Starting phenix.real_space_refine on Tue Nov 21 20:47:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v26_31637/11_2023/7v26_31637.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v26_31637/11_2023/7v26_31637.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v26_31637/11_2023/7v26_31637.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v26_31637/11_2023/7v26_31637.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v26_31637/11_2023/7v26_31637.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v26_31637/11_2023/7v26_31637.pdb" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 153 5.16 5 C 22299 2.51 5 N 5799 2.21 5 O 6906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A ARG 454": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 466": "NH1" <-> "NH2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "C GLU 516": "OE1" <-> "OE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 346": "NH1" <-> "NH2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E ARG 408": "NH1" <-> "NH2" Residue "E ARG 454": "NH1" <-> "NH2" Residue "E ARG 457": "NH1" <-> "NH2" Residue "E ARG 466": "NH1" <-> "NH2" Residue "E PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 60": "NH1" <-> "NH2" Residue "b ARG 192": "NH1" <-> "NH2" Residue "c ARG 60": "NH1" <-> "NH2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d ARG 192": "NH1" <-> "NH2" Residue "e ARG 60": "NH1" <-> "NH2" Residue "f ARG 192": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 35157 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8342 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "C" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8342 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 8342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1076, 8342 Classifications: {'peptide': 1076} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 53, 'TRANS': 1022} Chain breaks: 3 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "a" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "c" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "d" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} Chain: "e" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1664 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 16, 'TRANS': 206} Chain: "f" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 13, 'TRANS': 189} 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 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 chiralities: 15 Chain: "E" 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 chiralities: 15 Time building chain proxies: 16.50, per 1000 atoms: 0.47 Number of scatterers: 35157 At special positions: 0 Unit cell: (207.108, 192.464, 234.304, 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 153 16.00 O 6906 8.00 N 5799 7.00 C 22299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=1.93 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 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 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 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 E 15 " - pdb=" SG CYS E 136 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 291 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.03 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 538 " - pdb=" SG CYS E 590 " distance=2.03 Simple disulfide: pdb=" SG CYS E 617 " - pdb=" SG CYS E 649 " distance=2.03 Simple disulfide: pdb=" SG CYS E 662 " - pdb=" SG CYS E 671 " distance=2.03 Simple disulfide: pdb=" SG CYS E 738 " - pdb=" SG CYS E 760 " distance=2.03 Simple disulfide: pdb=" SG CYS E 743 " - pdb=" SG CYS E 749 " distance=2.03 Simple disulfide: pdb=" SG CYS E1032 " - pdb=" SG CYS E1043 " distance=2.03 Simple disulfide: pdb=" SG CYS E1082 " - pdb=" SG CYS E1126 " distance=2.03 Simple disulfide: pdb=" SG CYS a 22 " - pdb=" SG CYS a 97 " distance=2.03 Simple disulfide: pdb=" SG CYS a 147 " - pdb=" SG CYS a 203 " distance=2.03 Simple disulfide: pdb=" SG CYS b 22 " - pdb=" SG CYS b 90 " distance=2.03 Simple disulfide: pdb=" SG CYS b 137 " - pdb=" SG CYS b 196 " distance=2.03 Simple disulfide: pdb=" SG CYS c 22 " - pdb=" SG CYS c 97 " distance=2.03 Simple disulfide: pdb=" SG CYS c 147 " - pdb=" SG CYS c 203 " distance=2.03 Simple disulfide: pdb=" SG CYS d 22 " - pdb=" SG CYS d 90 " distance=2.04 Simple disulfide: pdb=" SG CYS d 137 " - pdb=" SG CYS d 196 " distance=2.03 Simple disulfide: pdb=" SG CYS e 22 " - pdb=" SG CYS e 97 " distance=2.03 Simple disulfide: pdb=" SG CYS e 147 " - pdb=" SG CYS e 203 " distance=2.03 Simple disulfide: pdb=" SG CYS f 22 " - pdb=" SG CYS f 90 " distance=2.03 Simple disulfide: pdb=" SG CYS f 137 " - pdb=" SG CYS f 196 " 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 NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A 717 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A1098 " " NAG A1310 " - " ASN A1134 " " NAG A1311 " - " ASN A 17 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 331 " " NAG A1314 " - " ASN A 234 " " NAG A1315 " - " ASN A 149 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C 717 " " NAG C1309 " - " ASN C 801 " " NAG C1310 " - " ASN C1098 " " NAG C1311 " - " ASN C1134 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 17 " " NAG C1314 " - " ASN C1074 " " NAG C1315 " - " ASN C 