Starting phenix.real_space_refine on Wed Feb 21 08:30:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3m_25663/02_2024/7t3m_25663.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3m_25663/02_2024/7t3m_25663.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3m_25663/02_2024/7t3m_25663.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3m_25663/02_2024/7t3m_25663.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3m_25663/02_2024/7t3m_25663.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t3m_25663/02_2024/7t3m_25663.pdb" } resolution = 3.0 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= 0.012 sd= 1.242 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19134 2.51 5 N 4926 2.21 5 O 5907 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 281": "OE1" <-> "OE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 780": "OE1" <-> "OE2" Residue "G TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30099 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "C" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "D" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "G" Number of atoms: 8013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8013 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 51, 'TRANS': 973} Chain breaks: 7 Chain: "H" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Chain: "J" Number of atoms: 832 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 110, 832 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "K" Number of atoms: 832 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 110, 832 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 110, 832 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "B" 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: "E" 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: "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: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "G" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 15.81, per 1000 atoms: 0.53 Number of scatterers: 30099 At special positions: 0 Unit cell: (154.8, 161.1, 201.6, 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 132 16.00 O 5907 8.00 N 4926 7.00 C 19134 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 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 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.03 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 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 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 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=2.03 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 D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 166 " distance=2.03 Simple disulfide: pdb=" SG CYS G 291 " - pdb=" SG CYS G 301 " distance=2.03 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS G 538 " - pdb=" SG CYS G 590 " distance=2.04 Simple disulfide: pdb=" SG CYS G 617 " - pdb=" SG CYS G 649 " distance=2.03 Simple disulfide: pdb=" SG CYS G 662 " - pdb=" SG CYS G 671 " distance=2.03 Simple disulfide: pdb=" SG CYS G 738 " - pdb=" SG CYS G 760 " distance=2.03 Simple disulfide: pdb=" SG CYS G 743 " - pdb=" SG CYS G 749 " distance=2.03 Simple disulfide: pdb=" SG CYS G1032 " - pdb=" SG CYS G1043 " distance=2.03 Simple disulfide: pdb=" SG CYS G1082 " - pdb=" SG CYS G1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A1201 " - " ASN A 61 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A 165 " " NAG A1204 " - " ASN A 234 " " NAG A1205 " - " ASN A 282 " " NAG A1206 " - " ASN A 331 " " NAG A1207 " - " ASN A 343 " " NAG A1208 " - " ASN A 603 " " NAG A1209 " - " ASN A 616 " " NAG A1210 " - " ASN A 657 " " NAG A1211 " - " ASN A 709 " " NAG A1212 " - " ASN A 801 " " NAG A1213 " - " ASN A1074 " " NAG A1214 " - " ASN A1098 " " NAG A1215 " - " ASN A1134 " " NAG B 1 " - " ASN A 717 " " NAG C1201 " - " ASN C 61 " " NAG C1202 " - " ASN C 122 " " NAG C1203 " - " ASN C 165 " " NAG C1204 " - " ASN C 234 " " NAG C1205 " - " ASN C 282 " " NAG C1206 " - " ASN C 331 " " NAG C1207 " - " ASN C 343 " " NAG C1208 " - " ASN C 603 " " NAG C1209 " - " ASN C 616 " " NAG C1210 " - " ASN C 657 " " NAG C1211 " - " ASN C 709 " " NAG C1212 " - " ASN C 801 " " NAG C1213 " - " ASN C1074 " " NAG C1214 " - " ASN C1098 " " NAG C1215 " - " ASN C1134 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN G 717 " " NAG G1201 " - " ASN G 61 " " NAG G1202 " - " ASN G 122 " " NAG G1203 " - " ASN G 165 " " NAG G1204 " - " ASN G 234 " " NAG G1205 " - " ASN G 282 " " NAG G1206 " - " ASN G 331 " " NAG G1207 " - " ASN G 343 " " NAG G1208 " - " ASN G 603 " " NAG G1209 " - " ASN G 616 " " NAG G1210 " - " ASN G 657 " " NAG G1211 " - " ASN G 709 " " NAG G1212 " - " ASN G 801 " " NAG G1213 " - " ASN G1074 " " NAG G1214 " - " ASN G1098 " " NAG G1215 " - " ASN G1134 " Time building additional restraints: 11.10 Conformation dependent library (CDL) restraints added in 5.1 seconds 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 63 sheets defined 21.7% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.914A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 4.602A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (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 'A' and resid 1140 through 1148 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.646A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.913A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.675A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1033 removed outlier: 4.603A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (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 'C' and resid 1140 through 1148 Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.955A pdb=" N LYS D 64 " --> pdb=" O PRO D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR D 87 " --> pdb=" O PRO D 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 304 Processing helix chain 'G' and resid 338 through 343 Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 383 through 387 removed outlier: 3.645A pdb=" N LEU G 387 " --> pdb=" O PRO G 384 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 3.914A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'G' and resid 737 through 743 Processing helix chain 'G' and resid 746 through 754 Processing helix chain 'G' and resid 758 through 783 removed outlier: 3.676A pdb=" N GLU G 773 " --> pdb=" O GLY G 769 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN G 774 " --> pdb=" O ILE G 770 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASP G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS G 776 " --> pdb=" O VAL G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 826 Processing helix chain 'G' and resid 866 through 884 Processing helix chain 'G' and resid 886 through 890 Processing helix chain 'G' and resid 897 through 909 Processing helix chain 'G' and resid 913 through 918 Processing helix chain 'G' and resid 919 through 940 Processing helix chain 'G' and resid 945 through 965 removed outlier: 3.602A pdb=" N VAL G 951 " --> pdb=" O LYS G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 966 through 968 No H-bonds generated for 'chain 'G' and resid 966 through 968' Processing helix chain 'G' and resid 976 through 984 Processing helix chain 'G' and resid 985 through 988 Processing helix chain 'G' and resid 989 through 1033 removed outlier: 4.603A pdb=" N ARG G 995 " --> pdb=" O VAL G 991 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 996 " --> pdb=" O GLN G 992 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA G1016 " --> pdb=" O LEU G1012 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU G1017 " --> pdb=" O ILE G1013 " (cutoff:3.500A) Processing helix chain 'G' and resid 1116 through 1118 No H-bonds generated for 'chain 'G' and resid 1116 through 1118' Processing helix chain 'G' and resid 1140 through 1148 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.956A pdb=" N LYS H 64 " --> pdb=" O PRO H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR H 87 " --> pdb=" O PRO H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.956A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.615A pdb=" N THR I 87 " --> pdb=" O PRO I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 27B through 31 removed outlier: 3.898A pdb=" N ASN J 31 " --> pdb=" O ILE J 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 27B through 31 removed outlier: 3.897A pdb=" N ASN K 31 " --> pdb=" O ILE K 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 27B through 31 removed outlier: 3.898A pdb=" N ASN L 31 " --> pdb=" O ILE L 28 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 8.299A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.674A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.788A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 140 removed outlier: 8.031A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.467A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 359 removed outlier: 3.855A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 538 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.573A pdb=" N PHE A 565 " --> pdb=" O PHE G 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.503A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL A1094 " --> pdb=" O THR A1105 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.617A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.786A 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 1083 removed outlier: 5.066A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 29 through 31 removed outlier: 8.299A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.675A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.788A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 135 through 140 removed outlier: 8.030A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.467A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 359 removed outlier: 3.856A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AC9, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.504A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.616A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 788 through 790 removed outlier: 5.768A pdb=" N ILE C 788 " --> pdb=" O ASN G 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 1081 through 1083 removed outlier: 5.066A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 3 through 7 removed outlier: 3.537A pdb=" N THR D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 18 " --> pdb=" O MET D 82 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET D 82 " --> pdb=" O LEU D 18 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 29 through 31 removed outlier: 8.299A pdb=" N ASN G 61 " --> pdb=" O TYR G 269 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N TYR G 269 " --> pdb=" O ASN G 61 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G 227 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER G 205 " --> pdb=" O PRO G 225 " (cutoff:3.500A) removed outlier: 9.712A pdb=" N HIS G 207 " --> pdb=" O LEU G 223 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LEU G 223 " --> pdb=" O HIS G 207 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL G 36 " --> pdb=" O LEU G 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 48 through 55 removed outlier: 3.675A pdb=" N ASP G 53 " --> pdb=" O ARG G 273 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 271 " --> pdb=" O PHE G 55 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP G 287 " --> pdb=" O LYS G 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 84 through 85 removed outlier: 3.788A pdb=" N GLY G 103 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ARG G 102 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 135 through 140 removed outlier: 8.030A pdb=" N VAL G 159 " --> pdb=" O CYS G 136 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 311 through 319 removed outlier: 5.468A pdb=" N ILE G 312 " --> pdb=" O THR G 599 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR G 599 " --> pdb=" O ILE G 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN G 314 " --> pdb=" O VAL G 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 597 " --> pdb=" O GLN G 314 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER G 316 " --> pdb=" O VAL G 595 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 356 through 359 removed outlier: 3.855A pdb=" N ASN G 394 " --> pdb=" O GLU G 516 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'G' and resid 538 through 543 Processing sheet with id=AE8, first strand: chain 'G' and resid 654 through 660 removed outlier: 5.503A pdb=" N THR G 696 " --> pdb=" O VAL G 656 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASN G 658 " --> pdb=" O THR G 696 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE G 670 " --> pdb=" O ILE G 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER G 711 " --> pdb=" O THR G1076 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR G1076 " --> pdb=" O SER G 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 713 " --> pdb=" O ASN G1074 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN G1074 " --> pdb=" O ALA G 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU G1072 " --> pdb=" O PRO G 715 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLY G1059 " --> pdb=" O SER G1055 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N SER G1055 " --> pdb=" O GLY G1059 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL G1061 " --> pdb=" O PRO G1053 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU G1063 " --> pdb=" O SER G1051 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER G1051 " --> pdb=" O LEU G1063 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL G1065 " --> pdb=" O LEU G1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 711 through 728 removed outlier: 6.717A pdb=" N SER G 711 " --> pdb=" O THR G1076 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N THR G1076 " --> pdb=" O SER G 711 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 713 " --> pdb=" O ASN G1074 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN G1074 " --> pdb=" O ALA G 713 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU G1072 " --> pdb=" O PRO G 715 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA G1078 " --> pdb=" O PHE G1095 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE G1095 " --> pdb=" O ALA G1078 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL G1094 " --> pdb=" O THR G1105 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 733 through 736 removed outlier: 4.616A pdb=" N LYS G 733 " --> pdb=" O LEU G 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 1081 through 1083 removed outlier: 5.065A pdb=" N ALA G1087 " --> pdb=" O SER G1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.536A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.573A pdb=" N VAL H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.537A pdb=" N THR I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU I 18 " --> pdb=" O MET I 82 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET I 82 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.572A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.572A pdb=" N VAL I 12 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AG2, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR J 105 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU J 13 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP J 35 " --> pdb=" O VAL J 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR J 105 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU J 13 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER J 90 " --> pdb=" O VAL J 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL J 97 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AG5, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.814A pdb=" N THR K 105 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU K 13 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP K 35 " --> pdb=" O VAL K 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 9 through 13 removed outlier: 3.814A pdb=" N THR K 105 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU K 13 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER K 90 " --> pdb=" O VAL K 97 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL K 97 " --> pdb=" O SER K 90 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AG8, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.815A pdb=" N THR L 105 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER L 90 " --> pdb=" O VAL L 97 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 97 " --> pdb=" O SER L 90 " (cutoff:3.500A) 1159 hydrogen bonds defined for protein. 3144 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: 17.97 Time building geometry restraints manager: 11.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 9552 1.34 - 1.46: 7540 1.46 - 1.58: 13514 1.58 - 1.70: 0 1.70 - 1.82: 171 Bond restraints: 30777 Sorted by residual: bond pdb=" N VAL C 130 " pdb=" CA VAL C 130 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.94e+00 bond pdb=" N VAL A 130 " pdb=" CA VAL A 130 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.69e+00 bond pdb=" N VAL G 130 " pdb=" CA VAL G 130 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.57e+00 bond pdb=" N PHE H 100A" pdb=" CA PHE H 100A" ideal model delta sigma weight residual 1.459 1.492 -0.033 1.41e-02 5.03e+03 5.47e+00 bond pdb=" C TYR H 100B" pdb=" N PRO H 100C" ideal model delta sigma weight residual 1.326 1.357 -0.031 1.44e-02 4.82e+03 4.54e+00 ... (remaining 30772 not shown) Histogram of bond angle deviations from ideal: 100.38 - 107.68: 1128 107.68 - 114.99: 18229 114.99 - 122.29: 16974 122.29 - 129.60: 5426 129.60 - 136.90: 120 Bond angle restraints: 41877 Sorted by residual: angle pdb=" CB MET I 82C" pdb=" CG MET I 82C" pdb=" SD MET I 82C" ideal model delta sigma weight residual 112.70 122.25 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET H 82C" pdb=" CG MET H 82C" pdb=" SD MET H 82C" ideal model delta sigma weight residual 112.70 122.23 -9.53 3.00e+00 1.11e-01 1.01e+01 angle pdb=" CB MET D 82C" pdb=" CG MET D 82C" pdb=" SD MET D 82C" ideal model delta sigma weight residual 112.70 122.22 -9.52 3.00e+00 1.11e-01 1.01e+01 angle pdb=" OG1 THR H 32 " pdb=" CB THR H 32 " pdb=" CG2 THR H 32 " ideal model delta sigma weight residual 109.30 103.30 6.00 2.00e+00 2.50e-01 9.00e+00 angle pdb=" C ASN A 87 " pdb=" N ASP A 88 " pdb=" CA ASP A 88 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.97e+00 ... (remaining 41872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 17271 17.15 - 34.30: 1328 34.30 - 51.46: 253 51.46 - 68.61: 102 68.61 - 85.76: 39 Dihedral angle restraints: 18993 sinusoidal: 8040 harmonic: 10953 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -35.19 -50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -35.19 -50.81 1 1.00e+01 1.00e-02 3.53e+01 dihedral pdb=" CB CYS G1082 " pdb=" SG CYS G1082 " pdb=" SG CYS G1126 " pdb=" CB CYS G1126 " ideal model delta sinusoidal sigma weight residual -86.00 -35.20 -50.80 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 18990 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3796 0.051 - 0.102: 859 0.102 - 0.153: 226 0.153 - 0.203: 12 0.203 - 0.254: 9 Chirality restraints: 4902 Sorted by residual: chirality pdb=" CA VAL A 130 " pdb=" N VAL A 130 " pdb=" C VAL A 130 " pdb=" CB VAL A 130 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA VAL G 130 " pdb=" N VAL G 130 " pdb=" C VAL G 130 " pdb=" CB VAL G 130 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL C 130 " pdb=" N VAL C 130 " pdb=" C VAL C 130 " pdb=" CB VAL C 130 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4899 not shown) Planarity restraints: 5379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 83 " 0.043 5.00e-02 4.00e+02 6.59e-02 6.94e+00 pdb=" N PRO D 84 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 84 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 83 " 0.043 5.00e-02 4.00e+02 6.58e-02 6.94e+00 pdb=" N PRO H 84 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO H 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 84 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP I 83 " 0.043 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO I 84 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO I 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO I 84 " 0.036 5.00e-02 4.00e+02 ... (remaining 5376 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1603 2.73 - 3.28: 28428 3.28 - 3.82: 46881 3.82 - 4.36: 54132 4.36 - 4.90: 99294 Nonbonded interactions: 230338 Sorted by model distance: nonbonded pdb=" OG1 THR H 31 " pdb=" CG2 VAL H 34 " model vdw 2.194 3.460 nonbonded pdb=" OG1 THR D 31 " pdb=" CG2 VAL D 34 " model vdw 2.196 3.460 nonbonded pdb=" OG1 THR I 31 " pdb=" CG2 VAL I 34 " model vdw 2.198 3.460 nonbonded pdb=" NZ LYS A 811 " pdb=" OG SER A 813 " model vdw 2.244 2.520 nonbonded pdb=" NZ LYS G 811 " pdb=" OG SER G 813 " model vdw 2.245 2.520 ... (remaining 230333 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 19.110 Check model and map are aligned: 0.470 Set scattering table: 0.290 Process input model: 82.220 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.340 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:14.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.003 0.042 30777 Z= 0.204 Angle : 0.588 11.903 41877 Z= 0.294 Chirality : 0.047 0.254 4902 Planarity : 0.004 0.066 5331 Dihedral : 13.239 85.761 11814 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.03 % Allowed : 0.70 % Favored : 99.27 % 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: -0.02 (0.14), residues: 3711 helix: 1.44 (0.20), residues: 699 sheet: 0.95 (0.18), residues: 849 loop : -0.94 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 64 HIS 0.002 0.000 HIS L 8 PHE 0.021 0.001 PHE D 100A TYR 0.011 0.001 TYR G 266 ARG 0.002 0.000 ARG H 11 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 902 MET cc_start: 0.8459 (mmm) cc_final: 0.8242 (mmp) outliers start: 1 outliers final: 1 residues processed: 228 average time/residue: 1.1128 time to fit residues: 312.8110 Evaluate side-chains 145 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 144 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 1118 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 8.9990 chunk 284 optimal weight: 5.9990 chunk 157 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 293 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 218 optimal weight: 7.9990 chunk 340 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 703 ASN A 901 GLN A 926 GLN C 703 ASN C 901 GLN C 926 GLN C1002 GLN G 703 ASN G 901 GLN G 926 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 30777 Z= 0.505 Angle : 0.712 11.712 41877 Z= 0.369 Chirality : 0.051 0.220 4902 Planarity : 0.005 0.049 5331 Dihedral : 7.853 59.893 5111 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 7.05 % Favored : 91.10 % 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: -0.18 (0.14), residues: 3711 helix: 1.64 (0.22), residues: 681 sheet: 0.80 (0.18), residues: 849 loop : -1.13 (0.13), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 47 HIS 0.005 0.001 HIS G 49 PHE 0.034 0.003 PHE G 906 TYR 0.026 0.002 TYR L 86 ARG 0.006 0.001 ARG G1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 159 time to evaluate : 3.645 Fit side-chains REVERT: A 318 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7876 (p90) outliers start: 61 outliers final: 28 residues processed: 194 average time/residue: 1.2340 time to fit residues: 291.2057 Evaluate side-chains 161 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 3.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain G residue 1092 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 4 LEU Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 4 LEU Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 283 optimal weight: 0.6980 chunk 231 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 341 optimal weight: 0.5980 chunk 368 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 338 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 273 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 926 GLN ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN G 926 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30777 Z= 0.171 Angle : 0.545 10.909 41877 Z= 0.278 Chirality : 0.044 0.223 4902 Planarity : 0.004 0.043 5331 Dihedral : 7.028 57.545 5109 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.03 % Allowed : 10.05 % Favored : 88.92 % 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: 0.05 (0.14), residues: 3711 helix: 1.85 (0.22), residues: 681 sheet: 1.02 (0.18), residues: 855 loop : -1.03 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 64 HIS 0.002 0.001 HIS C1048 PHE 0.013 0.001 PHE D 100A TYR 0.013 0.001 TYR G1067 ARG 0.002 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 143 time to evaluate : 3.456 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.7925 (p90) REVERT: C 166 CYS cc_start: 0.4618 (m) cc_final: 0.4227 (m) REVERT: G 1141 LEU cc_start: 0.8442 (tm) cc_final: 0.8182 (tp) outliers start: 34 outliers final: 22 residues processed: 162 average time/residue: 1.2318 time to fit residues: 244.1616 Evaluate side-chains 153 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 102 ILE Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 75 LYS Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 0.9980 chunk 256 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 162 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 342 optimal weight: 0.5980 chunk 362 optimal weight: 3.9990 chunk 178 optimal weight: 5.9990 chunk 324 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 703 ASN A 901 GLN A 926 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 926 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN G 926 GLN J 89 GLN K 89 GLN L 89 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30777 Z= 0.406 Angle : 0.651 11.034 41877 Z= 0.333 Chirality : 0.048 0.225 4902 Planarity : 0.005 0.046 5331 Dihedral : 7.256 59.903 5109 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.48 % Allowed : 11.69 % Favored : 85.83 % 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: -0.25 (0.14), residues: 3711 helix: 1.71 (0.22), residues: 687 sheet: 0.73 (0.17), residues: 861 loop : -1.23 (0.12), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 HIS 0.004 0.001 HIS C1048 PHE 0.023 0.002 PHE A 906 TYR 0.020 0.002 TYR L 86 ARG 0.004 0.001 ARG G1039 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 147 time to evaluate : 3.550 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.7952 (p90) REVERT: A 489 TYR cc_start: 0.7339 (OUTLIER) cc_final: 0.6373 (m-80) REVERT: C 153 MET cc_start: 0.4877 (ppp) cc_final: 0.4546 (ppp) REVERT: G 153 MET cc_start: 0.5509 (ppp) cc_final: 0.5258 (ppp) REVERT: G 177 MET cc_start: 0.5399 (mmm) cc_final: 0.5196 (mmm) REVERT: H 82 MET cc_start: 0.7586 (tpp) cc_final: 0.7385 (mmp) REVERT: K 83 GLU cc_start: 0.6156 (mm-30) cc_final: 0.5699 (pp20) outliers start: 82 outliers final: 48 residues processed: 209 average time/residue: 1.1333 time to fit residues: 294.7400 Evaluate side-chains 185 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 135 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 489 TYR Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 269 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 250 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 325 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30777 Z= 0.241 Angle : 0.570 10.772 41877 Z= 0.291 Chirality : 0.045 0.231 4902 Planarity : 0.004 0.044 5331 Dihedral : 6.918 59.465 5109 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.30 % Allowed : 13.14 % Favored : 84.56 % 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: -0.21 (0.14), residues: 3711 helix: 1.82 (0.22), residues: 678 sheet: 0.74 (0.18), residues: 864 loop : -1.22 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 47 HIS 0.002 0.001 HIS C1048 PHE 0.012 0.001 PHE G1121 TYR 0.016 0.001 TYR G1067 ARG 0.003 0.000 ARG G 995 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 141 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.5239 (mmm) cc_final: 0.4590 (mpp) REVERT: A 318 PHE cc_start: 0.8663 (OUTLIER) cc_final: 0.7925 (p90) REVERT: A 489 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6290 (m-80) REVERT: A 900 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8225 (mtm) REVERT: C 96 GLU cc_start: 0.4219 (OUTLIER) cc_final: 0.2789 (pm20) REVERT: C 153 MET cc_start: 0.4913 (ppp) cc_final: 0.4542 (ppp) REVERT: C 318 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8241 (p90) REVERT: C 900 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8321 (mtm) REVERT: C 981 LEU cc_start: 0.7904 (pp) cc_final: 0.7690 (mt) REVERT: G 153 MET cc_start: 0.5330 (ppp) cc_final: 0.4952 (ppp) REVERT: K 83 GLU cc_start: 0.6062 (mm-30) cc_final: 0.5679 (pp20) REVERT: L 83 GLU cc_start: 0.6291 (mm-30) cc_final: 0.6043 (pp20) outliers start: 76 outliers final: 46 residues processed: 195 average time/residue: 1.1080 time to fit residues: 268.4531 Evaluate side-chains 185 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 133 time to evaluate : 3.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 198 ASP Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 2.9990 chunk 326 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 120 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN K 52 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30777 Z= 0.336 Angle : 0.625 11.808 41877 Z= 0.316 Chirality : 0.047 0.232 4902 Planarity : 0.004 0.042 5331 Dihedral : 6.980 59.969 5109 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.12 % Allowed : 13.44 % Favored : 83.44 % 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: -0.23 (0.14), residues: 3711 helix: 1.81 (0.22), residues: 678 sheet: 0.70 (0.17), residues: 939 loop : -1.29 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 47 HIS 0.003 0.001 HIS C1048 PHE 0.017 0.002 PHE C 338 TYR 0.016 0.001 TYR L 86 ARG 0.003 0.000 ARG C 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 142 time to evaluate : 3.514 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.4218 (OUTLIER) cc_final: 0.3458 (pp20) REVERT: A 177 MET cc_start: 0.5249 (mmm) cc_final: 0.4909 (mmm) REVERT: A 318 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7942 (p90) REVERT: A 489 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: C 96 GLU cc_start: 0.4064 (OUTLIER) cc_final: 0.3522 (pp20) REVERT: C 153 MET cc_start: 0.4954 (ppp) cc_final: 0.4747 (ppp) REVERT: C 177 MET cc_start: 0.5117 (mmm) cc_final: 0.4731 (mmm) REVERT: C 318 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.8201 (p90) REVERT: C 489 TYR cc_start: 0.7520 (OUTLIER) cc_final: 0.6834 (m-80) REVERT: C 900 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8392 (mtm) REVERT: G 96 GLU cc_start: 0.4182 (OUTLIER) cc_final: 0.3549 (pp20) REVERT: G 153 MET cc_start: 0.5333 (ppp) cc_final: 0.4954 (ppp) REVERT: G 318 PHE cc_start: 0.8693 (OUTLIER) cc_final: 0.8141 (p90) REVERT: K 83 GLU cc_start: 0.6074 (mm-30) cc_final: 0.5791 (pp20) REVERT: L 83 GLU cc_start: 0.6334 (mm-30) cc_final: 0.6021 (pp20) outliers start: 103 outliers final: 57 residues processed: 219 average time/residue: 1.0559 time to fit residues: 291.0164 Evaluate side-chains 201 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 135 time to evaluate : 3.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 318 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 407 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 206 optimal weight: 0.8980 chunk 264 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 305 optimal weight: 0.7980 chunk 202 optimal weight: 0.5980 chunk 361 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 220 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30777 Z= 0.240 Angle : 0.579 10.865 41877 Z= 0.294 Chirality : 0.045 0.234 4902 Planarity : 0.004 0.041 5331 Dihedral : 6.768 58.801 5109 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.79 % Allowed : 14.35 % Favored : 82.86 % 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: -0.15 (0.14), residues: 3711 helix: 1.87 (0.22), residues: 681 sheet: 0.74 (0.17), residues: 939 loop : -1.24 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 47 HIS 0.002 0.001 HIS C1048 PHE 0.013 0.001 PHE C1121 TYR 0.016 0.001 TYR G1067 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 140 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8666 (OUTLIER) cc_final: 0.7920 (p90) REVERT: A 489 TYR cc_start: 0.7366 (OUTLIER) cc_final: 0.6318 (m-80) REVERT: C 96 GLU cc_start: 0.3947 (OUTLIER) cc_final: 0.3520 (pp20) REVERT: C 153 MET cc_start: 0.4950 (ppp) cc_final: 0.4700 (ppp) REVERT: C 177 MET cc_start: 0.5150 (mmm) cc_final: 0.4689 (mmm) REVERT: C 318 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.8228 (p90) REVERT: C 489 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: C 900 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8318 (mtm) REVERT: D 83 ASP cc_start: 0.6741 (t0) cc_final: 0.6359 (p0) REVERT: G 96 GLU cc_start: 0.4028 (OUTLIER) cc_final: 0.3551 (pp20) REVERT: G 153 MET cc_start: 0.5342 (ppp) cc_final: 0.4949 (ppp) REVERT: G 318 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.8110 (p90) REVERT: G 376 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8613 (p) REVERT: K 83 GLU cc_start: 0.6006 (mm-30) cc_final: 0.5721 (pp20) REVERT: L 83 GLU cc_start: 0.6274 (mm-30) cc_final: 0.5992 (pp20) outliers start: 92 outliers final: 62 residues processed: 212 average time/residue: 1.0250 time to fit residues: 274.8646 Evaluate side-chains 206 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 135 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 318 PHE Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 66 ASP Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 246 optimal weight: 1.9990 chunk 178 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 284 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30777 Z= 0.250 Angle : 0.579 10.743 41877 Z= 0.295 Chirality : 0.045 0.234 4902 Planarity : 0.004 0.042 5331 Dihedral : 6.694 58.420 5109 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.85 % Allowed : 14.44 % Favored : 82.71 % 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: -0.14 (0.14), residues: 3711 helix: 1.93 (0.22), residues: 681 sheet: 0.73 (0.17), residues: 939 loop : -1.24 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.002 0.001 HIS A1064 PHE 0.012 0.001 PHE C 338 TYR 0.016 0.001 TYR G1067 ARG 0.002 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 141 time to evaluate : 3.451 Fit side-chains revert: symmetry clash REVERT: A 318 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7900 (p90) REVERT: A 489 TYR cc_start: 0.7418 (OUTLIER) cc_final: 0.6387 (m-80) REVERT: C 96 GLU cc_start: 0.4030 (OUTLIER) cc_final: 0.3617 (pp20) REVERT: C 177 MET cc_start: 0.4977 (mmm) cc_final: 0.4705 (mmm) REVERT: C 318 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8250 (p90) REVERT: C 489 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: C 900 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8327 (mtm) REVERT: D 83 ASP cc_start: 0.6695 (t0) cc_final: 0.6335 (p0) REVERT: G 96 GLU cc_start: 0.4072 (OUTLIER) cc_final: 0.3588 (pp20) REVERT: G 153 MET cc_start: 0.5397 (ppp) cc_final: 0.4991 (ppp) REVERT: G 157 PHE cc_start: 0.6369 (t80) cc_final: 0.5842 (t80) REVERT: G 318 PHE cc_start: 0.8691 (OUTLIER) cc_final: 0.8117 (p90) REVERT: K 82 ASP cc_start: 0.7480 (OUTLIER) cc_final: 0.7272 (p0) REVERT: K 83 GLU cc_start: 0.6032 (mm-30) cc_final: 0.5748 (pp20) REVERT: L 83 GLU cc_start: 0.6236 (mm-30) cc_final: 0.5994 (pp20) outliers start: 94 outliers final: 70 residues processed: 213 average time/residue: 0.9809 time to fit residues: 266.0496 Evaluate side-chains 210 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 131 time to evaluate : 3.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 96 GLU Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 318 PHE Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 82 ASP Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 0.9980 chunk 346 optimal weight: 0.7980 chunk 315 optimal weight: 3.9990 chunk 336 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 264 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 304 optimal weight: 0.9980 chunk 318 optimal weight: 10.0000 chunk 335 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 978 ASN C 245 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN D 77 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30777 Z= 0.162 Angle : 0.548 12.512 41877 Z= 0.277 Chirality : 0.044 0.233 4902 Planarity : 0.004 0.040 5331 Dihedral : 6.441 55.981 5109 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.30 % Allowed : 15.11 % Favored : 82.59 % 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: 0.03 (0.14), residues: 3711 helix: 2.08 (0.22), residues: 681 sheet: 0.79 (0.17), residues: 984 loop : -1.14 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 64 HIS 0.001 0.000 HIS A1064 PHE 0.012 0.001 PHE C1121 TYR 0.016 0.001 TYR G1067 ARG 0.002 0.000 ARG G 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 139 time to evaluate : 3.635 Fit side-chains revert: symmetry clash REVERT: A 96 GLU cc_start: 0.4049 (OUTLIER) cc_final: 0.2711 (pm20) REVERT: A 318 PHE cc_start: 0.8636 (OUTLIER) cc_final: 0.7872 (p90) REVERT: A 489 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.6631 (m-80) REVERT: C 208 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8042 (p) REVERT: C 318 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.8263 (p90) REVERT: C 489 TYR cc_start: 0.7533 (OUTLIER) cc_final: 0.6898 (m-80) REVERT: C 900 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8234 (mtm) REVERT: D 83 ASP cc_start: 0.6608 (t0) cc_final: 0.6328 (p0) REVERT: G 96 GLU cc_start: 0.3962 (OUTLIER) cc_final: 0.3495 (pp20) REVERT: G 153 MET cc_start: 0.5413 (ppp) cc_final: 0.5152 (ppp) REVERT: G 376 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8618 (p) REVERT: K 83 GLU cc_start: 0.6064 (mm-30) cc_final: 0.5811 (pp20) REVERT: L 82 ASP cc_start: 0.7345 (OUTLIER) cc_final: 0.7129 (p0) outliers start: 76 outliers final: 59 residues processed: 202 average time/residue: 1.0451 time to fit residues: 265.4095 Evaluate side-chains 200 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 131 time to evaluate : 3.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 407 VAL Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 376 THR Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 1.9990 chunk 356 optimal weight: 3.9990 chunk 217 optimal weight: 0.0770 chunk 168 optimal weight: 0.9980 chunk 247 optimal weight: 0.2980 chunk 373 optimal weight: 0.9990 chunk 343 optimal weight: 3.9990 chunk 297 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 229 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 978 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 926 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 30777 Z= 0.158 Angle : 0.544 11.622 41877 Z= 0.275 Chirality : 0.044 0.228 4902 Planarity : 0.004 0.040 5331 Dihedral : 6.325 55.382 5109 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.18 % Allowed : 15.50 % Favored : 82.32 % 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: 0.11 (0.14), residues: 3711 helix: 2.20 (0.22), residues: 681 sheet: 0.83 (0.17), residues: 984 loop : -1.10 (0.13), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 64 HIS 0.001 0.000 HIS A1064 PHE 0.052 0.001 PHE A 157 TYR 0.015 0.001 TYR G1067 ARG 0.003 0.000 ARG L 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 139 time to evaluate : 3.349 Fit side-chains revert: symmetry clash REVERT: A 489 TYR cc_start: 0.7367 (OUTLIER) cc_final: 0.6699 (m-80) REVERT: C 208 THR cc_start: 0.8243 (OUTLIER) cc_final: 0.8040 (p) REVERT: C 318 PHE cc_start: 0.8655 (OUTLIER) cc_final: 0.8290 (p90) REVERT: C 489 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6889 (m-80) REVERT: D 83 ASP cc_start: 0.6567 (t0) cc_final: 0.6262 (p0) REVERT: G 96 GLU cc_start: 0.3937 (OUTLIER) cc_final: 0.3464 (pp20) REVERT: G 153 MET cc_start: 0.5336 (ppp) cc_final: 0.4996 (ppp) REVERT: G 318 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.8091 (p90) REVERT: H 43 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7261 (mtmm) REVERT: K 83 GLU cc_start: 0.6078 (mm-30) cc_final: 0.5843 (pp20) outliers start: 72 outliers final: 61 residues processed: 199 average time/residue: 1.0526 time to fit residues: 263.9976 Evaluate side-chains 197 residues out of total 3303 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 130 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 167 THR Chi-restraints excluded: chain A residue 175 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 138 ASP Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 175 PHE Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 489 TYR Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 96 GLU Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain G residue 175 PHE Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain G residue 240 THR Chi-restraints excluded: chain G residue 318 PHE Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 590 CYS Chi-restraints excluded: chain G residue 720 ILE Chi-restraints excluded: chain G residue 754 LEU Chi-restraints excluded: chain G residue 772 VAL Chi-restraints excluded: chain G residue 915 VAL Chi-restraints excluded: chain G residue 934 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 15 THR Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain J residue 74 THR Chi-restraints excluded: chain J residue 97 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain K residue 66 ASP Chi-restraints excluded: chain K residue 74 THR Chi-restraints excluded: chain K residue 97 VAL Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain L residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 2.9990 chunk 316 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 274 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 305 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A 978 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 926 GLN ** G 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 GLN K 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.116075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.085363 restraints weight = 61559.393| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.69 r_work: 0.3145 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3156 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30777 Z= 0.209 Angle : 0.554 11.053 41877 Z= 0.281 Chirality : 0.044 0.228 4902 Planarity : 0.004 0.041 5331 Dihedral : 6.374 56.225 5109 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.30 % Allowed : 15.53 % Favored : 82.17 % 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: 0.08 (0.14), residues: 3711 helix: 2.15 (0.22), residues: 684 sheet: 0.81 (0.17), residues: 984 loop : -1.12 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 64 HIS 0.002 0.000 HIS A1064 PHE 0.045 0.001 PHE G 157 TYR 0.017 0.001 TYR G 200 ARG 0.002 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7036.83 seconds wall clock time: 129 minutes 5.96 seconds (7745.96 seconds total)