Starting phenix.real_space_refine on Sun Feb 18 18:20:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/02_2024/7y45_33601_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/02_2024/7y45_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_33601/02_2024/7y45_33601.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/02_2024/7y45_33601.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/02_2024/7y45_33601_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y45_33601/02_2024/7y45_33601_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 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. Process input model Symmetric amino acids flipped Residue "C PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 923": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22638 Number of models: 1 Model: "" Number of chains: 22 Chain: "C" 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: "D" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "E" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "A" 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: "B" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2399 Classifications: {'peptide': 294} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 278} Chain: "G" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "F" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "H" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 75 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "M" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 60 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" 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: "D" 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: "E" 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: "A" 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: "B" 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: "G" 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: "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: 11.82, per 1000 atoms: 0.52 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 D 127 " - pdb=" SG CYS D 150 " distance=2.04 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=2.04 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: 9.05 Conformation dependent library (CDL) restraints added in 3.9 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: 4.95 Creating SS restraints... Processing helix chain 'C' and resid 34 through 37 No H-bonds generated for 'chain 'C' and resid 34 through 37' Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.625A pdb=" N HIS C 52 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN C 53 " --> pdb=" O ASP C 49 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 88 through 95 Processing helix chain 'C' and resid 100 through 121 Processing helix chain 'C' and resid 128 through 150 removed outlier: 3.602A pdb=" N CYS C 145 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 162 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 216 through 219 No H-bonds generated for 'chain 'C' and resid 216 through 219' 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 276 Processing helix chain 'C' and resid 283 through 312 removed outlier: 3.567A pdb=" N PHE C 291 " --> pdb=" O GLU C 287 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER C 305 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 331 removed outlier: 3.972A pdb=" N ILE C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 353 Processing helix chain 'C' and resid 361 through 366 Processing helix chain 'C' and resid 416 through 427 Processing helix chain 'C' and resid 451 through 463 Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 511 through 517 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 removed outlier: 4.013A pdb=" N ALA C 626 " --> pdb=" O ILE C 622 " (cutoff:3.500A) Processing helix chain 'C' and resid 641 through 647 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 671 Processing helix chain 'C' and resid 675 through 684 Processing helix chain 'C' and resid 695 through 707 removed outlier: 4.346A pdb=" N LEU C 699 " --> pdb=" O PRO C 695 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE C 700 " --> pdb=" O GLN C 696 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 707 " --> pdb=" O GLU C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 722 through 727 removed outlier: 3.687A pdb=" N LYS C 727 " --> pdb=" O PRO C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 740 through 745 Processing helix chain 'C' and resid 756 through 795 removed outlier: 3.751A pdb=" N PHE C 769 " --> pdb=" O GLY C 765 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 772 " --> pdb=" O ILE C 768 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER C 782 " --> pdb=" O TYR C 778 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C 783 " --> pdb=" O THR C 779 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE C 784 " --> pdb=" O LEU C 780 " (cutoff:3.500A) Proline residue: C 785 - end of helix Proline residue: C 789 - end of helix Processing helix chain 'C' and resid 804 through 811 Processing helix chain 'C' and resid 814 through 824 Proline residue: C 818 - end of helix removed outlier: 4.312A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR C 824 " --> pdb=" O ILE C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 847 through 853 Processing helix chain 'C' and resid 857 through 876 Processing helix chain 'C' and resid 880 through 883 No H-bonds generated for 'chain 'C' and resid 880 through 883' Processing helix chain 'C' and resid 887 through 890 No H-bonds generated for 'chain 'C' and resid 887 through 890' Processing helix chain 'C' and resid 908 through 938 removed outlier: 4.045A pdb=" N ALA C 932 " --> pdb=" O VAL C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 947 No H-bonds generated for 'chain 'C' and resid 944 through 947' Processing helix chain 'C' and resid 952 through 970 removed outlier: 3.587A pdb=" N ALA C 965 " --> pdb=" O GLU C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 977 No H-bonds generated for 'chain 'C' and resid 974 through 977' Processing helix chain 'C' and resid 987 through 989 No H-bonds generated for 'chain 'C' and resid 987 through 989' Processing helix chain 'C' and resid 992 through 1011 removed outlier: 3.557A pdb=" N PHE C1007 " --> pdb=" O GLU C1003 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C1008 " --> pdb=" O MET C1004 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C1009 " --> pdb=" O ARG C1005 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ARG C1010 " --> pdb=" O ARG C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1021 Processing helix chain 'D' and resid 15 through 17 No H-bonds generated for 'chain 'D' and resid 15 through 17' Processing helix chain 'D' and resid 30 through 60 removed outlier: 3.749A 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: 3.761A pdb=" N SER D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 203 No H-bonds generated for 'chain 'D' and resid 201 through 203' Processing helix chain 'D' and resid 221 through 225 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 249 through 252 No H-bonds generated for 'chain 'D' and resid 249 through 252' Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 16 through 39 Processing helix chain 'A' and resid 34 through 37 No H-bonds generated for 'chain 'A' and resid 34 through 37' Processing helix chain 'A' and resid 48 through 55 removed outlier: 3.625A pdb=" N HIS A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 53 " --> pdb=" O ASP A 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 100 through 121 Processing helix chain 'A' and resid 128 through 150 removed outlier: 3.602A pdb=" N CYS A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 162 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 216 through 219 No H-bonds generated for 'chain 'A' and resid 216 through 219' 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 276 Processing helix chain 'A' and resid 283 through 312 removed outlier: 3.567A pdb=" N PHE A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 305 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.972A pdb=" N ILE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 353 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 427 Processing helix chain 'A' and resid 451 through 463 Processing helix chain 'A' and resid 467 through 472 Processing helix chain 'A' and resid 511 through 517 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 removed outlier: 4.013A pdb=" N ALA A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 647 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 671 Processing helix chain 'A' and resid 675 through 684 Processing helix chain 'A' and resid 695 through 707 removed outlier: 4.346A pdb=" N LEU A 699 " --> pdb=" O PRO A 695 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE A 700 " --> pdb=" O GLN A 696 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 707 " --> pdb=" O GLU A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 722 through 727 removed outlier: 3.687A pdb=" N LYS A 727 " --> pdb=" O PRO A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 745 Processing helix chain 'A' and resid 756 through 795 removed outlier: 3.751A pdb=" N PHE A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 772 " --> pdb=" O ILE A 768 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 782 " --> pdb=" O TYR A 778 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE A 784 " --> pdb=" O LEU A 780 " (cutoff:3.500A) Proline residue: A 785 - end of helix Proline residue: A 789 - end of helix Processing helix chain 'A' and resid 804 through 811 Processing helix chain 'A' and resid 814 through 824 Proline residue: A 818 - end of helix removed outlier: 4.312A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N TYR A 824 " --> pdb=" O ILE A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 853 Processing helix chain 'A' and resid 857 through 876 Processing helix chain 'A' and resid 880 through 883 No H-bonds generated for 'chain 'A' and resid 880 through 883' Processing helix chain 'A' and resid 887 through 890 No H-bonds generated for 'chain 'A' and resid 887 through 890' Processing helix chain 'A' and resid 908 through 938 removed outlier: 4.046A pdb=" N ALA A 932 " --> pdb=" O VAL A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 947 No H-bonds generated for 'chain 'A' and resid 944 through 947' Processing helix chain 'A' and resid 952 through 970 removed outlier: 3.587A pdb=" N ALA A 965 " --> pdb=" O GLU A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 977 No H-bonds generated for 'chain 'A' and resid 974 through 977' Processing helix chain 'A' and resid 987 through 989 No H-bonds generated for 'chain 'A' and resid 987 through 989' Processing helix chain 'A' and resid 992 through 1011 removed outlier: 3.557A pdb=" N PHE A1007 " --> pdb=" O GLU A1003 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A1008 " --> pdb=" O MET A1004 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A1009 " --> pdb=" O ARG A1005 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG A1010 " --> pdb=" O ARG A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1021 Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 30 through 60 removed outlier: 3.750A 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: 3.761A pdb=" N SER B 105 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU B 112 " --> pdb=" O LYS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 203 No H-bonds generated for 'chain 'B' and resid 201 through 203' Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 249 through 252 No H-bonds generated for 'chain 'B' and resid 249 through 252' Processing helix chain 'G' and resid 8 through 12 Processing helix chain 'G' and resid 16 through 39 Processing sheet with id= A, first strand: chain 'C' and resid 176 through 181 removed outlier: 12.081A pdb=" N GLN C 168 " --> pdb=" O LYS C 194 " (cutoff:3.500A) removed outlier: 9.425A pdb=" N LYS C 194 " --> pdb=" O GLN C 168 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU C 170 " --> pdb=" O GLU C 192 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU C 190 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 253 " --> pdb=" O HIS C 209 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER C 207 " --> pdb=" O ARG C 255 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 212 through 214 Processing sheet with id= C, first strand: chain 'C' and resid 356 through 358 Processing sheet with id= D, first strand: chain 'C' and resid 612 through 616 removed outlier: 3.596A pdb=" N SER C 375 " --> pdb=" O ILE C 614 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP C 376 " --> pdb=" O THR C 715 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE C 730 " --> pdb=" O VAL C 714 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N GLY C 716 " --> pdb=" O ILE C 730 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL C 732 " --> pdb=" O GLY C 716 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 390 through 392 Processing sheet with id= F, first strand: chain 'C' and resid 526 through 529 removed outlier: 7.177A pdb=" N LEU C 583 " --> pdb=" O SER C 519 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE C 521 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE C 585 " --> pdb=" O ILE C 521 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU C 523 " --> pdb=" O PHE C 585 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N GLY C 587 " --> pdb=" O LEU C 523 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N PHE C 555 " --> pdb=" O VAL C 586 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU C 588 " --> pdb=" O LEU C 553 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N LEU C 553 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA C 590 " --> pdb=" O ARG C 551 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG C 551 " --> pdb=" O ALA C 590 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR C 503 " --> pdb=" O LEU C 560 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU C 494 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS C 476 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 662 through 666 removed outlier: 6.714A pdb=" N GLU C 687 " --> pdb=" O CYS C 663 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL C 665 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL C 689 " --> pdb=" O VAL C 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 202 through 205 removed outlier: 6.523A pdb=" N ARG C 204 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL C 258 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 78 through 80 removed outlier: 3.514A pdb=" N THR D 266 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 88 through 92 removed outlier: 7.939A pdb=" N ILE D 89 " --> pdb=" O GLU D 298 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS D 300 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N PHE D 91 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLU D 302 " --> pdb=" O PHE D 91 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 210 through 212 Processing sheet with id= L, first strand: chain 'A' and resid 176 through 181 removed outlier: 12.081A pdb=" N GLN A 168 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N LYS A 194 " --> pdb=" O GLN A 168 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 170 " --> pdb=" O GLU A 192 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 190 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR A 253 " --> pdb=" O HIS A 209 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 207 " --> pdb=" O ARG A 255 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 212 through 214 Processing sheet with id= N, first strand: chain 'A' and resid 356 through 358 Processing sheet with id= O, first strand: chain 'A' and resid 612 through 616 removed outlier: 3.595A pdb=" N SER A 375 " --> pdb=" O ILE A 614 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP A 376 " --> pdb=" O THR A 715 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 730 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLY A 716 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL A 732 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 390 through 392 Processing sheet with id= Q, first strand: chain 'A' and resid 526 through 529 removed outlier: 7.176A pdb=" N LEU A 583 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE A 521 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N PHE A 585 " --> pdb=" O ILE A 521 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU A 523 " --> pdb=" O PHE A 585 " (cutoff:3.500A) removed outlier: 11.226A pdb=" N GLY A 587 " --> pdb=" O LEU A 523 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N PHE A 555 " --> pdb=" O VAL A 586 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU A 588 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU A 553 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA A 590 " --> pdb=" O ARG A 551 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ARG A 551 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR A 503 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU A 494 " --> pdb=" O LYS A 476 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N LYS A 476 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 662 through 666 removed outlier: 6.715A pdb=" N GLU A 687 " --> pdb=" O CYS A 663 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N VAL A 665 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 689 " --> pdb=" O VAL A 665 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'A' and resid 202 through 205 removed outlier: 6.523A pdb=" N ARG A 204 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL A 258 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 78 through 80 removed outlier: 3.514A pdb=" N THR B 266 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 88 through 92 removed outlier: 7.937A pdb=" N ILE B 89 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LYS B 300 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE B 91 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU B 302 " --> pdb=" O PHE B 91 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' 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: 7.30 Time building geometry restraints manager: 9.79 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: 6815 1.34 - 1.46: 5034 1.46 - 1.59: 10961 1.59 - 1.71: 76 1.71 - 1.83: 172 Bond restraints: 23058 Sorted by residual: bond pdb=" C39 PCW G 102 " pdb=" C40 PCW G 102 " ideal model delta sigma weight residual 1.333 1.543 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C39 PCW E 102 " pdb=" C40 PCW E 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 A1108 " pdb=" C20 PCW A1108 " 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 C1108 " pdb=" C20 PCW C1108 " ideal model delta sigma weight residual 1.333 1.539 -0.206 2.00e-02 2.50e+03 1.06e+02 bond pdb=" C19 PCW E 102 " pdb=" C20 PCW E 102 " ideal model delta sigma weight residual 1.333 1.537 -0.204 2.00e-02 2.50e+03 1.04e+02 ... (remaining 23053 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.52: 645 105.52 - 112.65: 12087 112.65 - 119.78: 8336 119.78 - 126.91: 9798 126.91 - 134.04: 236 Bond angle restraints: 31102 Sorted by residual: angle pdb=" C PRO A 84 " pdb=" N THR A 85 " pdb=" CA THR A 85 " ideal model delta sigma weight residual 123.03 111.77 11.26 1.79e+00 3.12e-01 3.95e+01 angle pdb=" C PRO C 84 " pdb=" N THR C 85 " pdb=" CA THR C 85 " ideal model delta sigma weight residual 123.03 111.79 11.24 1.79e+00 3.12e-01 3.95e+01 angle pdb=" C SER A 310 " pdb=" N LEU A 311 " pdb=" CA LEU A 311 " ideal model delta sigma weight residual 122.06 111.41 10.65 1.86e+00 2.89e-01 3.28e+01 angle pdb=" C SER C 310 " pdb=" N LEU C 311 " pdb=" CA LEU C 311 " ideal model delta sigma weight residual 122.06 111.49 10.57 1.86e+00 2.89e-01 3.23e+01 angle pdb=" N ILE A 592 " pdb=" CA ILE A 592 " pdb=" C ILE A 592 " ideal model delta sigma weight residual 108.53 116.71 -8.18 1.45e+00 4.76e-01 3.18e+01 ... (remaining 31097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 13616 27.86 - 55.71: 1093 55.71 - 83.57: 161 83.57 - 111.42: 58 111.42 - 139.28: 38 Dihedral angle restraints: 14966 sinusoidal: 7310 harmonic: 7656 Sorted by residual: dihedral pdb=" C33 PCW A1113 " pdb=" C31 PCW A1113 " pdb=" C32 PCW A1113 " pdb=" O2 PCW A1113 " ideal model delta sinusoidal sigma weight residual 191.83 52.55 139.28 1 3.00e+01 1.11e-03 1.88e+01 dihedral pdb=" C33 PCW C1113 " pdb=" C31 PCW C1113 " pdb=" C32 PCW C1113 " pdb=" O2 PCW C1113 " ideal model delta sinusoidal sigma weight residual 191.83 52.68 139.15 1 3.00e+01 1.11e-03 1.87e+01 dihedral pdb=" C33 PCW C1111 " pdb=" C31 PCW C1111 " pdb=" C32 PCW C1111 " pdb=" O2 PCW C1111 " ideal model delta sinusoidal sigma weight residual -168.17 -29.87 -138.30 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 14963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2810 0.075 - 0.150: 591 0.150 - 0.225: 64 0.225 - 0.300: 29 0.300 - 0.375: 20 Chirality restraints: 3514 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 -2.23 -0.17 2.00e-02 2.50e+03 6.84e+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 -2.24 -0.16 2.00e-02 2.50e+03 6.77e+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 -2.33 -0.07 2.00e-02 2.50e+03 1.13e+01 ... (remaining 3511 not shown) Planarity restraints: 3816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 122 " 0.090 5.00e-02 4.00e+02 1.41e-01 3.19e+01 pdb=" N PRO B 123 " -0.244 5.00e-02 4.00e+02 pdb=" CA PRO B 123 " 0.079 5.00e-02 4.00e+02 pdb=" CD PRO B 123 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " -0.090 5.00e-02 4.00e+02 1.41e-01 3.18e+01 pdb=" N PRO D 123 " 0.244 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.079 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 594 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO A 595 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO A 595 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 595 " 0.055 5.00e-02 4.00e+02 ... (remaining 3813 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.84: 7039 2.84 - 3.42: 22919 3.42 - 3.99: 40223 3.99 - 4.57: 55568 4.57 - 5.14: 83468 Nonbonded interactions: 209217 Sorted by model distance: nonbonded pdb=" N ASN C 127 " pdb=" OD1 ASN C 127 " model vdw 2.266 2.520 nonbonded pdb=" N ASN A 127 " pdb=" OD1 ASN A 127 " model vdw 2.266 2.520 nonbonded pdb=" O2 PCW C1112 " pdb=" O3 PCW C1112 " model vdw 2.291 2.432 nonbonded pdb=" O2 PCW A1112 " pdb=" O3 PCW A1112 " model vdw 2.291 2.432 nonbonded pdb=" O2 PCW A1111 " pdb=" O3 PCW A1111 " model vdw 2.297 2.432 ... (remaining 209212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = (chain 'F' and resid 1 through 4) selection = (chain 'H' and resid 1 through 4) selection = (chain 'K' and resid 1 through 4) selection = (chain 'L' and resid 1 through 4) } ncs_group { reference = chain 'I' selection = chain 'M' } ncs_group { reference = chain 'J' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 4.220 Check model and map are aligned: 0.300 Set scattering table: 0.190 Process input model: 58.490 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 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 0.210 23058 Z= 0.630 Angle : 1.478 12.473 31102 Z= 0.748 Chirality : 0.068 0.375 3514 Planarity : 0.009 0.141 3808 Dihedral : 20.374 139.275 10036 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.99 % Favored : 89.33 % Rotamer: Outliers : 11.22 % Allowed : 10.11 % Favored : 78.67 % 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: 1160 sheet: -2.75 (0.29), residues: 254 loop : -2.77 (0.15), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 156 HIS 0.008 0.002 HIS A 919 PHE 0.030 0.003 PHE A 923 TYR 0.035 0.002 TYR B 206 ARG 0.009 0.001 ARG B 137 *********************** 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 576 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 322 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 PHE cc_start: 0.7830 (m-80) cc_final: 0.7529 (m-80) REVERT: C 173 ARG cc_start: 0.3216 (mtt180) cc_final: 0.2361 (ptt180) REVERT: C 324 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8862 (tp) REVERT: C 488 TYR cc_start: 0.4527 (OUTLIER) cc_final: 0.4257 (p90) REVERT: C 493 HIS cc_start: 0.4768 (OUTLIER) cc_final: 0.4154 (m-70) REVERT: C 698 LYS cc_start: 0.4825 (OUTLIER) cc_final: 0.4233 (tttt) REVERT: C 816 MET cc_start: 0.8081 (mmm) cc_final: 0.7605 (mmm) REVERT: C 949 MET cc_start: 0.8455 (mmm) cc_final: 0.8084 (mtp) REVERT: C 975 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7915 (p0) REVERT: D 106 MET cc_start: 0.8232 (mmm) cc_final: 0.7969 (mmm) REVERT: D 142 ASP cc_start: 0.7018 (t0) cc_final: 0.6781 (t0) REVERT: D 154 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8009 (ttt180) REVERT: D 272 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7230 (ttm) REVERT: D 305 SER cc_start: 0.7577 (t) cc_final: 0.7301 (p) REVERT: A 173 ARG cc_start: 0.3246 (mtt180) cc_final: 0.2491 (ptt180) REVERT: A 185 VAL cc_start: 0.7489 (t) cc_final: 0.7261 (p) REVERT: A 488 TYR cc_start: 0.4507 (OUTLIER) cc_final: 0.4249 (p90) REVERT: A 493 HIS cc_start: 0.5462 (OUTLIER) cc_final: 0.4356 (m-70) REVERT: A 615 MET cc_start: 0.5860 (ttm) cc_final: 0.5467 (ttp) REVERT: A 708 GLN cc_start: 0.6476 (OUTLIER) cc_final: 0.6262 (mt0) REVERT: A 816 MET cc_start: 0.8225 (mmm) cc_final: 0.7806 (mmm) REVERT: A 846 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7547 (p0) REVERT: A 975 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7687 (p0) REVERT: B 23 LYS cc_start: 0.8326 (mttt) cc_final: 0.8003 (mmtp) REVERT: B 73 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7553 (p) REVERT: B 106 MET cc_start: 0.8454 (mmm) cc_final: 0.8187 (mmm) REVERT: B 142 ASP cc_start: 0.7097 (t0) cc_final: 0.6751 (t0) REVERT: B 154 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.8106 (ttt180) REVERT: B 156 TRP cc_start: 0.8513 (OUTLIER) cc_final: 0.8253 (m-10) REVERT: B 272 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.7550 (ttm) outliers start: 254 outliers final: 40 residues processed: 516 average time/residue: 0.4130 time to fit residues: 309.2855 Evaluate side-chains 201 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 145 time to evaluate : 2.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 LYS Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 488 TYR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 571 PHE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 943 SER Chi-restraints excluded: chain C residue 952 LYS Chi-restraints excluded: chain C residue 975 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 79 SER Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 488 TYR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 608 SER Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 832 MET Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 872 ILE Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 975 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 154 ARG Chi-restraints excluded: chain B residue 156 TRP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 272 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 206 optimal weight: 0.8980 chunk 80 optimal weight: 0.0270 chunk 125 optimal weight: 6.9990 chunk 154 optimal weight: 50.0000 chunk 239 optimal weight: 7.9990 overall best weight: 2.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 209 HIS C 434 GLN C 474 ASN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS C 638 ASN C 696 GLN C 720 ASN C 744 GLN C 904 GLN C1019 GLN D 56 GLN D 258 GLN A 118 GLN A 129 ASN A 209 HIS A 383 GLN A 434 GLN A 474 ASN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 638 ASN A 696 GLN A 720 ASN A 744 GLN A 904 GLN A1019 GLN B 56 GLN B 258 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23058 Z= 0.281 Angle : 0.701 9.283 31102 Z= 0.342 Chirality : 0.048 0.426 3514 Planarity : 0.006 0.069 3808 Dihedral : 17.438 134.912 5189 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.58 % Allowed : 13.47 % Favored : 82.95 % 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: -1.56 (0.15), residues: 2642 helix: -0.13 (0.15), residues: 1180 sheet: -2.26 (0.27), residues: 288 loop : -1.59 (0.16), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 89 HIS 0.008 0.002 HIS A 620 PHE 0.021 0.002 PHE C 393 TYR 0.019 0.002 TYR B 248 ARG 0.009 0.001 ARG C 445 *********************** 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 251 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 170 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 LYS cc_start: 0.7698 (mmmt) cc_final: 0.7299 (mmmm) REVERT: C 173 ARG cc_start: 0.2933 (mtt180) cc_final: 0.2132 (ptt180) REVERT: C 267 MET cc_start: 0.5920 (ppp) cc_final: 0.5374 (ppp) REVERT: C 324 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9010 (tp) REVERT: C 512 GLU cc_start: 0.5281 (OUTLIER) cc_final: 0.4919 (mp0) REVERT: C 589 MET cc_start: 0.7558 (mmm) cc_final: 0.6730 (mpp) REVERT: C 615 MET cc_start: 0.5293 (OUTLIER) cc_final: 0.5055 (ttp) REVERT: C 846 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8159 (p0) REVERT: C 952 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7525 (mptt) REVERT: D 14 LYS cc_start: 0.7274 (tptt) cc_final: 0.6482 (mmtm) REVERT: D 106 MET cc_start: 0.8578 (mmm) cc_final: 0.8283 (mmm) REVERT: D 142 ASP cc_start: 0.7545 (t0) cc_final: 0.7115 (t0) REVERT: A 41 MET cc_start: 0.5417 (ppp) cc_final: 0.5181 (ptm) REVERT: A 153 LYS cc_start: 0.7657 (mmmt) cc_final: 0.7248 (mmmm) REVERT: A 173 ARG cc_start: 0.3136 (mtt180) cc_final: 0.2360 (ptt180) REVERT: A 185 VAL cc_start: 0.7359 (t) cc_final: 0.7011 (p) REVERT: A 267 MET cc_start: 0.5999 (ppp) cc_final: 0.5480 (ppp) REVERT: A 396 GLN cc_start: 0.6487 (tp40) cc_final: 0.5911 (mt0) REVERT: A 507 MET cc_start: 0.5670 (ttp) cc_final: 0.5467 (ttm) REVERT: A 512 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.4168 (mp0) REVERT: A 571 PHE cc_start: 0.4767 (OUTLIER) cc_final: 0.4478 (m-10) REVERT: A 816 MET cc_start: 0.8291 (mmm) cc_final: 0.7966 (mmm) REVERT: A 846 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7750 (p0) REVERT: B 23 LYS cc_start: 0.8551 (mttt) cc_final: 0.8030 (mmtm) REVERT: B 106 MET cc_start: 0.8653 (mmm) cc_final: 0.8334 (mmm) REVERT: B 203 GLN cc_start: 0.7547 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: G 7 ASP cc_start: 0.7208 (t0) cc_final: 0.6965 (t0) outliers start: 81 outliers final: 39 residues processed: 245 average time/residue: 0.3811 time to fit residues: 141.2333 Evaluate side-chains 189 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 141 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 512 GLU Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 638 ASN Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 952 LYS Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 160 CYS Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 261 THR Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 512 GLU Chi-restraints excluded: chain A residue 515 LEU Chi-restraints excluded: chain A residue 571 PHE Chi-restraints excluded: chain A residue 638 ASN Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 160 CYS Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 199 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 259 optimal weight: 5.9990 chunk 213 optimal weight: 6.9990 chunk 238 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 489 GLN ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23058 Z= 0.207 Angle : 0.570 8.792 31102 Z= 0.281 Chirality : 0.044 0.393 3514 Planarity : 0.005 0.057 3808 Dihedral : 16.277 123.288 5118 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.00 % Allowed : 14.22 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.16), residues: 2642 helix: 0.72 (0.15), residues: 1196 sheet: -1.83 (0.28), residues: 288 loop : -1.07 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 89 HIS 0.008 0.001 HIS A 557 PHE 0.017 0.002 PHE A 923 TYR 0.013 0.001 TYR C 869 ARG 0.012 0.000 ARG A 445 *********************** 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 214 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 146 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: C 173 ARG cc_start: 0.3001 (mtt180) cc_final: 0.2206 (ptt180) REVERT: C 324 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9100 (tp) REVERT: C 816 MET cc_start: 0.8205 (mmm) cc_final: 0.7816 (mmm) REVERT: D 14 LYS cc_start: 0.7539 (tptt) cc_final: 0.6678 (mmtm) REVERT: D 106 MET cc_start: 0.8565 (mmm) cc_final: 0.8239 (mmm) REVERT: D 142 ASP cc_start: 0.7596 (t0) cc_final: 0.7185 (t0) REVERT: A 164 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6700 (tmm) REVERT: A 173 ARG cc_start: 0.3140 (mtt180) cc_final: 0.2380 (ptt180) REVERT: A 185 VAL cc_start: 0.7342 (t) cc_final: 0.6976 (p) REVERT: A 396 GLN cc_start: 0.6410 (tp40) cc_final: 0.5860 (mt0) REVERT: A 493 HIS cc_start: 0.4852 (OUTLIER) cc_final: 0.3935 (m-70) REVERT: A 708 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6718 (tt0) REVERT: A 816 MET cc_start: 0.8349 (mmm) cc_final: 0.8012 (mmm) REVERT: B 23 LYS cc_start: 0.8626 (mttt) cc_final: 0.8054 (mmtm) REVERT: B 106 MET cc_start: 0.8660 (mmm) cc_final: 0.8332 (mmm) REVERT: B 203 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.7474 (mp10) outliers start: 68 outliers final: 35 residues processed: 203 average time/residue: 0.3501 time to fit residues: 110.1955 Evaluate side-chains 173 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 133 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain C residue 986 SER Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 203 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 241 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 228 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 243 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 243 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23058 Z= 0.162 Angle : 0.521 8.292 31102 Z= 0.254 Chirality : 0.043 0.416 3514 Planarity : 0.004 0.050 3808 Dihedral : 15.084 115.992 5098 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.39 % Allowed : 15.64 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.16), residues: 2642 helix: 1.13 (0.15), residues: 1210 sheet: -1.02 (0.29), residues: 304 loop : -0.88 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 89 HIS 0.008 0.001 HIS A 557 PHE 0.014 0.001 PHE A 306 TYR 0.013 0.001 TYR C 869 ARG 0.010 0.000 ARG C 889 *********************** 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 199 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 145 time to evaluate : 2.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 173 ARG cc_start: 0.3057 (mtt180) cc_final: 0.2241 (ptt180) REVERT: C 230 GLU cc_start: 0.7665 (mp0) cc_final: 0.6980 (tt0) REVERT: C 291 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.8198 (p90) REVERT: C 493 HIS cc_start: 0.4306 (OUTLIER) cc_final: 0.3785 (m-70) REVERT: C 534 MET cc_start: 0.4558 (OUTLIER) cc_final: 0.4225 (mtp) REVERT: C 816 MET cc_start: 0.8219 (mmm) cc_final: 0.7846 (mmm) REVERT: D 106 MET cc_start: 0.8556 (mmm) cc_final: 0.8179 (mmm) REVERT: D 142 ASP cc_start: 0.7610 (t0) cc_final: 0.7171 (t0) REVERT: A 164 MET cc_start: 0.7134 (OUTLIER) cc_final: 0.6817 (tmm) REVERT: A 173 ARG cc_start: 0.3086 (mtt180) cc_final: 0.2381 (ptt180) REVERT: A 230 GLU cc_start: 0.7316 (mp0) cc_final: 0.6841 (tt0) REVERT: A 493 HIS cc_start: 0.4545 (OUTLIER) cc_final: 0.3984 (m-70) REVERT: A 708 GLN cc_start: 0.7104 (OUTLIER) cc_final: 0.6814 (tt0) REVERT: A 816 MET cc_start: 0.8352 (mmm) cc_final: 0.8029 (mmm) REVERT: B 23 LYS cc_start: 0.8651 (mttt) cc_final: 0.8031 (mmtm) outliers start: 54 outliers final: 28 residues processed: 188 average time/residue: 0.3555 time to fit residues: 105.4475 Evaluate side-chains 166 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 608 SER Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 1000 LEU Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 157 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 0.5980 chunk 144 optimal weight: 20.0000 chunk 3 optimal weight: 40.0000 chunk 190 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 217 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 130 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 577 ASN ** A 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23058 Z= 0.282 Angle : 0.593 7.765 31102 Z= 0.291 Chirality : 0.046 0.424 3514 Planarity : 0.005 0.087 3808 Dihedral : 14.841 123.814 5088 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.65 % Allowed : 15.46 % Favored : 81.89 % 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: 0.04 (0.16), residues: 2642 helix: 1.15 (0.15), residues: 1178 sheet: -0.91 (0.28), residues: 316 loop : -0.84 (0.17), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 894 HIS 0.011 0.001 HIS A 398 PHE 0.025 0.002 PHE A 923 TYR 0.020 0.002 TYR D 44 ARG 0.014 0.001 ARG A 889 *********************** 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 196 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 136 time to evaluate : 2.487 Fit side-chains revert: symmetry clash REVERT: C 173 ARG cc_start: 0.3465 (mtt180) cc_final: 0.2504 (ptt180) REVERT: C 230 GLU cc_start: 0.7549 (mp0) cc_final: 0.6964 (tt0) REVERT: C 291 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8496 (p90) REVERT: C 490 LEU cc_start: 0.4362 (OUTLIER) cc_final: 0.3705 (pt) REVERT: C 493 HIS cc_start: 0.4363 (OUTLIER) cc_final: 0.3793 (m-70) REVERT: C 534 MET cc_start: 0.4297 (OUTLIER) cc_final: 0.3930 (mtp) REVERT: C 578 PHE cc_start: 0.1487 (OUTLIER) cc_final: 0.0442 (p90) REVERT: C 816 MET cc_start: 0.8238 (mmm) cc_final: 0.7883 (mmm) REVERT: D 23 LYS cc_start: 0.7935 (mmtp) cc_final: 0.7701 (mmtm) REVERT: D 106 MET cc_start: 0.8575 (mmm) cc_final: 0.8133 (mtp) REVERT: A 185 VAL cc_start: 0.7439 (OUTLIER) cc_final: 0.7134 (p) REVERT: A 391 MET cc_start: 0.6901 (mmp) cc_final: 0.6620 (mmp) REVERT: A 396 GLN cc_start: 0.6576 (tm-30) cc_final: 0.5784 (mt0) REVERT: A 493 HIS cc_start: 0.4743 (OUTLIER) cc_final: 0.4121 (m-70) REVERT: A 578 PHE cc_start: 0.1883 (OUTLIER) cc_final: 0.0644 (p90) REVERT: A 708 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: A 816 MET cc_start: 0.8419 (mmm) cc_final: 0.8029 (mmm) REVERT: B 23 LYS cc_start: 0.8678 (mttt) cc_final: 0.8124 (mmtm) REVERT: B 106 MET cc_start: 0.8625 (mmm) cc_final: 0.8128 (mtp) outliers start: 60 outliers final: 34 residues processed: 186 average time/residue: 0.3564 time to fit residues: 104.2191 Evaluate side-chains 168 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 125 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 935 ILE Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 708 GLN Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 269 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 2.9990 chunk 229 optimal weight: 0.9980 chunk 50 optimal weight: 20.0000 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 0.0370 chunk 255 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 20.0000 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 HIS ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23058 Z= 0.161 Angle : 0.501 7.486 31102 Z= 0.244 Chirality : 0.043 0.438 3514 Planarity : 0.004 0.053 3808 Dihedral : 14.191 125.809 5086 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.16 % Allowed : 16.52 % Favored : 81.32 % 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: 0.36 (0.16), residues: 2642 helix: 1.48 (0.16), residues: 1184 sheet: -0.74 (0.29), residues: 318 loop : -0.76 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 89 HIS 0.008 0.001 HIS A 557 PHE 0.014 0.001 PHE C 306 TYR 0.015 0.001 TYR C 488 ARG 0.007 0.000 ARG C 889 *********************** 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 184 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 135 time to evaluate : 2.385 Fit side-chains revert: symmetry clash REVERT: C 173 ARG cc_start: 0.3405 (mtt180) cc_final: 0.2423 (ptt180) REVERT: C 230 GLU cc_start: 0.7720 (mp0) cc_final: 0.7201 (tt0) REVERT: C 291 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8246 (p90) REVERT: C 391 MET cc_start: 0.7044 (mmt) cc_final: 0.6537 (mmp) REVERT: C 493 HIS cc_start: 0.4212 (OUTLIER) cc_final: 0.3750 (m-70) REVERT: C 534 MET cc_start: 0.4336 (OUTLIER) cc_final: 0.4049 (mtp) REVERT: C 578 PHE cc_start: 0.1512 (OUTLIER) cc_final: 0.0304 (p90) REVERT: C 816 MET cc_start: 0.8204 (mmm) cc_final: 0.7867 (mmm) REVERT: D 23 LYS cc_start: 0.7948 (mmtp) cc_final: 0.7673 (mmtt) REVERT: D 106 MET cc_start: 0.8525 (mmm) cc_final: 0.8046 (mtp) REVERT: A 164 MET cc_start: 0.7182 (tmm) cc_final: 0.6930 (tmm) REVERT: A 230 GLU cc_start: 0.7710 (mp0) cc_final: 0.7049 (tt0) REVERT: A 391 MET cc_start: 0.7010 (mmp) cc_final: 0.6663 (mmp) REVERT: A 396 GLN cc_start: 0.6547 (tm-30) cc_final: 0.5631 (mt0) REVERT: A 490 LEU cc_start: 0.4464 (OUTLIER) cc_final: 0.3869 (pt) REVERT: A 493 HIS cc_start: 0.4491 (OUTLIER) cc_final: 0.3823 (m-70) REVERT: A 578 PHE cc_start: 0.1761 (OUTLIER) cc_final: 0.0605 (p90) REVERT: A 816 MET cc_start: 0.8407 (mmm) cc_final: 0.7991 (mmm) REVERT: B 23 LYS cc_start: 0.8692 (mttt) cc_final: 0.8121 (mmtm) REVERT: B 106 MET cc_start: 0.8557 (mmm) cc_final: 0.8050 (mtp) outliers start: 49 outliers final: 30 residues processed: 178 average time/residue: 0.3621 time to fit residues: 101.2061 Evaluate side-chains 163 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 126 time to evaluate : 2.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 881 MET Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 85 ILE Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 157 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 186 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 254 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23058 Z= 0.304 Angle : 0.587 7.416 31102 Z= 0.286 Chirality : 0.046 0.441 3514 Planarity : 0.005 0.056 3808 Dihedral : 14.262 130.795 5083 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.61 % Allowed : 16.17 % Favored : 81.23 % 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: 0.21 (0.16), residues: 2642 helix: 1.30 (0.15), residues: 1178 sheet: -0.82 (0.29), residues: 314 loop : -0.75 (0.16), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 894 HIS 0.009 0.001 HIS A 557 PHE 0.025 0.002 PHE A 923 TYR 0.017 0.002 TYR C 869 ARG 0.009 0.000 ARG C 889 *********************** 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 190 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 131 time to evaluate : 2.606 Fit side-chains revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7667 (mp0) cc_final: 0.7028 (tt0) REVERT: C 291 PHE cc_start: 0.8995 (OUTLIER) cc_final: 0.8559 (p90) REVERT: C 386 MET cc_start: 0.6514 (ptp) cc_final: 0.6162 (ptp) REVERT: C 490 LEU cc_start: 0.4563 (OUTLIER) cc_final: 0.3985 (pt) REVERT: C 493 HIS cc_start: 0.4405 (OUTLIER) cc_final: 0.3842 (m-70) REVERT: C 534 MET cc_start: 0.4040 (OUTLIER) cc_final: 0.3710 (mmm) REVERT: C 578 PHE cc_start: 0.1688 (OUTLIER) cc_final: 0.0384 (p90) REVERT: C 816 MET cc_start: 0.8238 (mmm) cc_final: 0.7885 (mmm) REVERT: D 23 LYS cc_start: 0.8026 (mmtp) cc_final: 0.7824 (mmtt) REVERT: D 106 MET cc_start: 0.8589 (mmm) cc_final: 0.8157 (mtp) REVERT: D 234 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.8966 (tp) REVERT: A 230 GLU cc_start: 0.7827 (mp0) cc_final: 0.7141 (tt0) REVERT: A 396 GLN cc_start: 0.6444 (tm-30) cc_final: 0.5420 (mt0) REVERT: A 578 PHE cc_start: 0.1803 (OUTLIER) cc_final: 0.0652 (p90) REVERT: A 589 MET cc_start: 0.7829 (mmm) cc_final: 0.7506 (mmt) REVERT: B 106 MET cc_start: 0.8587 (mmm) cc_final: 0.8145 (mtp) outliers start: 59 outliers final: 40 residues processed: 180 average time/residue: 0.3368 time to fit residues: 98.2353 Evaluate side-chains 170 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 123 time to evaluate : 2.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 279 VAL Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 415 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 534 MET Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 894 TRP Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 157 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 269 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 894 TRP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 269 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 23 optimal weight: 0.1980 chunk 200 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23058 Z= 0.183 Angle : 0.511 7.652 31102 Z= 0.249 Chirality : 0.043 0.441 3514 Planarity : 0.004 0.055 3808 Dihedral : 13.736 130.895 5081 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.30 % Allowed : 16.48 % Favored : 81.23 % 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: 0.48 (0.16), residues: 2642 helix: 1.56 (0.16), residues: 1176 sheet: -0.69 (0.29), residues: 312 loop : -0.66 (0.16), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 89 HIS 0.009 0.001 HIS A 557 PHE 0.013 0.001 PHE A 923 TYR 0.015 0.001 TYR A 488 ARG 0.008 0.000 ARG C 889 *********************** 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 183 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 131 time to evaluate : 2.565 Fit side-chains revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7804 (mp0) cc_final: 0.7185 (tt0) REVERT: C 291 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8380 (p90) REVERT: C 386 MET cc_start: 0.6534 (ptp) cc_final: 0.5951 (ptp) REVERT: C 391 MET cc_start: 0.6959 (mmt) cc_final: 0.6520 (mmp) REVERT: C 490 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.3948 (pt) REVERT: C 493 HIS cc_start: 0.4116 (OUTLIER) cc_final: 0.3698 (m-70) REVERT: C 578 PHE cc_start: 0.1656 (OUTLIER) cc_final: 0.0390 (p90) REVERT: C 816 MET cc_start: 0.8200 (mmm) cc_final: 0.7870 (mmm) REVERT: D 23 LYS cc_start: 0.8095 (mmtp) cc_final: 0.7857 (mmtt) REVERT: D 106 MET cc_start: 0.8522 (mmm) cc_final: 0.8069 (mtp) REVERT: D 121 ASN cc_start: 0.6273 (m-40) cc_final: 0.6067 (m-40) REVERT: A 164 MET cc_start: 0.6804 (tmm) cc_final: 0.6540 (tmm) REVERT: A 230 GLU cc_start: 0.7735 (mp0) cc_final: 0.7145 (tt0) REVERT: A 396 GLN cc_start: 0.6408 (tm-30) cc_final: 0.5425 (mt0) REVERT: A 490 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.3884 (pt) REVERT: A 578 PHE cc_start: 0.1844 (OUTLIER) cc_final: 0.0678 (p90) REVERT: A 816 MET cc_start: 0.8125 (mmm) cc_final: 0.7820 (mmm) REVERT: B 106 MET cc_start: 0.8523 (mmm) cc_final: 0.8028 (mtp) outliers start: 52 outliers final: 36 residues processed: 174 average time/residue: 0.3264 time to fit residues: 92.4161 Evaluate side-chains 162 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 120 time to evaluate : 2.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 485 THR Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 655 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 79 SER Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 9.9990 chunk 222 optimal weight: 0.9990 chunk 237 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 186 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 chunk 214 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 236 optimal weight: 0.0010 chunk 155 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23058 Z= 0.143 Angle : 0.491 6.985 31102 Z= 0.239 Chirality : 0.042 0.445 3514 Planarity : 0.004 0.073 3808 Dihedral : 13.176 128.000 5081 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.86 % Allowed : 17.14 % Favored : 81.01 % 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: 0.71 (0.16), residues: 2642 helix: 1.77 (0.16), residues: 1176 sheet: -0.55 (0.29), residues: 314 loop : -0.56 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 89 HIS 0.008 0.001 HIS A 557 PHE 0.013 0.001 PHE C 306 TYR 0.015 0.001 TYR C 869 ARG 0.003 0.000 ARG C 889 *********************** 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 169 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 127 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7776 (mp0) cc_final: 0.7218 (tt0) REVERT: C 291 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.8319 (p90) REVERT: C 386 MET cc_start: 0.6531 (ptp) cc_final: 0.6040 (ptp) REVERT: C 391 MET cc_start: 0.6909 (mmt) cc_final: 0.6474 (mmp) REVERT: C 490 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.3938 (pt) REVERT: C 493 HIS cc_start: 0.4163 (OUTLIER) cc_final: 0.3695 (m-70) REVERT: C 578 PHE cc_start: 0.1656 (OUTLIER) cc_final: 0.0439 (p90) REVERT: C 816 MET cc_start: 0.8208 (mmm) cc_final: 0.7883 (mmm) REVERT: D 23 LYS cc_start: 0.8133 (mmtp) cc_final: 0.7908 (mmtt) REVERT: D 106 MET cc_start: 0.8501 (mmm) cc_final: 0.8008 (mtp) REVERT: D 121 ASN cc_start: 0.6272 (m-40) cc_final: 0.6067 (m-40) REVERT: D 234 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8879 (tp) REVERT: A 164 MET cc_start: 0.6701 (tmm) cc_final: 0.6390 (tmm) REVERT: A 230 GLU cc_start: 0.7719 (mp0) cc_final: 0.7152 (tt0) REVERT: A 396 GLN cc_start: 0.6388 (tm-30) cc_final: 0.5538 (mt0) REVERT: A 490 LEU cc_start: 0.4509 (OUTLIER) cc_final: 0.3958 (pt) REVERT: A 493 HIS cc_start: 0.4601 (OUTLIER) cc_final: 0.3952 (m-70) REVERT: A 578 PHE cc_start: 0.1753 (OUTLIER) cc_final: 0.0700 (p90) REVERT: A 816 MET cc_start: 0.8103 (mmm) cc_final: 0.7806 (mmm) REVERT: B 106 MET cc_start: 0.8491 (mmm) cc_final: 0.7993 (mtp) outliers start: 42 outliers final: 26 residues processed: 162 average time/residue: 0.3103 time to fit residues: 83.9512 Evaluate side-chains 155 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 121 time to evaluate : 2.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.5980 chunk 153 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 242 optimal weight: 0.1980 chunk 209 optimal weight: 0.4980 chunk 21 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 166 optimal weight: 9.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 946 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23058 Z= 0.185 Angle : 0.510 9.209 31102 Z= 0.248 Chirality : 0.043 0.445 3514 Planarity : 0.004 0.074 3808 Dihedral : 12.977 128.054 5079 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.86 % Allowed : 17.27 % Favored : 80.87 % 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: 0.72 (0.16), residues: 2642 helix: 1.77 (0.16), residues: 1176 sheet: -0.50 (0.29), residues: 314 loop : -0.56 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 89 HIS 0.008 0.001 HIS A 557 PHE 0.016 0.001 PHE A 923 TYR 0.015 0.001 TYR C 869 ARG 0.004 0.000 ARG C 445 ********************** 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 172 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 130 time to evaluate : 2.582 Fit side-chains revert: symmetry clash REVERT: C 230 GLU cc_start: 0.7855 (mp0) cc_final: 0.7198 (tt0) REVERT: C 291 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8389 (p90) REVERT: C 386 MET cc_start: 0.6462 (ptp) cc_final: 0.5938 (ptp) REVERT: C 391 MET cc_start: 0.6983 (mmt) cc_final: 0.6522 (mmp) REVERT: C 396 GLN cc_start: 0.6313 (tm-30) cc_final: 0.5547 (pt0) REVERT: C 490 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.3862 (pt) REVERT: C 493 HIS cc_start: 0.4159 (OUTLIER) cc_final: 0.3674 (m-70) REVERT: C 578 PHE cc_start: 0.1722 (OUTLIER) cc_final: 0.0551 (p90) REVERT: C 816 MET cc_start: 0.8207 (mmm) cc_final: 0.7876 (mmm) REVERT: D 23 LYS cc_start: 0.8140 (mmtp) cc_final: 0.7909 (mmtt) REVERT: D 106 MET cc_start: 0.8520 (mmm) cc_final: 0.8042 (mtp) REVERT: D 121 ASN cc_start: 0.6286 (m-40) cc_final: 0.6077 (m-40) REVERT: D 234 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8904 (tp) REVERT: A 164 MET cc_start: 0.6646 (tmm) cc_final: 0.6365 (tmm) REVERT: A 230 GLU cc_start: 0.7737 (mp0) cc_final: 0.7178 (tt0) REVERT: A 396 GLN cc_start: 0.6396 (tm-30) cc_final: 0.5578 (mt0) REVERT: A 490 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.4037 (pt) REVERT: A 493 HIS cc_start: 0.4800 (OUTLIER) cc_final: 0.4008 (m-70) REVERT: A 578 PHE cc_start: 0.1766 (OUTLIER) cc_final: 0.0585 (p90) REVERT: A 734 MET cc_start: 0.7795 (mmm) cc_final: 0.7369 (mmm) REVERT: A 816 MET cc_start: 0.8122 (mmm) cc_final: 0.7818 (mmm) REVERT: B 106 MET cc_start: 0.8539 (mmm) cc_final: 0.8041 (mtp) outliers start: 42 outliers final: 30 residues processed: 168 average time/residue: 0.3116 time to fit residues: 86.2700 Evaluate side-chains 164 residues out of total 2264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 291 PHE Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 493 HIS Chi-restraints excluded: chain C residue 515 LEU Chi-restraints excluded: chain C residue 578 PHE Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 686 THR Chi-restraints excluded: chain C residue 719 VAL Chi-restraints excluded: chain C residue 846 ASN Chi-restraints excluded: chain C residue 872 ILE Chi-restraints excluded: chain C residue 881 MET Chi-restraints excluded: chain C residue 974 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 64 ASP Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 485 THR Chi-restraints excluded: chain A residue 490 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain A residue 578 PHE Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 719 VAL Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 846 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 201 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain G residue 13 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 9.9990 chunk 209 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 HIS C 708 GLN ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 486 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 HIS A 708 GLN A 946 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.141250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.095461 restraints weight = 40627.910| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.38 r_work: 0.2957 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23058 Z= 0.201 Angle : 0.514 6.874 31102 Z= 0.252 Chirality : 0.043 0.440 3514 Planarity : 0.004 0.062 3808 Dihedral : 12.844 128.006 5079 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.94 % Allowed : 17.40 % Favored : 80.65 % 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: 0.70 (0.16), residues: 2642 helix: 1.77 (0.16), residues: 1174 sheet: -0.66 (0.29), residues: 326 loop : -0.53 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 89 HIS 0.009 0.001 HIS A 557 PHE 0.017 0.001 PHE A 923 TYR 0.015 0.001 TYR C 869 ARG 0.004 0.000 ARG A 517 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4309.69 seconds wall clock time: 79 minutes 25.51 seconds (4765.51 seconds total)