149 " " NAG E1301 " - " ASN E 61 " " NAG E1302 " - " ASN E 165 " " NAG E1303 " - " ASN E 234 " " NAG E1304 " - " ASN E 282 " " NAG E1305 " - " ASN E 331 " " NAG E1306 " - " ASN E 616 " " NAG E1307 " - " ASN E 709 " " NAG E1308 " - " ASN E 717 " " NAG E1309 " - " ASN E 801 " " NAG E1310 " - " ASN E1074 " " NAG E1311 " - " ASN E1098 " " NAG E1312 " - " ASN E1134 " " NAG E1313 " - " ASN E 17 " " NAG E1314 " - " ASN E 149 " " NAG E1315 " - " ASN E 343 " Time building additional restraints: 12.56 Conformation dependent library (CDL) restraints added in 6.0 seconds 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8406 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 77 sheets defined 15.8% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 removed outlier: 3.529A pdb=" N GLU A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.610A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.659A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.550A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.536A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 912 through 916 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.923A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.179A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.604A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 755 Processing helix chain 'C' and resid 758 through 782 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 891 removed outlier: 4.242A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 removed outlier: 3.636A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.107A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.811A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 5.356A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1118 No H-bonds generated for 'chain 'C' and resid 1116 through 1118' Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.388A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 304 removed outlier: 3.560A pdb=" N GLU E 298 " --> pdb=" O ASP E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 364 through 370 removed outlier: 3.754A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.683A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.658A pdb=" N ASN E 422 " --> pdb=" O ILE E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 737 through 743 Processing helix chain 'E' and resid 746 through 755 removed outlier: 3.936A pdb=" N GLN E 755 " --> pdb=" O ASN E 751 " (cutoff:3.500A) Processing helix chain 'E' and resid 758 through 782 Processing helix chain 'E' and resid 816 through 826 Processing helix chain 'E' and resid 866 through 884 Processing helix chain 'E' and resid 897 through 909 removed outlier: 3.615A pdb=" N ILE E 909 " --> pdb=" O ARG E 905 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 918 removed outlier: 3.546A pdb=" N GLU E 918 " --> pdb=" O ASN E 914 " (cutoff:3.500A) Processing helix chain 'E' and resid 919 through 941 Processing helix chain 'E' and resid 946 through 967 removed outlier: 3.581A pdb=" N SER E 967 " --> pdb=" O VAL E 963 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 983 removed outlier: 3.682A pdb=" N ILE E 980 " --> pdb=" O VAL E 976 " (cutoff:3.500A) Processing helix chain 'E' and resid 985 through 1033 Processing helix chain 'E' and resid 1140 through 1145 removed outlier: 3.822A pdb=" N GLU E1144 " --> pdb=" O PRO E1140 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 92 removed outlier: 3.884A pdb=" N THR c 92 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 88 through 92 removed outlier: 3.952A pdb=" N THR e 92 " --> pdb=" O PRO e 89 " (cutoff:3.500A) Processing helix chain 'e' and resid 193 through 197 removed outlier: 3.843A pdb=" N LEU e 196 " --> pdb=" O SER e 193 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY e 197 " --> pdb=" O SER e 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 193 through 197' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.315A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 200 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 51 removed outlier: 4.507A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 3.610A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.800A pdb=" N PHE A 238 " --> pdb=" O LEU A 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.800A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 146 removed outlier: 3.822A pdb=" N HIS A 146 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER A 151 " --> pdb=" O HIS A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 4.110A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE A 598 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR A 612 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 327 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.909A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.122A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 670 through 675 removed outlier: 3.560A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN A 675 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER A 691 " --> pdb=" O GLN A 675 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 727 removed outlier: 7.373A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.240A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 859 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.997A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.546A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.628A pdb=" N LEU C 277 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR C 286 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AC4, first strand: chain 'C' and resid 131 through 135 removed outlier: 7.956A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 154 through 156 removed outlier: 6.282A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 205 removed outlier: 5.917A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.856A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 311 through 312 removed outlier: 3.856A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 325 through 326 removed outlier: 7.865A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.550A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 396 through 397 removed outlier: 3.550A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.836A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 664 through 667 removed outlier: 6.709A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 702 through 703 Processing sheet with id=AD6, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AD7, first strand: chain 'C' and resid 717 through 728 removed outlier: 3.577A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD9, first strand: chain 'C' and resid 1120 through 1121 removed outlier: 3.504A pdb=" N ILE C1081 " --> pdb=" O HIS C1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'E' and resid 28 through 30 removed outlier: 3.726A pdb=" N PHE E 65 " --> pdb=" O TYR E 265 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR E 265 " --> pdb=" O PHE E 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA E 263 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 50 through 53 removed outlier: 3.613A pdb=" N ASP E 53 " --> pdb=" O ARG E 273 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASP E 287 " --> pdb=" O LYS E 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.712A pdb=" N VAL E 193 " --> pdb=" O TYR E 204 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 204 " --> pdb=" O VAL E 193 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 195 " --> pdb=" O LYS E 202 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE E 197 " --> pdb=" O TYR E 200 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE E 201 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ASP E 228 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE E 203 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AE6, first strand: chain 'E' and resid 127 through 131 removed outlier: 6.904A pdb=" N ILE E 128 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU E 169 " --> pdb=" O ILE E 128 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 130 " --> pdb=" O THR E 167 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 134 through 135 removed outlier: 3.913A pdb=" N SER E 162 " --> pdb=" O GLN E 134 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 151 through 156 removed outlier: 4.271A pdb=" N SER E 151 " --> pdb=" O HIS E 146 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS E 146 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET E 153 " --> pdb=" O TYR E 144 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER E 155 " --> pdb=" O GLY E 142 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLY E 142 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL E 143 " --> pdb=" O ARG E 246 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 311 through 319 removed outlier: 3.897A pdb=" N GLY E 311 " --> pdb=" O THR E 599 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR E 599 " --> pdb=" O GLY E 311 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR E 315 " --> pdb=" O VAL E 595 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL E 595 " --> pdb=" O THR E 315 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN E 317 " --> pdb=" O GLY E 593 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY E 593 " --> pdb=" O ASN E 317 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N GLY E 594 " --> pdb=" O GLN E 613 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN E 613 " --> pdb=" O GLY E 594 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR E 612 " --> pdb=" O CYS E 649 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N CYS E 649 " --> pdb=" O TYR E 612 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY E 648 " --> pdb=" O THR E 645 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 325 through 327 removed outlier: 6.379A pdb=" N ILE E 326 " --> pdb=" O ASN E 542 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL E 539 " --> pdb=" O GLY E 550 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY E 548 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP E 574 " --> pdb=" O ILE E 587 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 354 through 358 removed outlier: 4.021A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE E 358 " --> pdb=" O VAL E 395 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AF4, first strand: chain 'E' and resid 452 through 453 removed outlier: 3.595A pdb=" N GLN E 493 " --> pdb=" O TYR E 453 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 654 through 655 removed outlier: 6.535A pdb=" N GLU E 654 " --> pdb=" O ALA E 694 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR E 696 " --> pdb=" O GLU E 654 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER E 691 " --> pdb=" O GLN E 675 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER E 673 " --> pdb=" O ILE E 693 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE E 670 " --> pdb=" O ILE E 666 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE E 664 " --> pdb=" O ALA E 672 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 711 through 727 removed outlier: 6.487A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E1068 " --> pdb=" O THR E 719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 725 " --> pdb=" O PHE E1062 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET E1050 " --> pdb=" O VAL E1065 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N TYR E1067 " --> pdb=" O HIS E1048 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N HIS E1048 " --> pdb=" O TYR E1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 711 through 727 removed outlier: 6.487A pdb=" N SER E 711 " --> pdb=" O THR E1076 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E1076 " --> pdb=" O SER E 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA E 713 " --> pdb=" O ASN E1074 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASN E1074 " --> pdb=" O ALA E 713 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLU E1072 " --> pdb=" O PRO E 715 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E1068 " --> pdb=" O THR E 719 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU E 725 " --> pdb=" O PHE E1062 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 734 through 736 Processing sheet with id=AF9, first strand: chain 'E' and resid 1120 through 1122 removed outlier: 3.524A pdb=" N ILE E1081 " --> pdb=" O HIS E1088 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS E1082 " --> pdb=" O VAL E1133 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 1094 through 1097 Processing sheet with id=AG2, first strand: chain 'a' and resid 5 through 7 removed outlier: 3.791A pdb=" N VAL a 80 " --> pdb=" O CYS a 22 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 11 through 12 removed outlier: 3.918A pdb=" N VAL a 12 " --> pdb=" O THR a 117 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR a 114 " --> pdb=" O TYR a 95 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA a 93 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA a 51 " --> pdb=" O TRP a 38 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ARG a 40 " --> pdb=" O TRP a 49 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N TRP a 49 " --> pdb=" O ARG a 40 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG a 60 " --> pdb=" O LEU a 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 149 through 150 Processing sheet with id=AG5, first strand: chain 'a' and resid 157 through 161 removed outlier: 3.945A pdb=" N THR a 158 " --> pdb=" O ASN a 206 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN a 206 " --> pdb=" O THR a 158 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 18 through 20 removed outlier: 3.712A pdb=" N ILE b 77 " --> pdb=" O ILE b 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU b 75 " --> pdb=" O ILE b 20 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N SER b 65 " --> pdb=" O THR b 76 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 48 through 50 removed outlier: 7.050A pdb=" N TRP b 37 " --> pdb=" O MET b 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 117 through 121 removed outlier: 3.543A pdb=" N SER b 140 " --> pdb=" O SER b 117 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'c' and resid 5 through 6 Processing sheet with id=AH1, first strand: chain 'c' and resid 11 through 12 removed outlier: 3.561A pdb=" N ALA c 51 " --> pdb=" O TRP c 38 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG c 40 " --> pdb=" O TRP c 49 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N TRP c 49 " --> pdb=" O ARG c 40 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU c 52 " --> pdb=" O ARG c 60 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG c 60 " --> pdb=" O LEU c 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'c' and resid 11 through 12 removed outlier: 3.561A pdb=" N ARG c 99 " --> pdb=" O CYS c 109 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS c 109 " --> pdb=" O ARG c 99 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'c' and resid 129 through 130 removed outlier: 3.680A pdb=" N ASP c 151 " --> pdb=" O TYR c 183 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR c 183 " --> pdb=" O ASP c 151 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'c' and resid 157 through 161 removed outlier: 3.576A pdb=" N THR c 158 " --> pdb=" O ASN c 206 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TYR c 201 " --> pdb=" O VAL c 218 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 46 through 48 removed outlier: 3.684A pdb=" N SER d 92 " --> pdb=" O VAL d 99 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL d 99 " --> pdb=" O SER d 92 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 46 through 48 removed outlier: 3.591A pdb=" N ALA d 86 " --> pdb=" O LEU d 106 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 64 through 68 removed outlier: 3.611A pdb=" N SER d 67 " --> pdb=" O SER d 74 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER d 74 " --> pdb=" O SER d 67 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 117 through 121 removed outlier: 3.571A pdb=" N SER d 140 " --> pdb=" O SER d 117 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL d 136 " --> pdb=" O PHE d 121 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 11 through 12 removed outlier: 9.138A pdb=" N VAL e 12 " --> pdb=" O LEU e 115 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR e 117 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL e 36 " --> pdb=" O LEU e 52 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LEU e 52 " --> pdb=" O VAL e 36 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N TRP e 38 " --> pdb=" O LEU e 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 18 through 21 Processing sheet with id=AI2, first strand: chain 'f' and resid 21 through 22 removed outlier: 4.271A pdb=" N CYS f 22 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA f 73 " --> pdb=" O CYS f 22 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'f' and resid 47 through 50 removed outlier: 6.445A pdb=" N TRP f 37 " --> pdb=" O MET f 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR f 89 " --> pdb=" O TYR f 38 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER f 92 " --> pdb=" O VAL f 99 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL f 99 " --> pdb=" O SER f 92 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'f' and resid 47 through 50 removed outlier: 6.445A pdb=" N TRP f 37 " --> pdb=" O MET f 49 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR f 89 " --> pdb=" O TYR f 38 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'f' and resid 119 through 121 removed outlier: 3.784A pdb=" N THR f 119 " --> pdb=" O LEU f 138 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU f 138 " --> pdb=" O THR f 119 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL f 136 " --> pdb=" O PHE f 121 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2535 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 15.17 Time building geometry restraints manager: 13.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 11192 1.35 - 1.47: 9112 1.47 - 1.59: 15477 1.59 - 1.71: 0 1.71 - 1.83: 192 Bond restraints: 35973 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.55e+00 bond pdb=" C1 NAG A1315 " pdb=" O5 NAG A1315 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C1 NAG C1314 " pdb=" O5 NAG C1314 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" C1 NAG C1306 " pdb=" O5 NAG C1306 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.46e+00 bond pdb=" C1 NAG E1301 " pdb=" O5 NAG E1301 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 35968 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 1203 107.09 - 113.81: 20265 113.81 - 120.54: 12645 120.54 - 127.26: 14575 127.26 - 133.99: 365 Bond angle restraints: 49053 Sorted by residual: angle pdb=" N VAL a 90 " pdb=" CA VAL a 90 " pdb=" C VAL a 90 " ideal model delta sigma weight residual 113.71 107.87 5.84 9.50e-01 1.11e+00 3.78e+01 angle pdb=" N VAL b 60 " pdb=" CA VAL b 60 " pdb=" C VAL b 60 " ideal model delta sigma weight residual 106.21 109.88 -3.67 1.07e+00 8.73e-01 1.18e+01 angle pdb=" C ASN C 616 " pdb=" N CYS C 617 " pdb=" CA CYS C 617 " ideal model delta sigma weight residual 122.08 126.97 -4.89 1.47e+00 4.63e-01 1.11e+01 angle pdb=" C CYS A 336 " pdb=" N PRO A 337 " pdb=" CA PRO A 337 " ideal model delta sigma weight residual 119.84 123.68 -3.84 1.25e+00 6.40e-01 9.45e+00 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 111.90 109.45 2.45 8.10e-01 1.52e+00 9.17e+00 ... (remaining 49048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 19745 17.99 - 35.98: 1142 35.98 - 53.98: 154 53.98 - 71.97: 26 71.97 - 89.96: 17 Dihedral angle restraints: 21084 sinusoidal: 7995 harmonic: 13089 Sorted by residual: dihedral pdb=" CB CYS f 137 " pdb=" SG CYS f 137 " pdb=" SG CYS f 196 " pdb=" CB CYS f 196 " ideal model delta sinusoidal sigma weight residual -86.00 -175.71 89.71 1 1.00e+01 1.00e-02 9.55e+01 dihedral pdb=" CB CYS E 738 " pdb=" SG CYS E 738 " pdb=" SG CYS E 760 " pdb=" CB CYS E 760 " ideal model delta sinusoidal sigma weight residual 93.00 4.16 88.84 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual -86.00 -169.91 83.91 1 1.00e+01 1.00e-02 8.58e+01 ... (remaining 21081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 4883 0.056 - 0.111: 791 0.111 - 0.167: 83 0.167 - 0.222: 2 0.222 - 0.278: 1 Chirality restraints: 5760 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C1 NAG C1314 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG C1314 " pdb=" O5 NAG C1314 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" C2 NAG E1312 " pdb=" C1 NAG E1312 " pdb=" C3 NAG E1312 " pdb=" N2 NAG E1312 " both_signs ideal model delta sigma weight residual False -2.49 -2.32 -0.17 2.00e-01 2.50e+01 7.31e-01 ... (remaining 5757 not shown) Planarity restraints: 6303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 431 " 0.011 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C GLY A 431 " -0.040 2.00e-02 2.50e+03 pdb=" O GLY A 431 " 0.015 2.00e-02 2.50e+03 pdb=" N CYS A 432 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR f 184 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO f 185 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO f 185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO f 185 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR d 184 " -0.032 5.00e-02 4.00e+02 4.81e-02 3.70e+00 pdb=" N PRO d 185 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO d 185 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO d 185 " -0.027 5.00e-02 4.00e+02 ... (remaining 6300 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5919 2.77 - 3.30: 32692 3.30 - 3.83: 57619 3.83 - 4.37: 64768 4.37 - 4.90: 112098 Nonbonded interactions: 273096 Sorted by model distance: nonbonded pdb=" O ASN E 501 " pdb=" ND2 ASN f 33 " model vdw 2.234 2.520 nonbonded pdb=" O VAL C1040 " pdb=" OG SER E1030 " model vdw 2.250 2.440 nonbonded pdb=" OG1 THR d 19 " pdb=" OG SER d 74 " model vdw 2.252 2.440 nonbonded pdb=" OG1 THR C 33 " pdb=" O GLY C 219 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR e 101 " pdb=" OG1 THR e 105 " model vdw 2.274 2.440 ... (remaining 273091 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 'E' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'd' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.270 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: 14.230 Check model and map are aligned: 0.440 Set scattering table: 0.340 Process input model: 88.010 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 0.046 35973 Z= 0.174 Angle : 0.534 5.993 49053 Z= 0.295 Chirality : 0.042 0.278 5760 Planarity : 0.003 0.050 6258 Dihedral : 10.875 89.962 12516 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.84 (0.11), residues: 4470 helix: 0.63 (0.20), residues: 629 sheet: -2.82 (0.14), residues: 966 loop : -3.41 (0.09), residues: 2875 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 674 time to evaluate : 4.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 680 average time/residue: 0.5209 time to fit residues: 557.0460 Evaluate side-chains 357 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 355 time to evaluate : 4.028 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3267 time to fit residues: 6.6457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 377 optimal weight: 10.0000 chunk 338 optimal weight: 0.0870 chunk 187 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 181 optimal weight: 0.0070 chunk 350 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 213 optimal weight: 1.9990 chunk 260 optimal weight: 10.0000 chunk 405 optimal weight: 20.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 146 HIS A 173 GLN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 498 GLN A 501 ASN A 536 ASN A 564 GLN A 777 ASN A 784 GLN A 856 ASN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN A 926 GLN A 954 GLN ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN C 69 HIS C 134 GLN C 185 ASN C 188 ASN C 196 ASN C 271 GLN C 394 ASN C 409 GLN C 414 GLN C 498 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 580 GLN C 690 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN C 913 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C1036 GLN C1048 HIS C1101 HIS E 137 ASN E 196 ASN E 218 GLN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 ASN E 580 GLN E 603 ASN E 658 ASN E 690 GLN E 777 ASN ** E 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 787 GLN E 935 GLN E 954 GLN E1011 GLN E1048 HIS E1101 HIS E1106 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 178 GLN a 204 ASN ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 79 GLN c 178 GLN ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 178 GLN e 211 ASN ** f 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 170 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 35973 Z= 0.282 Angle : 0.621 14.813 49053 Z= 0.311 Chirality : 0.044 0.321 5760 Planarity : 0.004 0.067 6258 Dihedral : 3.446 21.973 4812 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 1.53 % Allowed : 12.85 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.12), residues: 4470 helix: 1.46 (0.21), residues: 646 sheet: -2.34 (0.15), residues: 1037 loop : -3.06 (0.10), residues: 2787 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 372 time to evaluate : 4.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 29 residues processed: 413 average time/residue: 0.4858 time to fit residues: 333.3458 Evaluate side-chains 322 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 293 time to evaluate : 4.034 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.3504 time to fit residues: 24.1265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 225 optimal weight: 1.9990 chunk 125 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 chunk 276 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 406 optimal weight: 0.9980 chunk 439 optimal weight: 0.9980 chunk 362 optimal weight: 0.6980 chunk 403 optimal weight: 30.0000 chunk 138 optimal weight: 4.9990 chunk 326 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 314 GLN A 334 ASN A 787 GLN ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1135 ASN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 655 HIS ** E 779 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 949 GLN E 953 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 191 HIS ** d 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 178 GLN ** f 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 35973 Z= 0.312 Angle : 0.624 13.371 49053 Z= 0.311 Chirality : 0.044 0.308 5760 Planarity : 0.004 0.048 6258 Dihedral : 3.756 23.938 4812 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 2.02 % Allowed : 15.85 % Favored : 82.13 % 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: -2.93 (0.12), residues: 4470 helix: 1.66 (0.21), residues: 644 sheet: -2.39 (0.15), residues: 1058 loop : -2.81 (0.11), residues: 2768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 315 time to evaluate : 4.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 33 residues processed: 377 average time/residue: 0.4493 time to fit residues: 286.0143 Evaluate side-chains 300 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 3.865 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 33 outliers final: 1 residues processed: 33 average time/residue: 0.3307 time to fit residues: 25.7188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 401 optimal weight: 0.8980 chunk 305 optimal weight: 5.9990 chunk 211 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 194 optimal weight: 3.9990 chunk 273 optimal weight: 0.9980 chunk 408 optimal weight: 7.9990 chunk 432 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 386 optimal weight: 0.0980 chunk 116 optimal weight: 7.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 872 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN ** E 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 779 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN e 78 ASN e 178 GLN ** f 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 ASN f 187 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35973 Z= 0.202 Angle : 0.575 16.315 49053 Z= 0.283 Chirality : 0.043 0.313 5760 Planarity : 0.004 0.048 6258 Dihedral : 3.676 24.383 4812 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.53 % Allowed : 17.61 % Favored : 80.86 % 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: -2.72 (0.12), residues: 4470 helix: 1.99 (0.21), residues: 630 sheet: -2.27 (0.15), residues: 1076 loop : -2.68 (0.11), residues: 2764 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 297 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 28 residues processed: 343 average time/residue: 0.4419 time to fit residues: 258.5561 Evaluate side-chains 294 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 266 time to evaluate : 3.652 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 28 outliers final: 1 residues processed: 28 average time/residue: 0.3198 time to fit residues: 22.0466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 359 optimal weight: 4.9990 chunk 245 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 321 optimal weight: 20.0000 chunk 178 optimal weight: 0.9980 chunk 368 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 220 optimal weight: 9.9990 chunk 387 optimal weight: 0.0050 chunk 109 optimal weight: 0.9980 overall best weight: 0.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 872 GLN A1088 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 607 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 81 GLN ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35973 Z= 0.176 Angle : 0.554 17.076 49053 Z= 0.272 Chirality : 0.043 0.312 5760 Planarity : 0.004 0.068 6258 Dihedral : 3.637 23.519 4812 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.32 % Allowed : 18.86 % Favored : 79.82 % 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: -2.54 (0.12), residues: 4470 helix: 2.16 (0.22), residues: 625 sheet: -2.15 (0.15), residues: 1082 loop : -2.55 (0.11), residues: 2763 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 286 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 22 residues processed: 326 average time/residue: 0.4507 time to fit residues: 252.1769 Evaluate side-chains 281 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 259 time to evaluate : 4.029 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 22 outliers final: 1 residues processed: 22 average time/residue: 0.2834 time to fit residues: 17.0551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 145 optimal weight: 6.9990 chunk 389 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 253 optimal weight: 0.0670 chunk 106 optimal weight: 2.9990 chunk 432 optimal weight: 6.9990 chunk 359 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 856 ASN A 919 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN E 239 GLN E 271 GLN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 178 GLN ** f 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 191 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35973 Z= 0.323 Angle : 0.643 15.327 49053 Z= 0.321 Chirality : 0.044 0.306 5760 Planarity : 0.004 0.054 6258 Dihedral : 4.087 25.587 4812 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 1.89 % Allowed : 19.74 % Favored : 78.37 % 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: -2.58 (0.12), residues: 4470 helix: 1.65 (0.21), residues: 652 sheet: -2.04 (0.15), residues: 1022 loop : -2.56 (0.11), residues: 2796 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 271 time to evaluate : 3.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 32 residues processed: 325 average time/residue: 0.4518 time to fit residues: 256.6659 Evaluate side-chains 283 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 251 time to evaluate : 3.862 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.3209 time to fit residues: 24.7982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 416 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 246 optimal weight: 4.9990 chunk 315 optimal weight: 0.9980 chunk 244 optimal weight: 0.0050 chunk 364 optimal weight: 6.9990 chunk 241 optimal weight: 0.9980 chunk 430 optimal weight: 5.9990 chunk 269 optimal weight: 0.8980 chunk 262 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN A 856 ASN ** C 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 41 GLN ** c 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 172 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 35973 Z= 0.219 Angle : 0.586 17.588 49053 Z= 0.291 Chirality : 0.044 0.307 5760 Planarity : 0.004 0.062 6258 Dihedral : 3.959 25.110 4812 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 1.04 % Allowed : 20.88 % Favored : 78.09 % 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: -2.47 (0.12), residues: 4470 helix: 1.73 (0.21), residues: 651 sheet: -1.96 (0.15), residues: 1023 loop : -2.49 (0.11), residues: 2796 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 272 time to evaluate : 3.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 15 residues processed: 300 average time/residue: 0.4417 time to fit residues: 225.9693 Evaluate side-chains 276 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 261 time to evaluate : 3.957 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 15 outliers final: 1 residues processed: 15 average time/residue: 0.3503 time to fit residues: 15.0865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 266 optimal weight: 9.9990 chunk 172 optimal weight: 0.5980 chunk 257 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 293 optimal weight: 0.2980 chunk 213 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 338 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 440 ASN ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 211 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 112 GLN ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 41 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 35973 Z= 0.171 Angle : 0.573 21.396 49053 Z= 0.282 Chirality : 0.043 0.313 5760 Planarity : 0.004 0.062 6258 Dihedral : 3.815 23.309 4812 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.75 % Allowed : 21.26 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.12), residues: 4470 helix: 1.91 (0.21), residues: 646 sheet: -1.82 (0.16), residues: 1030 loop : -2.40 (0.11), residues: 2794 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 275 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 12 residues processed: 297 average time/residue: 0.4344 time to fit residues: 220.9092 Evaluate side-chains 259 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 247 time to evaluate : 3.897 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.3318 time to fit residues: 12.7444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 391 optimal weight: 6.9990 chunk 412 optimal weight: 10.0000 chunk 376 optimal weight: 0.0980 chunk 401 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 315 optimal weight: 0.2980 chunk 123 optimal weight: 20.0000 chunk 362 optimal weight: 0.4980 chunk 379 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 856 ASN A 978 ASN ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 856 ASN ** E1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 170 GLN ** f 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35973 Z= 0.242 Angle : 0.603 23.087 49053 Z= 0.297 Chirality : 0.044 0.304 5760 Planarity : 0.004 0.060 6258 Dihedral : 3.934 24.620 4812 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.60 % Allowed : 21.68 % Favored : 77.73 % 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: -2.29 (0.12), residues: 4470 helix: 1.88 (0.21), residues: 652 sheet: -1.83 (0.16), residues: 1031 loop : -2.37 (0.11), residues: 2787 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8940 Ramachandran restraints generated. 4470 Oldfield, 0 Emsley, 4470 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 3.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 271 average time/residue: 0.3989 time to fit residues: 185.2031 Evaluate side-chains 251 residues out of total 3912 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 3.004 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 0.2622 time to fit residues: 8.6378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 447 random chunks: chunk 263 optimal weight: 4.9990 chunk 424 optimal weight: 0.4980 chunk 259 optimal weight: 2.9990 chunk 201 optimal weight: 0.5980 chunk 295 optimal weight: 2.9990 chunk 445 optimal weight: 1.9990 chunk 409 optimal weight: 0.0670 chunk 354 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 273 optimal weight: 0.8980 chunk 217 optimal weight: 6.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: