Starting phenix.real_space_refine on Tue Apr 16 17:03:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcb_34658/04_2024/8hcb_34658.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcb_34658/04_2024/8hcb_34658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcb_34658/04_2024/8hcb_34658.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcb_34658/04_2024/8hcb_34658.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcb_34658/04_2024/8hcb_34658.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hcb_34658/04_2024/8hcb_34658.pdb" } resolution = 4.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 775": "OD1" <-> "OD2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s 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: {'PCIS': 1, 'PTRANS': 11, '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: 17.75, per 1000 atoms: 0.50 Number of scatterers: 35187 At special positions: 0 Unit cell: (183.15, 146.85, 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=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 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=2.04 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=2.03 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: 13.28 Conformation dependent library (CDL) restraints added in 6.5 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: 79 helices and 73 sheets defined 18.9% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 384 through 390 removed outlier: 3.731A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.003A 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 502 through 505 Processing helix chain 'A' and resid 616 through 620 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.731A 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: 3.735A 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 Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.916A 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 918 removed outlier: 3.768A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 913 through 918' Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.561A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.015A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 4.109A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) removed outlier: 3.728A 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 337 through 343 removed outlier: 4.093A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.073A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 removed outlier: 3.514A pdb=" N TYR B 421 " --> pdb=" O ASN B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.891A pdb=" N GLU B 619 " --> pdb=" O ASN B 616 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 620' Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.653A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.669A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 782 Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 887 through 891 removed outlier: 4.142A pdb=" N GLY B 891 " --> pdb=" O PHE B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.531A pdb=" N GLN B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.645A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) 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 966 removed outlier: 3.944A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.253A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.707A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 372 removed outlier: 4.004A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA C 372 " --> pdb=" O LEU C 368 " (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 616 through 620 removed outlier: 4.120A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.561A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.715A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY C 891 " --> pdb=" O PHE C 888 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 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: 3.678A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.115A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.746A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.785A pdb=" N VAL E 88 " --> pdb=" O ALA E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 131 Processing helix chain 'F' and resid 28 through 32 removed outlier: 4.123A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 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: 3.960A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.780A pdb=" N SER L 132 " --> pdb=" O GLU L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.603A pdb=" N LYS L 193 " --> pdb=" O ALA L 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'H' and resid 65 through 72 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 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: 7.443A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.585A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 4.450A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.809A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 4.055A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 317 removed outlier: 3.586A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A 315 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.393A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (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 541 through 543 Processing sheet with id=AB1, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.784A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.747A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.715A 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 728 removed outlier: 7.004A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.004A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 4.373A 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: 3.854A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.994A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.079A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 264 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.013A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.061A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 135 through 141 removed outlier: 10.550A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.513A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.368A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.601A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.252A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.326A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.084A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 