Starting phenix.real_space_refine on Tue Apr 16 17:02:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hca_34657/04_2024/8hca_34657.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hca_34657/04_2024/8hca_34657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hca_34657/04_2024/8hca_34657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hca_34657/04_2024/8hca_34657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hca_34657/04_2024/8hca_34657.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hca_34657/04_2024/8hca_34657.pdb" } resolution = 4.35 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4818 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 22344 2.51 5 N 5802 2.21 5 O 6885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "G ASP 127": "OD1" <-> "OD2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 35187 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "B" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "C" Number of atoms: 8101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8101 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 57, 'TRANS': 974} Chain breaks: 8 Chain: "E" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "L" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1649 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 205} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1727 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 12, 'TRANS': 219} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 17.98, per 1000 atoms: 0.51 Number of scatterers: 35187 At special positions: 0 Unit cell: (161.7, 150.15, 244.2, 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 156 16.00 O 6885 8.00 N 5802 7.00 C 22344 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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 B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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 23 " - pdb=" SG CYS E 93 " distance=2.03 Simple disulfide: pdb=" SG CYS E 139 " - pdb=" SG CYS E 199 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 100 " distance=2.03 Simple disulfide: pdb=" SG CYS F 111 " - pdb=" SG CYS F 116 " distance=2.03 Simple disulfide: pdb=" SG CYS F 161 " - pdb=" SG CYS F 217 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS L 139 " - pdb=" SG CYS L 199 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.03 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 100 " distance=2.03 Simple disulfide: pdb=" SG CYS H 111 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 217 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 100 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 116 " distance=2.04 Simple disulfide: pdb=" SG CYS D 161 " - pdb=" SG CYS D 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " ASN A 616 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " ASN B 616 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 616 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 13.19 Conformation dependent library (CDL) restraints added in 6.3 seconds 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8322 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 73 sheets defined 19.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.827A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 3.851A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.510A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.605A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.558A pdb=" N ILE A 870 " --> pdb=" O THR A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.928A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.984A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASN A 919 " --> pdb=" O VAL A 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 919' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.104A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.836A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.304A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.126A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.808A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.005A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.209A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.551A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 372 removed outlier: 3.780A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.637A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 887 through 891 removed outlier: 3.823A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.544A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.623A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.844A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.693A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 133 Processing helix chain 'E' and resid 188 through 193 removed outlier: 4.303A pdb=" N LYS E 193 " --> pdb=" O ALA E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.669A pdb=" N THR F 31 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 65 through 71 Processing helix chain 'F' and resid 177 through 179 No H-bonds generated for 'chain 'F' and resid 177 through 179' Processing helix chain 'F' and resid 208 through 210 No H-bonds generated for 'chain 'F' and resid 208 through 210' Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.098A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 Processing helix chain 'L' and resid 188 through 193 Processing helix chain 'G' and resid 84 through 88 removed outlier: 4.156A pdb=" N VAL G 88 " --> pdb=" O ALA G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 132 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'H' and resid 65 through 71 Processing helix chain 'H' and resid 177 through 179 No H-bonds generated for 'chain 'H' and resid 177 through 179' Processing helix chain 'D' and resid 66 through 71 Processing helix chain 'D' and resid 177 through 179 No H-bonds generated for 'chain 'D' and resid 177 through 179' Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.311A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS A 206 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.969A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.071A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.654A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 314 removed outlier: 3.826A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 357 removed outlier: 4.155A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.738A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.634A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 43 " --> pdb=" O PHE A 565 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 567 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.828A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 666 " --> pdb=" O ILE A 670 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.543A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.930A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 727 removed outlier: 6.930A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.183A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.751A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 7.820A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.391A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.712A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.441A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.734A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 395 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N SER B 514 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA B 397 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 512 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER B 399 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL B 510 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 401 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 508 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.679A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.991A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE B 584 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.225A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.782A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 3.792A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.524A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.527A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.067A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 140 through 142 removed outlier: 3.878A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP C 142 " --> pdb=" O GLU C 156 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU C 156 " --> pdb=" O ASP C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 317 removed outlier: 3.656A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N THR C 315 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 325 through 326 removed outlier: 3.555A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 398 through 403 removed outlier: 3.710A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 660 removed outlier: 4.182A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE C 693 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N CYS C 671 " --> pdb=" O TYR C 695 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 713 through 727 removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C1047 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 713 through 727 removed outlier: 6.796A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.416A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF2, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF3, first strand: chain 'E' and resid 49 through 53 removed outlier: 6.815A pdb=" N TRP E 40 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 119 through 123 removed outlier: 3.665A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.705A pdb=" N TRP E 153 " --> pdb=" O GLN E 160 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS E 212 " --> pdb=" O CYS E 199 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 6 through 7 removed outlier: 3.619A pdb=" N PHE F 84 " --> pdb=" O SER F 75 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 35 through 38 removed outlier: 5.782A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER F 50 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR F 63 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.807A pdb=" N GLY F 160 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ALA F 158 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER F 201 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU F 199 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 165 " --> pdb=" O TYR F 197 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR F 197 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 172 through 175 removed outlier: 3.637A pdb=" N THR F 172 " --> pdb=" O ASN F 220 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR F 215 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.719A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 20 through 21 removed outlier: 3.952A pdb=" N ILE L 21 " --> pdb=" O LEU L 78 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR L 77 " --> pdb=" O SER L 70 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 49 through 53 removed outlier: 4.080A pdb=" N LEU L 52 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.598A pdb=" N VAL L 138 " --> pdb=" O PHE L 123 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.542A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 48 through 53 removed outlier: 6.472A pdb=" N LYS G 44 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU G 51 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU G 42 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP G 39 " --> pdb=" O MET G 94 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 67 through 70 Processing sheet with id=AG8, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.821A pdb=" N ASN G 143 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 159 through 160 removed outlier: 4.741A pdb=" N TRP G 153 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS G 212 " --> pdb=" O CYS G 199 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.850A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN H 86 " --> pdb=" O THR H 73 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.588A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 141 through 148 removed outlier: 4.186A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 141 through 148 removed outlier: 4.186A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP H 165 " --> pdb=" O TYR H 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 172 through 175 removed outlier: 4.942A pdb=" N TYR H 215 " --> pdb=" O VAL H 232 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.801A pdb=" N GLY D 10 " --> pdb=" O ILE D 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'D' and resid 18 through 23 removed outlier: 3.528A pdb=" N PHE D 84 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 35 through 39 removed outlier: 6.850A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 141 through 148 removed outlier: 4.084A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 202 " --> pdb=" O HIS D 185 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 173 through 175 removed outlier: 3.565A pdb=" N VAL D 219 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 228 " --> pdb=" O VAL D 219 " (cutoff:3.500A) 1127 hydrogen bonds defined for protein. 3093 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: 15.89 Time building geometry restraints manager: 14.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11196 1.34 - 1.46: 8829 1.46 - 1.58: 15765 1.58 - 1.70: 0 1.70 - 1.82: 195 Bond restraints: 35985 Sorted by residual: bond pdb=" C ARG A 328 " pdb=" N PHE A 329 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.07e-02 2.33e+03 5.69e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.17e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.59e+00 bond pdb=" C GLU H 169 " pdb=" N PRO H 170 " ideal model delta sigma weight residual 1.334 1.381 -0.047 2.34e-02 1.83e+03 4.09e+00 bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.99: 932 105.99 - 113.01: 19486 113.01 - 120.02: 11748 120.02 - 127.04: 16459 127.04 - 134.05: 359 Bond angle restraints: 48984 Sorted by residual: angle pdb=" CA PHE D 167 " pdb=" C PHE D 167 " pdb=" N PRO D 168 " ideal model delta sigma weight residual 120.58 117.63 2.95 7.40e-01 1.83e+00 1.59e+01 angle pdb=" C PRO C 987 " pdb=" N GLU C 988 " pdb=" CA GLU C 988 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 angle pdb=" N ARG A 328 " pdb=" CA ARG A 328 " pdb=" C ARG A 328 " ideal model delta sigma weight residual 109.31 114.61 -5.30 1.42e+00 4.96e-01 1.39e+01 angle pdb=" C ILE C 587 " pdb=" N THR C 588 " pdb=" CA THR C 588 " ideal model delta sigma weight residual 121.80 130.52 -8.72 2.44e+00 1.68e-01 1.28e+01 angle pdb=" C ARG A 273 " pdb=" N THR A 274 " pdb=" CA THR A 274 " ideal model delta sigma weight residual 122.77 118.22 4.55 1.33e+00 5.65e-01 1.17e+01 ... (remaining 48979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 20010 17.54 - 35.09: 1767 35.09 - 52.63: 337 52.63 - 70.18: 75 70.18 - 87.72: 41 Dihedral angle restraints: 22230 sinusoidal: 9294 harmonic: 12936 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 8.40 84.60 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual -86.00 -170.17 84.17 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -166.52 80.52 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 22227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 5189 0.085 - 0.170: 521 0.170 - 0.255: 7 0.255 - 0.340: 2 0.340 - 0.425: 5 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.51e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.90e+00 ... (remaining 5721 not shown) Planarity restraints: 6297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1305 " 0.044 2.00e-02 2.50e+03 3.65e-02 1.66e+01 pdb=" C7 NAG A1305 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A1305 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG A1305 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG A1305 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 205 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO D 206 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 206 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 206 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO A 330 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " 0.035 5.00e-02 4.00e+02 ... (remaining 6294 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6508 2.78 - 3.31: 30990 3.31 - 3.84: 57877 3.84 - 4.37: 62979 4.37 - 4.90: 110752 Nonbonded interactions: 269106 Sorted by model distance: nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.250 2.440 nonbonded pdb=" O CYS A1032 " pdb=" OG SER A1051 " model vdw 2.255 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR C 756 " pdb=" OD1 ASP C 994 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.270 2.440 ... (remaining 269101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.240 Construct map_model_manager: 0.020 Extract box with map and model: 5.940 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 93.410 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.400 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 0.070 35985 Z= 0.203 Angle : 0.595 9.908 48984 Z= 0.293 Chirality : 0.047 0.425 5724 Planarity : 0.004 0.070 6255 Dihedral : 13.561 87.722 13737 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.44 % Allowed : 0.34 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.12), residues: 4383 helix: 1.21 (0.20), residues: 657 sheet: 1.04 (0.17), residues: 960 loop : -1.31 (0.11), residues: 2766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 PHE 0.013 0.001 PHE A 541 TYR 0.008 0.001 TYR G 54 ARG 0.004 0.000 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7568 (OUTLIER) cc_final: 0.4652 (mtmm) REVERT: A 302 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7805 (p) REVERT: A 332 ILE cc_start: 0.8102 (pt) cc_final: 0.7630 (tp) REVERT: A 1050 MET cc_start: 0.8700 (pmm) cc_final: 0.8413 (pmm) REVERT: B 1050 MET cc_start: 0.8171 (pmm) cc_final: 0.7705 (pmm) REVERT: C 424 LYS cc_start: 0.8170 (tttt) cc_final: 0.7967 (ttmm) REVERT: E 192 GLU cc_start: 0.0092 (mm-30) cc_final: -0.0483 (pt0) REVERT: F 129 MET cc_start: 0.5922 (tpp) cc_final: 0.4545 (tpp) REVERT: L 170 GLU cc_start: 0.4642 (tp30) cc_final: 0.4157 (tt0) REVERT: G 40 TRP cc_start: 0.5618 (m100) cc_final: 0.5148 (m100) outliers start: 17 outliers final: 3 residues processed: 169 average time/residue: 0.4740 time to fit residues: 136.9354 Evaluate side-chains 100 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 95 time to evaluate : 3.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 372 optimal weight: 30.0000 chunk 334 optimal weight: 20.0000 chunk 185 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 345 optimal weight: 30.0000 chunk 133 optimal weight: 20.0000 chunk 210 optimal weight: 0.7980 chunk 257 optimal weight: 7.9990 chunk 400 optimal weight: 8.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 121 ASN A 448 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN B 607 GLN B 613 GLN B 751 ASN B 804 GLN B 955 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS E 142 ASN F 33 ASN F 86 GLN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 35985 Z= 0.344 Angle : 0.683 13.927 48984 Z= 0.350 Chirality : 0.047 0.446 5724 Planarity : 0.005 0.063 6255 Dihedral : 6.343 59.805 5904 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.61 % Favored : 95.35 % Rotamer: Outliers : 0.26 % Allowed : 6.70 % Favored : 93.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4383 helix: 1.63 (0.21), residues: 668 sheet: 0.80 (0.16), residues: 1079 loop : -1.30 (0.12), residues: 2636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP G 40 HIS 0.008 0.001 HIS A 66 PHE 0.029 0.002 PHE B 201 TYR 0.024 0.002 TYR C 313 ARG 0.007 0.001 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 4.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8602 (mt) cc_final: 0.8297 (mt) REVERT: A 332 ILE cc_start: 0.8009 (pt) cc_final: 0.7540 (tp) REVERT: A 731 MET cc_start: 0.8790 (ptp) cc_final: 0.8550 (ptm) REVERT: A 740 MET cc_start: 0.8409 (tpt) cc_final: 0.8065 (tpt) REVERT: A 1050 MET cc_start: 0.8903 (pmm) cc_final: 0.8541 (pmm) REVERT: B 559 PHE cc_start: 0.4169 (OUTLIER) cc_final: 0.3229 (m-80) REVERT: B 869 MET cc_start: 0.8807 (pmm) cc_final: 0.8562 (pmm) REVERT: B 1050 MET cc_start: 0.8332 (pmm) cc_final: 0.7698 (pmm) REVERT: E 154 LYS cc_start: 0.5160 (mppt) cc_final: 0.3417 (ptmm) REVERT: E 192 GLU cc_start: 0.0681 (mm-30) cc_final: 0.0302 (pt0) REVERT: F 87 MET cc_start: 0.4226 (tpt) cc_final: 0.3841 (tpt) REVERT: F 129 MET cc_start: 0.6331 (tpp) cc_final: 0.5074 (tpp) REVERT: L 94 MET cc_start: -0.0731 (mmt) cc_final: -0.1520 (tpp) REVERT: G 94 MET cc_start: -0.1931 (ptp) cc_final: -0.2486 (ptp) REVERT: D 34 MET cc_start: 0.1612 (tpt) cc_final: 0.1283 (mmm) outliers start: 10 outliers final: 2 residues processed: 130 average time/residue: 0.5037 time to fit residues: 113.0908 Evaluate side-chains 86 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 222 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 333 optimal weight: 30.0000 chunk 272 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 401 optimal weight: 0.6980 chunk 433 optimal weight: 20.0000 chunk 357 optimal weight: 20.0000 chunk 397 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 321 optimal weight: 0.0010 overall best weight: 3.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 394 ASN A 907 ASN A 954 HIS A1005 GLN A1011 GLN A1135 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN E 129 GLN L 50 HIS ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN D 126 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35985 Z= 0.259 Angle : 0.589 15.486 48984 Z= 0.299 Chirality : 0.045 0.405 5724 Planarity : 0.005 0.158 6255 Dihedral : 5.915 59.075 5904 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.84 % Favored : 95.12 % Rotamer: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4383 helix: 1.85 (0.21), residues: 659 sheet: 0.75 (0.16), residues: 1046 loop : -1.32 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 353 HIS 0.021 0.001 HIS A 954 PHE 0.030 0.002 PHE C 981 TYR 0.017 0.001 TYR H 98 ARG 0.012 0.001 ARG C 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 4.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8759 (tpt) cc_final: 0.8520 (tpt) REVERT: A 1050 MET cc_start: 0.8871 (pmm) cc_final: 0.8525 (pmm) REVERT: B 1050 MET cc_start: 0.8277 (pmm) cc_final: 0.7444 (pmm) REVERT: C 900 MET cc_start: 0.8617 (ppp) cc_final: 0.8203 (ppp) REVERT: C 1050 MET cc_start: 0.7967 (ptp) cc_final: 0.7228 (ptp) REVERT: E 17 GLU cc_start: 0.4935 (pp20) cc_final: 0.4332 (pm20) REVERT: E 65 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7451 (t0) REVERT: E 192 GLU cc_start: 0.0690 (mm-30) cc_final: 0.0282 (pt0) REVERT: F 87 MET cc_start: 0.4254 (tpt) cc_final: 0.3933 (tpt) REVERT: F 129 MET cc_start: 0.6428 (tpp) cc_final: 0.5162 (tpp) REVERT: L 128 GLU cc_start: 0.2213 (pp20) cc_final: 0.1985 (pp20) REVERT: G 94 MET cc_start: -0.1583 (ptp) cc_final: -0.2079 (ptp) REVERT: H 78 ASP cc_start: 0.6255 (m-30) cc_final: 0.5815 (m-30) REVERT: D 34 MET cc_start: 0.2137 (tpt) cc_final: 0.1631 (mmm) outliers start: 5 outliers final: 1 residues processed: 120 average time/residue: 0.4898 time to fit residues: 101.2710 Evaluate side-chains 80 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 4.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 396 optimal weight: 7.9990 chunk 301 optimal weight: 8.9990 chunk 208 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 191 optimal weight: 0.7980 chunk 269 optimal weight: 5.9990 chunk 402 optimal weight: 8.9990 chunk 426 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 381 optimal weight: 20.0000 chunk 114 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 607 GLN A1036 GLN A1058 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 188 ASN C 321 GLN C 437 ASN C 481 ASN ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1048 HIS ** F 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 GLN G 204 GLN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 35985 Z= 0.346 Angle : 0.684 13.043 48984 Z= 0.347 Chirality : 0.047 0.457 5724 Planarity : 0.005 0.062 6255 Dihedral : 6.329 59.891 5904 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 0.05 % Allowed : 5.22 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4383 helix: 1.27 (0.20), residues: 680 sheet: 0.44 (0.16), residues: 1082 loop : -1.46 (0.12), residues: 2621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 353 HIS 0.015 0.002 HIS C 207 PHE 0.030 0.002 PHE A 541 TYR 0.023 0.002 TYR C 313 ARG 0.012 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 105 time to evaluate : 4.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8779 (tpt) cc_final: 0.8520 (tpt) REVERT: A 1050 MET cc_start: 0.8886 (pmm) cc_final: 0.8525 (pmm) REVERT: B 869 MET cc_start: 0.8695 (pmm) cc_final: 0.8334 (pmm) REVERT: B 1050 MET cc_start: 0.8238 (pmm) cc_final: 0.7289 (pmm) REVERT: C 334 ASN cc_start: 0.7229 (m-40) cc_final: 0.6901 (p0) REVERT: C 1050 MET cc_start: 0.8141 (ptp) cc_final: 0.7631 (ptp) REVERT: E 17 GLU cc_start: 0.5033 (pp20) cc_final: 0.4581 (pm20) REVERT: E 192 GLU cc_start: 0.0509 (mm-30) cc_final: 0.0133 (pt0) REVERT: F 129 MET cc_start: 0.6485 (tpp) cc_final: 0.5263 (tpp) REVERT: L 121 PHE cc_start: 0.5033 (m-10) cc_final: 0.3905 (t80) REVERT: L 122 ILE cc_start: 0.5436 (tp) cc_final: 0.5082 (tp) REVERT: D 34 MET cc_start: 0.3185 (tpt) cc_final: 0.2250 (mmm) outliers start: 2 outliers final: 1 residues processed: 107 average time/residue: 0.5055 time to fit residues: 93.4037 Evaluate side-chains 81 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 4.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 355 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 317 optimal weight: 30.0000 chunk 175 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 chunk 294 optimal weight: 0.9980 chunk 0 optimal weight: 40.0000 chunk 217 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 607 GLN ** B 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 35985 Z= 0.301 Angle : 0.635 13.703 48984 Z= 0.322 Chirality : 0.046 0.449 5724 Planarity : 0.005 0.064 6255 Dihedral : 6.219 56.744 5904 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.73 % Favored : 94.23 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4383 helix: 1.32 (0.20), residues: 680 sheet: 0.38 (0.16), residues: 1085 loop : -1.53 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 886 HIS 0.006 0.001 HIS B1064 PHE 0.027 0.002 PHE A 541 TYR 0.025 0.002 TYR B 369 ARG 0.021 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 4.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8801 (tpt) cc_final: 0.8534 (tpt) REVERT: A 1050 MET cc_start: 0.8912 (pmm) cc_final: 0.8482 (pmm) REVERT: B 1050 MET cc_start: 0.8269 (pmm) cc_final: 0.7379 (pmm) REVERT: C 869 MET cc_start: 0.8172 (pmm) cc_final: 0.7844 (pmm) REVERT: C 1050 MET cc_start: 0.7856 (ptp) cc_final: 0.7401 (ptp) REVERT: E 17 GLU cc_start: 0.4959 (pp20) cc_final: 0.4679 (pm20) REVERT: E 192 GLU cc_start: 0.0792 (mm-30) cc_final: 0.0495 (pt0) REVERT: G 40 TRP cc_start: 0.7093 (m100) cc_final: 0.6359 (m100) REVERT: D 34 MET cc_start: 0.3597 (tpt) cc_final: 0.2437 (mmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.5032 time to fit residues: 91.3475 Evaluate side-chains 78 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 143 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 84 optimal weight: 4.9990 chunk 250 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 426 optimal weight: 8.9990 chunk 354 optimal weight: 0.0000 chunk 197 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 141 optimal weight: 10.0000 chunk 224 optimal weight: 0.8980 overall best weight: 2.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 474 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1083 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 203 HIS G 142 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35985 Z= 0.204 Angle : 0.568 18.261 48984 Z= 0.284 Chirality : 0.045 0.441 5724 Planarity : 0.004 0.057 6255 Dihedral : 5.829 56.442 5904 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.48 % Favored : 94.48 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.13), residues: 4383 helix: 1.68 (0.20), residues: 672 sheet: 0.37 (0.16), residues: 1067 loop : -1.42 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.008 0.001 HIS D 185 PHE 0.024 0.001 PHE A 541 TYR 0.018 0.001 TYR E 145 ARG 0.012 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8042 (ptp) cc_final: 0.7818 (ptp) REVERT: A 740 MET cc_start: 0.8754 (tpt) cc_final: 0.8469 (tpt) REVERT: A 1050 MET cc_start: 0.8899 (pmm) cc_final: 0.8591 (pmm) REVERT: B 1050 MET cc_start: 0.8224 (pmm) cc_final: 0.7525 (pmm) REVERT: C 869 MET cc_start: 0.7815 (pmm) cc_final: 0.7428 (pmm) REVERT: C 1050 MET cc_start: 0.8120 (ptp) cc_final: 0.7816 (ptp) REVERT: E 17 GLU cc_start: 0.5435 (pp20) cc_final: 0.5087 (pm20) REVERT: E 192 GLU cc_start: 0.0767 (mm-30) cc_final: 0.0506 (pt0) REVERT: F 129 MET cc_start: 0.6188 (tpp) cc_final: 0.4903 (tpp) REVERT: L 94 MET cc_start: 0.0502 (mmt) cc_final: -0.0268 (tpp) REVERT: G 40 TRP cc_start: 0.6974 (m100) cc_final: 0.6239 (m100) REVERT: D 34 MET cc_start: 0.4053 (tpt) cc_final: 0.2275 (mmm) outliers start: 1 outliers final: 0 residues processed: 105 average time/residue: 0.4860 time to fit residues: 88.8700 Evaluate side-chains 79 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 3.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 411 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 chunk 311 optimal weight: 30.0000 chunk 241 optimal weight: 8.9990 chunk 359 optimal weight: 20.0000 chunk 238 optimal weight: 9.9990 chunk 425 optimal weight: 0.0980 chunk 266 optimal weight: 9.9990 chunk 259 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 474 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN A1083 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 ASN B 564 GLN ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35985 Z= 0.270 Angle : 0.619 14.207 48984 Z= 0.313 Chirality : 0.045 0.443 5724 Planarity : 0.004 0.056 6255 Dihedral : 6.047 57.331 5904 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4383 helix: 1.52 (0.20), residues: 675 sheet: 0.28 (0.16), residues: 1114 loop : -1.50 (0.12), residues: 2594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.006 0.001 HIS D 185 PHE 0.025 0.002 PHE A 541 TYR 0.021 0.002 TYR B 266 ARG 0.008 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 4.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 740 MET cc_start: 0.8798 (tpt) cc_final: 0.8488 (tpt) REVERT: A 1050 MET cc_start: 0.8942 (pmm) cc_final: 0.8538 (pmm) REVERT: B 1050 MET cc_start: 0.8236 (pmm) cc_final: 0.7500 (pmm) REVERT: C 869 MET cc_start: 0.7921 (pmm) cc_final: 0.7457 (pmm) REVERT: C 900 MET cc_start: 0.8706 (ppp) cc_final: 0.7739 (ppp) REVERT: E 17 GLU cc_start: 0.5693 (pp20) cc_final: 0.5168 (pm20) REVERT: E 148 GLU cc_start: 0.4835 (pm20) cc_final: 0.4589 (pm20) REVERT: E 192 GLU cc_start: 0.1298 (mm-30) cc_final: 0.0992 (pt0) REVERT: F 129 MET cc_start: 0.5890 (tpp) cc_final: 0.4741 (tpp) REVERT: F 167 PHE cc_start: 0.3215 (t80) cc_final: 0.2680 (t80) REVERT: L 94 MET cc_start: 0.0472 (mmt) cc_final: -0.0059 (tpp) REVERT: G 40 TRP cc_start: 0.7162 (m100) cc_final: 0.6514 (m100) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.4943 time to fit residues: 88.1681 Evaluate side-chains 80 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 3.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 262 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 253 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 289 optimal weight: 2.9990 chunk 210 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 334 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN G 171 GLN ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35985 Z= 0.183 Angle : 0.550 12.773 48984 Z= 0.277 Chirality : 0.044 0.475 5724 Planarity : 0.004 0.056 6255 Dihedral : 5.610 56.040 5904 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.20 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.13), residues: 4383 helix: 1.80 (0.21), residues: 675 sheet: 0.35 (0.16), residues: 1079 loop : -1.41 (0.12), residues: 2629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 175 HIS 0.006 0.001 HIS D 185 PHE 0.020 0.001 PHE A 541 TYR 0.018 0.001 TYR H 64 ARG 0.009 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 4.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.5644 (tt) cc_final: 0.4214 (mp) REVERT: A 740 MET cc_start: 0.8759 (tpt) cc_final: 0.8494 (tpt) REVERT: A 1050 MET cc_start: 0.8886 (pmm) cc_final: 0.8623 (pmm) REVERT: B 1050 MET cc_start: 0.8203 (pmm) cc_final: 0.7389 (pmm) REVERT: C 869 MET cc_start: 0.7687 (pmm) cc_final: 0.7286 (pmm) REVERT: C 1050 MET cc_start: 0.7963 (ptp) cc_final: 0.7399 (ptp) REVERT: E 17 GLU cc_start: 0.5269 (pp20) cc_final: 0.4749 (pm20) REVERT: E 192 GLU cc_start: 0.1290 (mm-30) cc_final: 0.0990 (pt0) REVERT: F 129 MET cc_start: 0.5823 (tpp) cc_final: 0.4636 (tpp) REVERT: L 94 MET cc_start: 0.0445 (mmt) cc_final: -0.0045 (tpp) REVERT: L 192 GLU cc_start: 0.6231 (mm-30) cc_final: 0.5876 (mm-30) REVERT: L 216 ARG cc_start: 0.2430 (tmm-80) cc_final: 0.2045 (ptt180) REVERT: G 40 TRP cc_start: 0.7175 (m100) cc_final: 0.6610 (m100) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.5235 time to fit residues: 91.1956 Evaluate side-chains 81 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 4.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 386 optimal weight: 8.9990 chunk 407 optimal weight: 40.0000 chunk 371 optimal weight: 30.0000 chunk 396 optimal weight: 40.0000 chunk 238 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 311 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 357 optimal weight: 5.9990 chunk 374 optimal weight: 7.9990 chunk 394 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN A 907 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** C1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN G 142 ASN ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 35985 Z= 0.451 Angle : 0.793 14.538 48984 Z= 0.406 Chirality : 0.049 0.522 5724 Planarity : 0.005 0.076 6255 Dihedral : 7.044 59.339 5904 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 24.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.37 % Favored : 91.58 % Rotamer: Outliers : 0.03 % Allowed : 0.96 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.12), residues: 4383 helix: 0.87 (0.19), residues: 684 sheet: -0.10 (0.15), residues: 1117 loop : -1.75 (0.12), residues: 2582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.009 0.002 HIS C1064 PHE 0.028 0.003 PHE A 541 TYR 0.033 0.003 TYR H 64 ARG 0.011 0.001 ARG D 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 110 time to evaluate : 4.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8393 (p90) cc_final: 0.7841 (p90) REVERT: A 552 LEU cc_start: 0.6542 (tt) cc_final: 0.5033 (mp) REVERT: A 1050 MET cc_start: 0.8976 (pmm) cc_final: 0.8503 (pmm) REVERT: B 1050 MET cc_start: 0.8314 (pmm) cc_final: 0.7070 (pmm) REVERT: C 869 MET cc_start: 0.7949 (pmm) cc_final: 0.7477 (pmm) REVERT: C 900 MET cc_start: 0.8976 (ppp) cc_final: 0.8024 (ppp) REVERT: C 1050 MET cc_start: 0.8098 (ptp) cc_final: 0.7360 (ptp) REVERT: E 113 ARG cc_start: 0.7638 (mmp-170) cc_final: 0.6396 (ptt-90) REVERT: E 148 GLU cc_start: 0.4798 (pm20) cc_final: 0.4555 (pm20) REVERT: E 192 GLU cc_start: 0.0821 (mm-30) cc_final: 0.0614 (pt0) REVERT: F 167 PHE cc_start: 0.3647 (t80) cc_final: 0.3220 (t80) REVERT: L 192 GLU cc_start: 0.6217 (mm-30) cc_final: 0.5923 (mm-30) REVERT: H 149 SER cc_start: 0.5523 (m) cc_final: 0.5145 (t) REVERT: D 34 MET cc_start: 0.3834 (tpt) cc_final: 0.3268 (tpp) outliers start: 1 outliers final: 0 residues processed: 111 average time/residue: 0.6085 time to fit residues: 113.6763 Evaluate side-chains 84 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 4.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 260 optimal weight: 6.9990 chunk 418 optimal weight: 50.0000 chunk 255 optimal weight: 2.9990 chunk 198 optimal weight: 0.0980 chunk 291 optimal weight: 0.8980 chunk 439 optimal weight: 6.9990 chunk 404 optimal weight: 6.9990 chunk 349 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35985 Z= 0.188 Angle : 0.590 10.687 48984 Z= 0.298 Chirality : 0.046 0.468 5724 Planarity : 0.004 0.056 6255 Dihedral : 6.034 57.915 5904 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.13), residues: 4383 helix: 1.47 (0.20), residues: 684 sheet: 0.02 (0.16), residues: 1097 loop : -1.59 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.008 0.001 HIS D 185 PHE 0.026 0.001 PHE C 906 TYR 0.021 0.001 TYR H 64 ARG 0.005 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8766 Ramachandran restraints generated. 4383 Oldfield, 0 Emsley, 4383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 4.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 552 LEU cc_start: 0.6169 (tt) cc_final: 0.4614 (mp) REVERT: A 1050 MET cc_start: 0.8982 (pmm) cc_final: 0.8709 (pmm) REVERT: B 1050 MET cc_start: 0.8280 (pmm) cc_final: 0.7354 (pmm) REVERT: C 869 MET cc_start: 0.7704 (pmm) cc_final: 0.7249 (pmm) REVERT: C 900 MET cc_start: 0.8941 (ppp) cc_final: 0.8145 (ppp) REVERT: C 1050 MET cc_start: 0.7981 (ptp) cc_final: 0.7674 (ptp) REVERT: E 113 ARG cc_start: 0.7431 (mmp-170) cc_final: 0.6217 (ptt-90) REVERT: E 192 GLU cc_start: 0.0772 (mm-30) cc_final: 0.0424 (pt0) REVERT: F 129 MET cc_start: 0.5991 (tpp) cc_final: 0.4667 (tpp) REVERT: G 94 MET cc_start: -0.0789 (pmm) cc_final: -0.1987 (ptp) REVERT: H 149 SER cc_start: 0.5155 (m) cc_final: 0.4729 (t) REVERT: D 34 MET cc_start: 0.3162 (tpt) cc_final: 0.2643 (tpp) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.5131 time to fit residues: 91.4054 Evaluate side-chains 85 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 4.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 441 random chunks: chunk 277 optimal weight: 0.7980 chunk 372 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 322 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 0.0050 chunk 350 optimal weight: 2.9990 chunk 146 optimal weight: 6.9990 chunk 359 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 239 GLN ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** F 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 ASN ** G 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.068408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048971 restraints weight = 283086.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.047864 restraints weight = 201422.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.047782 restraints weight = 152929.551| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.5990 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: