Starting phenix.real_space_refine on Fri Mar 22 01:21:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rq6_24628/03_2024/7rq6_24628.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rq6_24628/03_2024/7rq6_24628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rq6_24628/03_2024/7rq6_24628.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rq6_24628/03_2024/7rq6_24628.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rq6_24628/03_2024/7rq6_24628.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rq6_24628/03_2024/7rq6_24628.pdb" } resolution = 4.18 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 504 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19944 2.51 5 N 5151 2.21 5 O 6138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 904": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31368 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8464 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "B" Number of atoms: 8464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8464 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "C" Number of atoms: 8464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1086, 8464 Classifications: {'peptide': 1086} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 58, 'TRANS': 1027} Chain breaks: 7 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 966 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "K" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "F" 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: "G" 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 15.84, per 1000 atoms: 0.50 Number of scatterers: 31368 At special positions: 0 Unit cell: (208.096, 200.092, 176.081, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 6138 8.00 N 5151 7.00 C 19944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 165 " " NAG A2003 " - " ASN A 234 " " NAG A2004 " - " ASN A 282 " " NAG A2005 " - " ASN A 331 " " NAG A2006 " - " ASN A 616 " " NAG A2007 " - " ASN A 657 " " NAG A2008 " - " ASN A 709 " " NAG A2009 " - " ASN A 717 " " NAG A2010 " - " ASN A 801 " " NAG A2011 " - " ASN A1074 " " NAG A2012 " - " ASN A1134 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 165 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 282 " " NAG B2005 " - " ASN B 331 " " NAG B2006 " - " ASN B 616 " " NAG B2007 " - " ASN B 657 " " NAG B2008 " - " ASN B 709 " " NAG B2009 " - " ASN B 717 " " NAG B2010 " - " ASN B 801 " " NAG B2011 " - " ASN B1074 " " NAG B2012 " - " ASN B1134 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 282 " " NAG C2005 " - " ASN C 331 " " NAG C2006 " - " ASN C 616 " " NAG C2007 " - " ASN C 657 " " NAG C2008 " - " ASN C 709 " " NAG C2009 " - " ASN C 717 " " NAG C2010 " - " ASN C 801 " " NAG C2011 " - " ASN C1074 " " NAG C2012 " - " ASN C1134 " " NAG F 1 " - " ASN A1098 " " NAG G 1 " - " ASN B1098 " " NAG I 1 " - " ASN C1098 " Time building additional restraints: 12.51 Conformation dependent library (CDL) restraints added in 6.0 seconds 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7368 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 65 sheets defined 20.0% alpha, 22.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.703A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 388' Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 removed outlier: 3.506A pdb=" N ALA A 623 " --> pdb=" O GLU A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.532A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.709A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.591A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.128A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 906 removed outlier: 4.194A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.576A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.821A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.643A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 86 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.599A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 371 Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.700A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 416 through 423 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.500A pdb=" N ALA B 623 " --> pdb=" O GLU B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.536A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.702A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.602A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 856 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.519A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 906 removed outlier: 4.142A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 907 through 909 No H-bonds generated for 'chain 'B' and resid 907 through 909' Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.539A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.811A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.664A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 86 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.612A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.699A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 384 through 388' Processing helix chain 'C' and resid 416 through 423 Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.503A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.521A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.697A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.607A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 852 through 856 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 4.133A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 906 removed outlier: 4.164A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 907 through 909 No H-bonds generated for 'chain 'C' and resid 907 through 909' Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.525A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.812A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.673A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 86 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 53 removed outlier: 3.868A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.900A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.510A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.313A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 585 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.565A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 516 through 517 removed outlier: 3.545A pdb=" N GLU A 516 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 4.406A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.650A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.130A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.825A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1082 removed outlier: 4.288A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC1, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.167A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.532A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR H 96 " --> pdb=" O MET H 100F" (cutoff:3.500A) removed outlier: 5.975A pdb=" N MET H 100F" --> pdb=" O TYR H 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC4, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.482A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LYS L 107 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA L 13 " --> pdb=" O LYS L 107 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 28 through 30 Processing sheet with id=AC6, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.411A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 50 through 53 removed outlier: 3.877A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 91 through 93 removed outlier: 4.064A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AD1, first strand: chain 'B' and resid 314 through 319 removed outlier: 6.045A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 325 through 328 removed outlier: 6.505A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 585 " --> pdb=" O VAL B 576 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 376 through 377 removed outlier: 3.631A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 516 through 517 removed outlier: 3.558A pdb=" N GLU B 516 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 4.402A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 702 through 703 Processing sheet with id=AD8, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.628A pdb=" N THR B1105 " --> pdb=" O VAL B1094 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.152A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B1047 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 718 through 728 Processing sheet with id=AE2, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AE3, first strand: chain 'B' and resid 1081 through 1082 removed outlier: 4.284A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.158A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.678A pdb=" N CYS D 92 " --> pdb=" O TRP D 103 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N TRP D 103 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ARG D 94 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR D 100E" --> pdb=" O TYR D 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 14 removed outlier: 6.311A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LYS E 107 " --> pdb=" O LEU E 11 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA E 13 " --> pdb=" O LYS E 107 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 28 through 30 Processing sheet with id=AF1, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.380A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU C 229 " --> pdb=" O PHE C 201 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 50 through 53 removed outlier: 3.866A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 91 through 93 removed outlier: 4.073A pdb=" N GLY C 268 " --> pdb=" O TYR C 91 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AF5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.492A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.443A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 585 " --> pdb=" O VAL C 576 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 376 through 377 removed outlier: 3.614A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 516 through 517 removed outlier: 3.536A pdb=" N GLU C 516 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AG1, first strand: chain 'C' and resid 654 through 655 removed outlier: 4.415A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.665A pdb=" N THR C1105 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.146A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 718 through 728 Processing sheet with id=AG5, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AG6, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 4.272A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.168A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.634A pdb=" N VAL J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR J 96 " --> pdb=" O MET J 100F" (cutoff:3.500A) removed outlier: 6.106A pdb=" N MET J 100F" --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AH2, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.326A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) 1022 hydrogen bonds defined for protein. 2682 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: 15.10 Time building geometry restraints manager: 13.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9792 1.34 - 1.46: 7981 1.46 - 1.59: 14138 1.59 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 32082 Sorted by residual: bond pdb=" CA GLY B 184 " pdb=" C GLY B 184 " ideal model delta sigma weight residual 1.518 1.497 0.020 1.07e-02 8.73e+03 3.60e+00 bond pdb=" CA VAL A 70 " pdb=" C VAL A 70 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.27e-02 6.20e+03 2.76e+00 bond pdb=" CA PHE A 543 " pdb=" C PHE A 543 " ideal model delta sigma weight residual 1.526 1.504 0.021 1.30e-02 5.92e+03 2.71e+00 bond pdb=" CA ASN C 185 " pdb=" C ASN C 185 " ideal model delta sigma weight residual 1.528 1.508 0.021 1.28e-02 6.10e+03 2.65e+00 bond pdb=" CA PHE C 543 " pdb=" C PHE C 543 " ideal model delta sigma weight residual 1.525 1.504 0.021 1.28e-02 6.10e+03 2.60e+00 ... (remaining 32077 not shown) Histogram of bond angle deviations from ideal: 99.53 - 106.42: 874 106.42 - 113.32: 17592 113.32 - 120.21: 10863 120.21 - 127.10: 14036 127.10 - 134.00: 303 Bond angle restraints: 43668 Sorted by residual: angle pdb=" N THR A 73 " pdb=" CA THR A 73 " pdb=" C THR A 73 " ideal model delta sigma weight residual 112.68 103.25 9.43 1.33e+00 5.65e-01 5.03e+01 angle pdb=" C PHE B 347 " pdb=" CA PHE B 347 " pdb=" CB PHE B 347 " ideal model delta sigma weight residual 116.54 109.69 6.85 1.15e+00 7.56e-01 3.55e+01 angle pdb=" C PHE C 347 " pdb=" CA PHE C 347 " pdb=" CB PHE C 347 " ideal model delta sigma weight residual 116.54 109.71 6.83 1.15e+00 7.56e-01 3.52e+01 angle pdb=" C PHE A 347 " pdb=" CA PHE A 347 " pdb=" CB PHE A 347 " ideal model delta sigma weight residual 116.54 109.72 6.82 1.15e+00 7.56e-01 3.52e+01 angle pdb=" N GLN C 563 " pdb=" CA GLN C 563 " pdb=" C GLN C 563 " ideal model delta sigma weight residual 108.00 116.69 -8.69 1.48e+00 4.57e-01 3.45e+01 ... (remaining 43663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 17765 17.46 - 34.91: 1567 34.91 - 52.37: 205 52.37 - 69.83: 53 69.83 - 87.28: 33 Dihedral angle restraints: 19623 sinusoidal: 8136 harmonic: 11487 Sorted by residual: dihedral pdb=" C GLN C 563 " pdb=" N GLN C 563 " pdb=" CA GLN C 563 " pdb=" CB GLN C 563 " ideal model delta harmonic sigma weight residual -122.60 -135.36 12.76 0 2.50e+00 1.60e-01 2.61e+01 dihedral pdb=" CA ARG B 158 " pdb=" C ARG B 158 " pdb=" N VAL B 159 " pdb=" CA VAL B 159 " ideal model delta harmonic sigma weight residual 180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA ARG A 158 " pdb=" C ARG A 158 " pdb=" N VAL A 159 " pdb=" CA VAL A 159 " ideal model delta harmonic sigma weight residual -180.00 -157.04 -22.96 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 19620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4762 0.096 - 0.192: 279 0.192 - 0.289: 15 0.289 - 0.385: 4 0.385 - 0.481: 1 Chirality restraints: 5061 Sorted by residual: chirality pdb=" CA GLN C 563 " pdb=" N GLN C 563 " pdb=" C GLN C 563 " pdb=" CB GLN C 563 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 chirality pdb=" C1 NAG C2008 " pdb=" ND2 ASN C 709 " pdb=" C2 NAG C2008 " pdb=" O5 NAG C2008 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C1 NAG B2008 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B2008 " pdb=" O5 NAG B2008 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.13e+00 ... (remaining 5058 not shown) Planarity restraints: 5616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 66 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.37e+01 pdb=" C GLY E 66 " -0.064 2.00e-02 2.50e+03 pdb=" O GLY E 66 " 0.024 2.00e-02 2.50e+03 pdb=" N PHE E 67 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 190 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.78e+00 pdb=" C ARG B 190 " 0.038 2.00e-02 2.50e+03 pdb=" O ARG B 190 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU B 191 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 190 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ARG A 190 " 0.036 2.00e-02 2.50e+03 pdb=" O ARG A 190 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 191 " -0.012 2.00e-02 2.50e+03 ... (remaining 5613 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1226 2.71 - 3.26: 31968 3.26 - 3.80: 49426 3.80 - 4.35: 58990 4.35 - 4.90: 99379 Nonbonded interactions: 240989 Sorted by model distance: nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.159 2.440 nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.160 2.440 nonbonded pdb=" OG1 THR B 618 " pdb=" OE1 GLU B 619 " model vdw 2.168 2.440 nonbonded pdb=" O GLN C 804 " pdb=" OG SER C 816 " model vdw 2.191 2.440 nonbonded pdb=" O GLN B 804 " pdb=" OG SER B 816 " model vdw 2.200 2.440 ... (remaining 240984 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 29.180 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 85.420 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 128.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 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 : 0.005 0.062 32082 Z= 0.294 Angle : 0.760 12.260 43668 Z= 0.421 Chirality : 0.050 0.481 5061 Planarity : 0.004 0.043 5577 Dihedral : 13.245 87.283 12138 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.30 % Favored : 91.62 % Rotamer: Outliers : 0.03 % Allowed : 0.93 % Favored : 99.04 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % 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: -1.63 (0.13), residues: 3891 helix: 1.44 (0.22), residues: 633 sheet: -0.90 (0.17), residues: 861 loop : -1.95 (0.12), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 103 HIS 0.009 0.001 HIS C 245 PHE 0.022 0.002 PHE C 906 TYR 0.027 0.001 TYR A 265 ARG 0.004 0.000 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7329 (p90) cc_final: 0.6780 (p90) REVERT: A 333 THR cc_start: 0.8046 (t) cc_final: 0.7825 (m) REVERT: H 100 MET cc_start: 0.7837 (tpp) cc_final: 0.7438 (tpp) REVERT: L 3 ARG cc_start: 0.7292 (mmp-170) cc_final: 0.6858 (tmm160) REVERT: L 74 THR cc_start: 0.6171 (p) cc_final: 0.5914 (p) REVERT: B 869 MET cc_start: 0.7042 (mtm) cc_final: 0.6806 (mtm) REVERT: D 100 MET cc_start: 0.7622 (tpp) cc_final: 0.7387 (tpp) REVERT: E 74 THR cc_start: 0.5246 (p) cc_final: 0.5043 (p) REVERT: J 100 MET cc_start: 0.7904 (tpp) cc_final: 0.7304 (tpp) REVERT: K 74 THR cc_start: 0.5835 (p) cc_final: 0.5567 (p) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.4047 time to fit residues: 178.8550 Evaluate side-chains 173 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 329 optimal weight: 0.9990 chunk 295 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 100 optimal weight: 0.9990 chunk 199 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 185 optimal weight: 0.0570 chunk 227 optimal weight: 1.9990 chunk 354 optimal weight: 2.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 460 ASN A 895 GLN L 31 ASN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 777 ASN B 895 GLN E 27 GLN C 422 ASN C 460 ASN C 895 GLN K 27 GLN K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32082 Z= 0.185 Angle : 0.578 10.486 43668 Z= 0.300 Chirality : 0.045 0.300 5061 Planarity : 0.004 0.044 5577 Dihedral : 5.804 55.122 5133 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.27 % Favored : 92.65 % Rotamer: Outliers : 0.15 % Allowed : 4.61 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.14), residues: 3891 helix: 1.60 (0.22), residues: 636 sheet: -0.73 (0.17), residues: 864 loop : -1.89 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 436 HIS 0.009 0.001 HIS B 245 PHE 0.027 0.001 PHE B 186 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 263 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8031 (t) cc_final: 0.7800 (m) REVERT: H 102 VAL cc_start: 0.8052 (t) cc_final: 0.7774 (t) REVERT: L 38 GLN cc_start: 0.6899 (mm110) cc_final: 0.6624 (tp40) REVERT: L 74 THR cc_start: 0.6486 (p) cc_final: 0.6222 (p) REVERT: B 1029 MET cc_start: 0.9093 (tpp) cc_final: 0.8878 (tpp) REVERT: D 102 VAL cc_start: 0.7613 (t) cc_final: 0.7411 (t) REVERT: E 38 GLN cc_start: 0.7942 (mm110) cc_final: 0.7340 (mm110) REVERT: J 3 GLN cc_start: 0.7970 (pm20) cc_final: 0.6874 (tm-30) REVERT: J 100 MET cc_start: 0.7935 (tpp) cc_final: 0.7417 (tpp) REVERT: J 102 VAL cc_start: 0.7783 (t) cc_final: 0.7366 (t) REVERT: K 74 THR cc_start: 0.6255 (p) cc_final: 0.6017 (p) outliers start: 5 outliers final: 0 residues processed: 268 average time/residue: 0.3974 time to fit residues: 178.4972 Evaluate side-chains 180 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 196 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 294 optimal weight: 9.9990 chunk 241 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 354 optimal weight: 3.9990 chunk 383 optimal weight: 2.9990 chunk 315 optimal weight: 0.6980 chunk 351 optimal weight: 8.9990 chunk 120 optimal weight: 8.9990 chunk 284 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 32082 Z= 0.274 Angle : 0.617 10.079 43668 Z= 0.321 Chirality : 0.045 0.276 5061 Planarity : 0.004 0.071 5577 Dihedral : 5.692 56.770 5133 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.56 % Favored : 91.36 % Rotamer: Outliers : 0.03 % Allowed : 5.34 % Favored : 94.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.57 (0.13), residues: 3891 helix: 1.40 (0.21), residues: 624 sheet: -0.71 (0.17), residues: 903 loop : -1.97 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 35A HIS 0.007 0.001 HIS A 245 PHE 0.023 0.002 PHE B 186 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG C 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 263 time to evaluate : 3.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 THR cc_start: 0.8115 (t) cc_final: 0.7910 (m) REVERT: H 102 VAL cc_start: 0.7929 (t) cc_final: 0.7507 (t) REVERT: L 38 GLN cc_start: 0.6891 (mm110) cc_final: 0.6552 (tp40) REVERT: L 74 THR cc_start: 0.6593 (p) cc_final: 0.6317 (p) REVERT: D 2 VAL cc_start: 0.7215 (t) cc_final: 0.6889 (m) REVERT: D 102 VAL cc_start: 0.7809 (t) cc_final: 0.7255 (t) REVERT: E 74 THR cc_start: 0.5600 (p) cc_final: 0.5354 (p) REVERT: C 473 TYR cc_start: 0.4908 (p90) cc_final: 0.4660 (p90) REVERT: J 100 MET cc_start: 0.7960 (tpp) cc_final: 0.7550 (tpp) REVERT: J 102 VAL cc_start: 0.7833 (t) cc_final: 0.7304 (t) REVERT: K 38 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7755 (mm-40) REVERT: K 74 THR cc_start: 0.6358 (p) cc_final: 0.6123 (p) outliers start: 1 outliers final: 0 residues processed: 264 average time/residue: 0.4151 time to fit residues: 180.7833 Evaluate side-chains 183 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 350 optimal weight: 1.9990 chunk 266 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 0.9990 chunk 238 optimal weight: 10.0000 chunk 356 optimal weight: 0.5980 chunk 376 optimal weight: 30.0000 chunk 186 optimal weight: 1.9990 chunk 337 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 978 ASN K 27 GLN K 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32082 Z= 0.209 Angle : 0.586 10.286 43668 Z= 0.302 Chirality : 0.045 0.284 5061 Planarity : 0.004 0.072 5577 Dihedral : 5.342 55.255 5133 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.61 % Favored : 92.32 % Rotamer: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.46 (0.14), residues: 3891 helix: 1.74 (0.22), residues: 603 sheet: -0.68 (0.18), residues: 852 loop : -1.90 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 103 HIS 0.006 0.001 HIS B 245 PHE 0.021 0.002 PHE A 377 TYR 0.017 0.001 TYR C 266 ARG 0.005 0.000 ARG K 3 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 267 time to evaluate : 3.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7108 (p90) cc_final: 0.6798 (p90) REVERT: L 38 GLN cc_start: 0.6839 (mm110) cc_final: 0.6461 (tp40) REVERT: L 74 THR cc_start: 0.6547 (p) cc_final: 0.6297 (p) REVERT: D 102 VAL cc_start: 0.7794 (t) cc_final: 0.7258 (t) REVERT: E 74 THR cc_start: 0.5466 (p) cc_final: 0.5218 (p) REVERT: C 265 TYR cc_start: 0.7148 (p90) cc_final: 0.6769 (p90) REVERT: C 473 TYR cc_start: 0.4829 (p90) cc_final: 0.4574 (p90) REVERT: J 3 GLN cc_start: 0.7683 (pm20) cc_final: 0.7171 (tm-30) REVERT: J 102 VAL cc_start: 0.7770 (t) cc_final: 0.7351 (t) REVERT: K 74 THR cc_start: 0.6324 (p) cc_final: 0.6030 (p) outliers start: 3 outliers final: 0 residues processed: 270 average time/residue: 0.3954 time to fit residues: 177.9339 Evaluate side-chains 183 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 313 optimal weight: 0.9980 chunk 213 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 321 optimal weight: 4.9990 chunk 260 optimal weight: 30.0000 chunk 0 optimal weight: 30.0000 chunk 192 optimal weight: 0.9980 chunk 338 optimal weight: 0.0030 chunk 95 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 149 ASN A 422 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 149 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32082 Z= 0.182 Angle : 0.576 10.452 43668 Z= 0.297 Chirality : 0.045 0.284 5061 Planarity : 0.004 0.060 5577 Dihedral : 5.069 54.869 5133 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 0.06 % Allowed : 2.09 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.14), residues: 3891 helix: 1.98 (0.22), residues: 603 sheet: -0.71 (0.18), residues: 849 loop : -1.83 (0.13), residues: 2439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 436 HIS 0.006 0.001 HIS C 245 PHE 0.017 0.001 PHE A 800 TYR 0.015 0.001 TYR C 266 ARG 0.005 0.000 ARG E 3 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 261 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7015 (p90) cc_final: 0.6749 (p90) REVERT: H 102 VAL cc_start: 0.7800 (t) cc_final: 0.7442 (t) REVERT: L 74 THR cc_start: 0.6542 (p) cc_final: 0.6268 (p) REVERT: B 869 MET cc_start: 0.7057 (mtm) cc_final: 0.6778 (mtm) REVERT: E 38 GLN cc_start: 0.7429 (mm110) cc_final: 0.6574 (tt0) REVERT: E 74 THR cc_start: 0.5441 (p) cc_final: 0.5180 (p) REVERT: C 265 TYR cc_start: 0.7065 (p90) cc_final: 0.6750 (p90) REVERT: J 3 GLN cc_start: 0.7754 (pm20) cc_final: 0.7256 (tm-30) REVERT: J 100 MET cc_start: 0.8050 (tpp) cc_final: 0.7525 (tpp) REVERT: J 102 VAL cc_start: 0.7910 (t) cc_final: 0.7281 (t) REVERT: K 74 THR cc_start: 0.6421 (p) cc_final: 0.6124 (p) outliers start: 2 outliers final: 0 residues processed: 263 average time/residue: 0.4288 time to fit residues: 188.6117 Evaluate side-chains 185 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 126 optimal weight: 30.0000 chunk 339 optimal weight: 6.9990 chunk 74 optimal weight: 0.0870 chunk 221 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 377 optimal weight: 8.9990 chunk 313 optimal weight: 6.9990 chunk 174 optimal weight: 0.3980 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 198 optimal weight: 5.9990 overall best weight: 0.9138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 777 ASN ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32082 Z= 0.176 Angle : 0.567 11.105 43668 Z= 0.292 Chirality : 0.044 0.284 5061 Planarity : 0.004 0.052 5577 Dihedral : 4.887 54.524 5133 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.99 % Favored : 92.93 % Rotamer: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.36 (0.14), residues: 3891 helix: 1.77 (0.22), residues: 624 sheet: -0.62 (0.18), residues: 843 loop : -1.85 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 35A HIS 0.005 0.001 HIS B 245 PHE 0.020 0.001 PHE L 91 TYR 0.025 0.001 TYR B 265 ARG 0.007 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7045 (p90) cc_final: 0.6816 (p90) REVERT: H 102 VAL cc_start: 0.7962 (t) cc_final: 0.7388 (t) REVERT: L 38 GLN cc_start: 0.6232 (mm110) cc_final: 0.5526 (tt0) REVERT: L 74 THR cc_start: 0.6548 (p) cc_final: 0.6267 (p) REVERT: D 3 GLN cc_start: 0.7680 (pm20) cc_final: 0.7077 (tm-30) REVERT: D 102 VAL cc_start: 0.7553 (t) cc_final: 0.7026 (t) REVERT: E 38 GLN cc_start: 0.7731 (mm110) cc_final: 0.6838 (tt0) REVERT: E 74 THR cc_start: 0.5466 (p) cc_final: 0.5210 (p) REVERT: J 3 GLN cc_start: 0.7761 (pm20) cc_final: 0.7365 (tm-30) REVERT: J 100 MET cc_start: 0.8035 (tpp) cc_final: 0.7645 (tpp) REVERT: J 102 VAL cc_start: 0.7894 (t) cc_final: 0.7239 (t) REVERT: K 74 THR cc_start: 0.6278 (p) cc_final: 0.6004 (p) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.3915 time to fit residues: 165.2855 Evaluate side-chains 179 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 3.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 363 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 275 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 210 optimal weight: 0.0000 chunk 375 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 173 optimal weight: 8.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN B 895 GLN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 32082 Z= 0.163 Angle : 0.569 9.820 43668 Z= 0.294 Chirality : 0.045 0.278 5061 Planarity : 0.004 0.075 5577 Dihedral : 4.769 54.093 5133 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 0.09 % Allowed : 1.39 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.31 (0.14), residues: 3891 helix: 1.92 (0.22), residues: 606 sheet: -0.53 (0.18), residues: 831 loop : -1.83 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 35A HIS 0.005 0.001 HIS C 245 PHE 0.015 0.001 PHE C 888 TYR 0.047 0.001 TYR L 36 ARG 0.018 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 252 time to evaluate : 3.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 VAL cc_start: 0.8008 (t) cc_final: 0.7532 (t) REVERT: L 38 GLN cc_start: 0.6274 (mm110) cc_final: 0.5591 (tt0) REVERT: L 74 THR cc_start: 0.6557 (p) cc_final: 0.6288 (p) REVERT: B 237 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7707 (ptm-80) REVERT: D 3 GLN cc_start: 0.7649 (pm20) cc_final: 0.7115 (tm-30) REVERT: E 3 ARG cc_start: 0.8405 (tmm160) cc_final: 0.7862 (tmm160) REVERT: E 38 GLN cc_start: 0.7716 (mm110) cc_final: 0.6910 (tt0) REVERT: E 74 THR cc_start: 0.5440 (p) cc_final: 0.5182 (p) REVERT: C 473 TYR cc_start: 0.4986 (p90) cc_final: 0.4725 (p90) REVERT: J 3 GLN cc_start: 0.7772 (pm20) cc_final: 0.7420 (tm-30) REVERT: J 100 MET cc_start: 0.7957 (tpp) cc_final: 0.7600 (tpp) REVERT: J 102 VAL cc_start: 0.7909 (t) cc_final: 0.7258 (t) REVERT: K 38 GLN cc_start: 0.7654 (mm110) cc_final: 0.6571 (tt0) REVERT: K 74 THR cc_start: 0.6290 (p) cc_final: 0.6007 (p) outliers start: 3 outliers final: 0 residues processed: 255 average time/residue: 0.3971 time to fit residues: 169.1073 Evaluate side-chains 180 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 232 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 224 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 73 optimal weight: 0.0040 chunk 72 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 256 optimal weight: 50.0000 chunk 185 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 295 optimal weight: 0.0670 overall best weight: 1.0934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 895 GLN B 928 ASN ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 32082 Z= 0.189 Angle : 0.580 9.728 43668 Z= 0.299 Chirality : 0.045 0.272 5061 Planarity : 0.004 0.056 5577 Dihedral : 4.788 55.014 5133 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 0.06 % Allowed : 0.96 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.38 (0.14), residues: 3891 helix: 1.63 (0.22), residues: 624 sheet: -0.52 (0.18), residues: 858 loop : -1.87 (0.13), residues: 2409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 35A HIS 0.005 0.001 HIS A 245 PHE 0.021 0.001 PHE A 888 TYR 0.021 0.001 TYR B 265 ARG 0.007 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 3.509 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: H 102 VAL cc_start: 0.8031 (t) cc_final: 0.7412 (t) REVERT: L 74 THR cc_start: 0.6536 (p) cc_final: 0.6242 (p) REVERT: D 3 GLN cc_start: 0.7660 (pm20) cc_final: 0.7174 (tm-30) REVERT: D 102 VAL cc_start: 0.7558 (t) cc_final: 0.7156 (t) REVERT: E 38 GLN cc_start: 0.7689 (mm110) cc_final: 0.6935 (tt0) REVERT: E 74 THR cc_start: 0.5478 (p) cc_final: 0.5216 (p) REVERT: C 237 ARG cc_start: 0.8244 (mtp-110) cc_final: 0.7639 (ptm-80) REVERT: C 473 TYR cc_start: 0.4912 (p90) cc_final: 0.4602 (p90) REVERT: J 3 GLN cc_start: 0.7795 (pm20) cc_final: 0.7579 (tm-30) REVERT: J 66 ARG cc_start: 0.7562 (mpp80) cc_final: 0.7152 (mmm160) REVERT: J 102 VAL cc_start: 0.7936 (t) cc_final: 0.7307 (t) REVERT: K 38 GLN cc_start: 0.7741 (mm110) cc_final: 0.6500 (tt0) REVERT: K 74 THR cc_start: 0.6137 (p) cc_final: 0.5841 (p) outliers start: 2 outliers final: 0 residues processed: 256 average time/residue: 0.3984 time to fit residues: 169.8962 Evaluate side-chains 175 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 3.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 341 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 350 optimal weight: 0.6980 chunk 210 optimal weight: 0.0370 chunk 152 optimal weight: 5.9990 chunk 275 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 331 optimal weight: 5.9990 chunk 349 optimal weight: 0.9980 overall best weight: 1.1060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32082 Z= 0.190 Angle : 0.581 9.755 43668 Z= 0.299 Chirality : 0.045 0.274 5061 Planarity : 0.004 0.054 5577 Dihedral : 4.794 54.891 5133 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.53 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.40 (0.14), residues: 3891 helix: 1.56 (0.22), residues: 624 sheet: -0.54 (0.18), residues: 840 loop : -1.86 (0.13), residues: 2427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 35A HIS 0.005 0.001 HIS A 245 PHE 0.023 0.001 PHE A 888 TYR 0.020 0.001 TYR K 36 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 3.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 102 VAL cc_start: 0.8085 (t) cc_final: 0.7588 (t) REVERT: L 74 THR cc_start: 0.6532 (p) cc_final: 0.6255 (p) REVERT: B 237 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7729 (ptm-80) REVERT: D 3 GLN cc_start: 0.7703 (pm20) cc_final: 0.7252 (tm-30) REVERT: D 102 VAL cc_start: 0.7651 (t) cc_final: 0.7160 (t) REVERT: E 3 ARG cc_start: 0.8405 (tmm160) cc_final: 0.7684 (tmm160) REVERT: E 38 GLN cc_start: 0.7669 (mm110) cc_final: 0.6965 (tt0) REVERT: E 74 THR cc_start: 0.5408 (p) cc_final: 0.5138 (p) REVERT: C 237 ARG cc_start: 0.8237 (mtp-110) cc_final: 0.7655 (ptm-80) REVERT: J 3 GLN cc_start: 0.7907 (pm20) cc_final: 0.7589 (tm-30) REVERT: J 63 LEU cc_start: 0.8426 (tp) cc_final: 0.8225 (tp) REVERT: J 102 VAL cc_start: 0.7920 (t) cc_final: 0.7265 (t) REVERT: K 74 THR cc_start: 0.6178 (p) cc_final: 0.5903 (p) outliers start: 0 outliers final: 0 residues processed: 257 average time/residue: 0.3946 time to fit residues: 169.0632 Evaluate side-chains 174 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 230 optimal weight: 1.9990 chunk 370 optimal weight: 40.0000 chunk 226 optimal weight: 0.9980 chunk 175 optimal weight: 40.0000 chunk 257 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 357 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 189 optimal weight: 0.2980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 32082 Z= 0.289 Angle : 0.641 9.703 43668 Z= 0.332 Chirality : 0.046 0.263 5061 Planarity : 0.004 0.056 5577 Dihedral : 5.190 57.315 5133 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.84 % Favored : 91.08 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.60 (0.14), residues: 3891 helix: 1.20 (0.21), residues: 624 sheet: -0.61 (0.18), residues: 861 loop : -1.97 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 35A HIS 0.005 0.001 HIS A 245 PHE 0.026 0.002 PHE A 888 TYR 0.023 0.001 TYR K 36 ARG 0.006 0.000 ARG B 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7782 Ramachandran restraints generated. 3891 Oldfield, 0 Emsley, 3891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 4.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.4457 (t80) cc_final: 0.4219 (t80) REVERT: A 265 TYR cc_start: 0.7175 (p90) cc_final: 0.6838 (p90) REVERT: H 102 VAL cc_start: 0.8023 (t) cc_final: 0.7511 (t) REVERT: L 38 GLN cc_start: 0.6635 (mm110) cc_final: 0.5014 (tt0) REVERT: L 74 THR cc_start: 0.6651 (p) cc_final: 0.6359 (p) REVERT: D 3 GLN cc_start: 0.7697 (pm20) cc_final: 0.7295 (tm-30) REVERT: D 102 VAL cc_start: 0.7649 (t) cc_final: 0.7142 (t) REVERT: E 3 ARG cc_start: 0.8475 (tmm160) cc_final: 0.7788 (tmm160) REVERT: E 38 GLN cc_start: 0.7499 (mm110) cc_final: 0.6953 (tt0) REVERT: E 74 THR cc_start: 0.5476 (p) cc_final: 0.5198 (p) REVERT: J 3 GLN cc_start: 0.7917 (pm20) cc_final: 0.7660 (tm-30) REVERT: J 102 VAL cc_start: 0.8001 (t) cc_final: 0.7348 (t) REVERT: K 38 GLN cc_start: 0.7533 (mm110) cc_final: 0.6306 (tt0) REVERT: K 44 PRO cc_start: 0.6736 (Cg_exo) cc_final: 0.6206 (Cg_endo) REVERT: K 74 THR cc_start: 0.6169 (p) cc_final: 0.5878 (p) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.3889 time to fit residues: 156.5241 Evaluate side-chains 174 residues out of total 3450 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 3.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 245 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 309 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 318 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.119702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.100232 restraints weight = 112053.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.094830 restraints weight = 142856.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.091995 restraints weight = 164247.355| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32082 Z= 0.201 Angle : 0.602 11.816 43668 Z= 0.309 Chirality : 0.045 0.281 5061 Planarity : 0.004 0.050 5577 Dihedral : 4.989 55.046 5133 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.92 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.48 (0.14), residues: 3891 helix: 1.39 (0.22), residues: 624 sheet: -0.59 (0.18), residues: 864 loop : -1.89 (0.13), residues: 2403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 886 HIS 0.005 0.001 HIS C 245 PHE 0.026 0.002 PHE C 888 TYR 0.023 0.001 TYR K 36 ARG 0.006 0.000 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5244.87 seconds wall clock time: 97 minutes 34.50 seconds (5854.50 seconds total)