 3514 Planarity : 0.009 0.141 3808 Dihedral : 19.083 139.272 8882 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.99 % Favored : 89.33 % Rotamer Outliers : 11.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.14), residues: 2642 helix: -2.21 (0.12), residues: 1162 sheet: -2.75 (0.29), residues: 254 loop : -2.77 (0.15), residues: 1226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 338 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 254 outliers final: 38 residues processed: 534 average time/residue: 0.3791 time to fit residues: 299.5302 Evaluate side-chains 195 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 157 time to evaluate : 2.262 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 2 residues processed: 38 average time/residue: 0.2394 time to fit residues: 19.4595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 154 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 118 GLN O 129 ASN O 209 HIS O 474 ASN ** O 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 638 ASN O 696 GLN O 708 GLN O 720 ASN O 744 GLN O 904 GLN O1019 GLN P 56 GLN P 243 GLN P 258 GLN R 118 GLN R 129 ASN R 209 HIS R 434 GLN R 474 ASN ** R 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 557 HIS R 638 ASN R 696 GLN R 744 GLN R 904 GLN R1019 GLN S 258 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 23058 Z= 0.301 Angle : 0.706 11.283 31102 Z= 0.353 Chirality : 0.046 0.297 3514 Planarity : 0.006 0.070 3808 Dihedral : 15.170 134.819 3922 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.15), residues: 2642 helix: -0.11 (0.15), residues: 1170 sheet: -2.19 (0.27), residues: 300 loop : -1.41 (0.17), residues: 1172 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 169 time to evaluate : 2.573 Fit side-chains revert: symmetry clash outliers start: 66 outliers final: 25 residues processed: 224 average time/residue: 0.3611 time to fit residues: 124.9638 Evaluate side-chains 160 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 135 time to evaluate : 2.614 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 2 residues processed: 25 average time/residue: 0.2150 time to fit residues: 13.4628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 199 optimal weight: 9.9990 chunk 163 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 213 optimal weight: 8.9990 chunk 238 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 192 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 489 GLN ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 ASN O 620 HIS R 483 ASN R 486 ASN R 489 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 23058 Z= 0.318 Angle : 0.665 9.617 31102 Z= 0.336 Chirality : 0.046 0.257 3514 Planarity : 0.005 0.058 3808 Dihedral : 14.115 124.133 3922 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2642 helix: 0.71 (0.15), residues: 1160 sheet: -1.66 (0.27), residues: 292 loop : -0.94 (0.17), residues: 1190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 148 time to evaluate : 2.419 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 21 residues processed: 188 average time/residue: 0.3405 time to fit residues: 101.7856 Evaluate side-chains 148 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 2.344 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 21 average time/residue: 0.2403 time to fit residues: 11.7875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 114 optimal weight: 0.3980 chunk 161 optimal weight: 4.9990 chunk 241 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 489 GLN ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 ASN ** O 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 146 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 577 ASN ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 23058 Z= 0.228 Angle : 0.534 7.487 31102 Z= 0.271 Chirality : 0.042 0.236 3514 Planarity : 0.004 0.057 3808 Dihedral : 13.348 123.684 3922 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 0.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2642 helix: 1.14 (0.16), residues: 1140 sheet: -1.39 (0.28), residues: 294 loop : -0.72 (0.17), residues: 1208 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 134 time to evaluate : 2.650 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 149 average time/residue: 0.3301 time to fit residues: 80.4652 Evaluate side-chains 132 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 2.590 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2211 time to fit residues: 7.3441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 3 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 0.7980 chunk 229 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 577 ASN ** O 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 489 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 683 HIS R 708 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 23058 Z= 0.276 Angle : 0.554 6.468 31102 Z= 0.281 Chirality : 0.043 0.212 3514 Planarity : 0.005 0.063 3808 Dihedral : 12.985 126.754 3922 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer Outliers : 1.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2642 helix: 1.16 (0.15), residues: 1164 sheet: -0.97 (0.28), residues: 314 loop : -0.75 (0.17), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 2.565 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 151 average time/residue: 0.3297 time to fit residues: 82.0048 Evaluate side-chains 135 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 121 time to evaluate : 2.489 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 14 average time/residue: 0.2996 time to fit residues: 10.5395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 3.9990 chunk 229 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 chunk 62 optimal weight: 0.0000 chunk 255 optimal weight: 0.9980 chunk 212 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 489 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 23058 Z= 0.184 Angle : 0.499 11.094 31102 Z= 0.254 Chirality : 0.041 0.259 3514 Planarity : 0.004 0.069 3808 Dihedral : 12.488 124.527 3922 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 2642 helix: 1.50 (0.16), residues: 1156 sheet: -0.92 (0.28), residues: 326 loop : -0.64 (0.17), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 3.141 Fit side-chains outliers start: 20 outliers final: 6 residues processed: 144 average time/residue: 0.3255 time to fit residues: 78.0540 Evaluate side-chains 121 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 2.654 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 6 average time/residue: 0.2072 time to fit residues: 5.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 186 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 215 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 254 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 557 HIS O 946 GLN ** R 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 489 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.5447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 23058 Z= 0.323 Angle : 0.571 8.980 31102 Z= 0.288 Chirality : 0.043 0.215 3514 Planarity : 0.004 0.059 3808 Dihedral : 12.744 129.270 3922 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer Outliers : 1.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.16), residues: 2642 helix: 1.31 (0.15), residues: 1168 sheet: -0.90 (0.28), residues: 324 loop : -0.66 (0.17), residues: 1150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 2.701 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 15 residues processed: 148 average time/residue: 0.3293 time to fit residues: 80.8844 Evaluate side-chains 133 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 2.483 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 2 residues processed: 15 average time/residue: 0.2451 time to fit residues: 9.7877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 200 optimal weight: 9.9990 chunk 231 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 946 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.5761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 23058 Z= 0.330 Angle : 0.575 9.770 31102 Z= 0.291 Chirality : 0.043 0.226 3514 Planarity : 0.004 0.060 3808 Dihedral : 12.979 133.969 3922 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.16), residues: 2642 helix: 1.28 (0.15), residues: 1166 sheet: -0.97 (0.27), residues: 346 loop : -0.67 (0.17), residues: 1130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 2.544 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 141 average time/residue: 0.3581 time to fit residues: 83.1552 Evaluate side-chains 130 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 2.612 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 10 outliers final: 1 residues processed: 10 average time/residue: 0.2934 time to fit residues: 8.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.9980 chunk 222 optimal weight: 8.9990 chunk 237 optimal weight: 0.0870 chunk 142 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 214 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 4.9990 chunk 155 optimal weight: 0.6980 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 271 ASN ** R 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 489 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 23058 Z= 0.151 Angle : 0.492 9.162 31102 Z= 0.250 Chirality : 0.040 0.215 3514 Planarity : 0.004 0.057 3808 Dihedral : 12.313 128.750 3922 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2642 helix: 1.64 (0.16), residues: 1168 sheet: -0.92 (0.27), residues: 348 loop : -0.48 (0.17), residues: 1126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 2.459 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 127 average time/residue: 0.3033 time to fit residues: 65.9268 Evaluate side-chains 121 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 2.404 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.2046 time to fit residues: 5.3743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 6.9990 chunk 153 optimal weight: 20.0000 chunk 118 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 242 optimal weight: 0.4980 chunk 209 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 161 optimal weight: 5.9990 chunk 128 optimal weight: 0.0870 chunk 166 optimal weight: 8.9990 overall best weight: 2.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 129 ASN ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 683 HIS ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 23058 Z= 0.229 Angle : 0.514 6.815 31102 Z= 0.260 Chirality : 0.041 0.218 3514 Planarity : 0.004 0.059 3808 Dihedral : 12.239 130.928 3922 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2642 helix: 1.67 (0.16), residues: 1164 sheet: -0.87 (0.27), residues: 350 loop : -0.50 (0.17), residues: 1128 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5284 Ramachandran restraints generated. 2642 Oldfield, 0 Emsley, 2642 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 2.604 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 125 average time/residue: 0.3090 time to fit residues: 66.1680 Evaluate side-chains 121 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 2.504 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2328 time to fit residues: 4.3000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 0.3980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.4980 chunk 209 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 489 GLN ** O 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 683 HIS O 946 GLN ** R 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 683 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.142947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097714 restraints weight = 40862.114| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.95 r_work: 0.3376 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work: 0.3337 rms_B_bonded: 2.74 restraints_weight: 0.1250 r_work: 0.3317 rms_B_bonded: 2.83 restraints_weight: 0.0625 r_work: 0.3295 rms_B_bonded: 2.98 restraints_weight: 0.0312 r_work: 0.3272 rms_B_bonded: 3.19 restraints_weight: 0.0156 r_work: 0.3245 rms_B_bonded: 3.46 restraints_weight: 0.0078 r_work: 0.3215 rms_B_bonded: 3.82 restraints_weight: 0.0039 r_work: 0.3181 rms_B_bonded: 4.26 restraints_weight: 0.0020 r_work: 0.3142 rms_B_bonded: 4.82 restraints_weight: 0.0010 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 23058 Z= 0.138 Angle : 0.469 8.215 31102 Z= 0.238 Chirality : 0.040 0.212 3514 Planarity : 0.004 0.072 3808 Dihedral : 11.647 125.306 3922 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2642 helix: 1.84 (0.16), residues: 1178 sheet: -0.69 (0.28), residues: 336 loop : -0.42 (0.17), residues: 1128 =============================================================================== Job complete usr+sys time: 3463.30 seconds wall clock time: 64 minutes 52.25 seconds (3892.25 seconds total)