3.600A pdb=" N SER B1123 " --> pdb=" O ALA B1087 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 29 removed outlier: 3.890A pdb=" N ALA C 264 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.983A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.274A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 141 removed outlier: 4.916A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N CYS C 136 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N TYR C 160 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP C 138 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N ARG C 158 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.549A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.534A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 539 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.740A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.747A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.044A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AE9, first strand: chain 'E' and resid 22 through 23 Processing sheet with id=AF1, first strand: chain 'E' and resid 49 through 53 removed outlier: 4.837A pdb=" N LEU E 51 " --> pdb=" O LEU E 42 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 42 " --> pdb=" O LEU E 51 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 121 through 123 removed outlier: 3.559A pdb=" N PHE E 123 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL E 138 " --> pdb=" O PHE E 123 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR E 178 " --> pdb=" O ASN E 143 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 159 through 160 removed outlier: 4.635A pdb=" N TRP E 153 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.542A pdb=" N VAL F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET F 87 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.211A pdb=" N GLY F 10 " --> pdb=" O ILE F 131 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.529A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N SER F 50 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TYR F 63 " --> pdb=" O SER F 50 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 141 through 148 removed outlier: 3.837A pdb=" N GLY F 160 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA F 158 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F 201 " --> pdb=" O CYS F 161 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR F 197 " --> pdb=" O ASP F 165 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 172 through 175 removed outlier: 4.555A pdb=" N TYR F 215 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 12 through 13 removed outlier: 3.703A pdb=" N VAL L 13 " --> pdb=" O GLU L 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'L' and resid 48 through 53 removed outlier: 3.989A pdb=" N SER L 48 " --> pdb=" O LYS L 44 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS L 44 " --> pdb=" O SER L 48 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU L 52 " --> pdb=" O TRP L 40 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 67 through 70 Processing sheet with id=AG3, first strand: chain 'L' and resid 119 through 123 removed outlier: 5.958A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 159 through 160 removed outlier: 4.720A pdb=" N TRP L 153 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS L 199 " --> pdb=" O LYS L 212 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 48 through 53 removed outlier: 6.839A pdb=" N LYS G 44 " --> pdb=" O PRO G 49 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU G 51 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LEU G 42 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TYR G 92 " --> pdb=" O TYR G 41 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 67 through 70 Processing sheet with id=AG7, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.698A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN G 143 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TYR G 178 " --> pdb=" O ASN G 143 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 159 through 160 removed outlier: 4.600A pdb=" N TRP G 153 " --> pdb=" O GLN G 160 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA G 198 " --> pdb=" O LYS G 154 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N CYS G 199 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS G 212 " --> pdb=" O CYS G 199 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.555A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER H 7 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU H 83 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 35 through 39 removed outlier: 6.941A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL H 48 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 141 through 148 removed outlier: 3.911A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'H' and resid 141 through 148 removed outlier: 3.911A pdb=" N GLY H 160 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ALA H 158 " --> pdb=" O PRO H 147 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER H 201 " --> pdb=" O CYS H 161 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N TYR H 197 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER H 198 " --> pdb=" O VAL H 190 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 172 through 175 Processing sheet with id=AH5, first strand: chain 'D' and resid 6 through 7 removed outlier: 4.202A pdb=" N SER D 21 " --> pdb=" O SER D 7 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'D' and resid 10 through 11 removed outlier: 5.897A 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 45 through 50 removed outlier: 4.778A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 141 through 148 removed outlier: 3.809A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 141 through 148 removed outlier: 3.809A pdb=" N GLY D 160 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA D 158 " --> pdb=" O PRO D 147 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP D 165 " --> pdb=" O TYR D 197 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N TYR D 197 " --> pdb=" O ASP D 165 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL D 190 " --> pdb=" O SER D 198 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 174 through 175 removed outlier: 4.882A pdb=" N TYR D 215 " --> pdb=" O VAL D 232 " (cutoff:3.500A) 1166 hydrogen bonds defined for protein. 3186 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: 14.89 Time building geometry restraints manager: 14.43 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: 11197 1.34 - 1.47: 8862 1.47 - 1.59: 15731 1.59 - 1.71: 0 1.71 - 1.83: 195 Bond restraints: 35985 Sorted by residual: bond pdb=" C PRO A 986 " pdb=" N PRO A 987 " ideal model delta sigma weight residual 1.335 1.382 -0.047 1.38e-02 5.25e+03 1.18e+01 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.54e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" C PHE B 898 " pdb=" N PRO B 899 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.90e+00 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.86e+00 ... (remaining 35980 not shown) Histogram of bond angle deviations from ideal: 93.79 - 101.84: 41 101.84 - 109.89: 5071 109.89 - 117.94: 22123 117.94 - 125.99: 21292 125.99 - 134.04: 457 Bond angle restraints: 48984 Sorted by residual: angle pdb=" C SER D 151 " pdb=" CA SER D 151 " pdb=" CB SER D 151 " ideal model delta sigma weight residual 115.89 110.71 5.18 1.32e+00 5.74e-01 1.54e+01 angle pdb=" CB PRO G 18 " pdb=" CG PRO G 18 " pdb=" CD PRO G 18 " ideal model delta sigma weight residual 106.10 93.79 12.31 3.20e+00 9.77e-02 1.48e+01 angle pdb=" CA PRO G 18 " pdb=" N PRO G 18 " pdb=" CD PRO G 18 " ideal model delta sigma weight residual 112.00 106.90 5.10 1.40e+00 5.10e-01 1.33e+01 angle pdb=" C ASN A 532 " pdb=" N LEU A 533 " pdb=" CA LEU A 533 " ideal model delta sigma weight residual 121.54 128.37 -6.83 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N PRO G 18 " pdb=" CD PRO G 18 " pdb=" CG PRO G 18 " ideal model delta sigma weight residual 103.20 97.94 5.26 1.50e+00 4.44e-01 1.23e+01 ... (remaining 48979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.09: 20073 18.09 - 36.19: 1698 36.19 - 54.28: 363 54.28 - 72.38: 66 72.38 - 90.47: 30 Dihedral angle restraints: 22230 sinusoidal: 9294 harmonic: 12936 Sorted by residual: 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 93.00 -176.53 -90.47 1 1.00e+01 1.00e-02 9.68e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 -176.81 -90.19 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 2.52 -88.52 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 22227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 5261 0.090 - 0.179: 451 0.179 - 0.269: 6 0.269 - 0.358: 2 0.358 - 0.448: 4 Chirality restraints: 5724 Sorted by residual: chirality pdb=" C1 NAG A1308 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1308 " pdb=" O5 NAG A1308 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" C1 NAG B1309 " pdb=" ND2 ASN B 709 " pdb=" C2 NAG B1309 " pdb=" O5 NAG B1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.00e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 5721 not shown) Planarity restraints: 6297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1306 " 0.044 2.00e-02 2.50e+03 3.63e-02 1.65e+01 pdb=" C7 NAG C1306 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C1306 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG C1306 " -0.058 2.00e-02 2.50e+03 pdb=" O7 NAG C1306 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO B 373 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 205 " -0.043 5.00e-02 4.00e+02 6.58e-02 6.93e+00 pdb=" N PRO D 206 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 206 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO D 206 " -0.036 5.00e-02 4.00e+02 ... (remaining 6294 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 5138 2.77 - 3.30: 31552 3.30 - 3.83: 58208 3.83 - 4.37: 63810 4.37 - 4.90: 112553 Nonbonded interactions: 271261 Sorted by model distance: nonbonded pdb=" OG SER D 28 " pdb=" OG1 THR D 31 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR A 430 " pdb=" O PHE A 515 " model vdw 2.244 2.440 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.255 2.440 nonbonded pdb=" O GLY B 880 " pdb=" OG SER B 884 " model vdw 2.272 2.440 nonbonded pdb=" O CYS B1032 " pdb=" OG SER B1051 " model vdw 2.279 2.440 ... (remaining 271256 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.020 Extract box with map and model: 5.760 Check model and map are aligned: 0.490 Set scattering table: 0.310 Process input model: 91.470 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 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 0.047 35985 Z= 0.198 Angle : 0.604 12.313 48984 Z= 0.302 Chirality : 0.047 0.448 5724 Planarity : 0.005 0.068 6255 Dihedral : 13.629 89.064 13737 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.39 % Allowed : 0.62 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.57 (0.12), residues: 4383 helix: 1.38 (0.20), residues: 648 sheet: 0.70 (0.16), residues: 1032 loop : -1.33 (0.11), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 36 HIS 0.004 0.000 HIS D 221 PHE 0.018 0.001 PHE A 543 TYR 0.033 0.001 TYR F 166 ARG 0.011 0.000 ARG E 59 *********************** 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: 15 poor density : 154 time to evaluate : 3.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 997 ILE cc_start: 0.9260 (pt) cc_final: 0.9034 (pt) REVERT: C 900 MET cc_start: 0.8355 (mpp) cc_final: 0.7979 (mpp) REVERT: F 84 PHE cc_start: 0.6808 (m-80) cc_final: 0.6501 (m-80) REVERT: D 34 MET cc_start: 0.7321 (mpp) cc_final: 0.7094 (mpp) REVERT: D 129 MET cc_start: 0.0045 (mmt) cc_final: -0.0191 (mmt) outliers start: 15 outliers final: 5 residues processed: 167 average time/residue: 0.4966 time to fit residues: 137.0461 Evaluate side-chains 112 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 3.988 ------------------------------------------------------------------------------- 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: 10.0000 chunk 334 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 chunk 225 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 345 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 257 optimal weight: 10.0000 chunk 400 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 334 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 907 ASN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 86 GLN L 6 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN ** L 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 35985 Z= 0.406 Angle : 0.693 11.675 48984 Z= 0.357 Chirality : 0.048 0.446 5724 Planarity : 0.005 0.059 6255 Dihedral : 6.878 59.760 5904 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.27 % Favored : 94.71 % Rotamer: Outliers : 0.08 % Allowed : 6.21 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.59 (0.12), residues: 4383 helix: 1.56 (0.20), residues: 681 sheet: 0.42 (0.16), residues: 1012 loop : -1.31 (0.11), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B1102 HIS 0.010 0.002 HIS A1064 PHE 0.043 0.002 PHE B 329 TYR 0.022 0.002 TYR C 796 ARG 0.010 0.001 ARG C 328 *********************** 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 123 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 120 time to evaluate : 3.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.6079 (pmm) cc_final: 0.5743 (pmm) REVERT: C 900 MET cc_start: 0.8826 (mpp) cc_final: 0.7913 (mpp) REVERT: E 94 MET cc_start: 0.0078 (tpp) cc_final: -0.0138 (tpp) REVERT: F 64 TYR cc_start: 0.4397 (m-10) cc_final: 0.3230 (m-80) REVERT: G 170 GLU cc_start: 0.0521 (mp0) cc_final: -0.0687 (mm-30) REVERT: H 87 MET cc_start: 0.5233 (mpp) cc_final: 0.4934 (mpp) REVERT: D 98 TYR cc_start: 0.5645 (m-10) cc_final: 0.5419 (m-10) outliers start: 3 outliers final: 1 residues processed: 122 average time/residue: 0.5468 time to fit residues: 111.1173 Evaluate side-chains 97 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 4.354 ------------------------------------------------------------------------------- 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: 4.9990 chunk 124 optimal weight: 1.9990 chunk 333 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 433 optimal weight: 7.9990 chunk 357 optimal weight: 8.9990 chunk 397 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 321 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 474 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 907 ASN E 129 GLN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN L 143 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35985 Z= 0.223 Angle : 0.534 8.976 48984 Z= 0.273 Chirality : 0.044 0.457 5724 Planarity : 0.004 0.055 6255 Dihedral : 6.342 58.864 5904 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.70 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.46 (0.13), residues: 4383 helix: 2.00 (0.21), residues: 664 sheet: 0.37 (0.16), residues: 1041 loop : -1.26 (0.12), residues: 2678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 64 HIS 0.005 0.001 HIS A1064 PHE 0.021 0.001 PHE B 329 TYR 0.013 0.001 TYR C1067 ARG 0.006 0.000 ARG B 346 *********************** 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 137 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 3.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 TYR cc_start: 0.0902 (m-80) cc_final: 0.0462 (m-80) REVERT: B 458 LYS cc_start: 0.5888 (mptt) cc_final: 0.4237 (ptpt) REVERT: C 900 MET cc_start: 0.8630 (mpp) cc_final: 0.7852 (mpp) REVERT: E 94 MET cc_start: 0.0216 (tpp) cc_final: -0.0049 (tpp) REVERT: F 64 TYR cc_start: 0.5020 (m-10) cc_final: 0.3916 (m-80) REVERT: G 170 GLU cc_start: 0.0567 (mp0) cc_final: -0.0628 (mm-30) REVERT: D 98 TYR cc_start: 0.5709 (m-10) cc_final: 0.5455 (m-10) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.5536 time to fit residues: 123.6254 Evaluate side-chains 98 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 3.983 ------------------------------------------------------------------------------- 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: 8.9990 chunk 301 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 269 optimal weight: 0.8980 chunk 402 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 210 optimal weight: 5.9990 chunk 381 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN B 185 ASN B 448 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN C 49 HIS C 196 ASN C 907 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 192 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 35985 Z= 0.326 Angle : 0.625 10.327 48984 Z= 0.318 Chirality : 0.046 0.451 5724 Planarity : 0.004 0.054 6255 Dihedral : 6.490 59.998 5904 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 4383 helix: 1.71 (0.20), residues: 661 sheet: 0.22 (0.16), residues: 1016 loop : -1.40 (0.11), residues: 2706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 124 HIS 0.006 0.001 HIS A1064 PHE 0.025 0.002 PHE C 906 TYR 0.023 0.002 TYR A 266 ARG 0.005 0.001 ARG D 19 *********************** 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 130 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 4.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7450 (tp) cc_final: 0.7213 (tt) REVERT: B 458 LYS cc_start: 0.5637 (mptt) cc_final: 0.4571 (ptpt) REVERT: C 486 PHE cc_start: 0.6471 (t80) cc_final: 0.5708 (t80) REVERT: C 900 MET cc_start: 0.8706 (mpp) cc_final: 0.8153 (mpp) REVERT: E 94 MET cc_start: 0.0993 (tpp) cc_final: 0.0551 (tpp) REVERT: F 64 TYR cc_start: 0.4652 (m-10) cc_final: 0.3791 (m-80) REVERT: L 128 GLU cc_start: -0.0988 (mp0) cc_final: -0.1210 (mp0) REVERT: H 87 MET cc_start: 0.5628 (mpp) cc_final: 0.5361 (mpp) REVERT: D 98 TYR cc_start: 0.5683 (m-10) cc_final: 0.5481 (m-10) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.5743 time to fit residues: 124.9990 Evaluate side-chains 100 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 4.148 ------------------------------------------------------------------------------- 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: 30.0000 chunk 241 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 317 optimal weight: 20.0000 chunk 175 optimal weight: 5.9990 chunk 363 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 217 optimal weight: 2.9990 chunk 382 optimal weight: 20.0000 chunk 107 optimal weight: 10.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN A 955 ASN A1071 GLN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 143 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3148 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= 0.219 Angle : 0.548 7.224 48984 Z= 0.279 Chirality : 0.045 0.459 5724 Planarity : 0.004 0.054 6255 Dihedral : 6.071 59.710 5904 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.11 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.63 (0.13), residues: 4383 helix: 1.82 (0.20), residues: 677 sheet: 0.20 (0.16), residues: 1026 loop : -1.34 (0.12), residues: 2680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.001 HIS A1064 PHE 0.025 0.001 PHE C 981 TYR 0.021 0.001 TYR G 54 ARG 0.004 0.000 ARG C 509 *********************** 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 133 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8369 (tp) cc_final: 0.7896 (mt) REVERT: A 582 LEU cc_start: 0.7617 (tp) cc_final: 0.7402 (tt) REVERT: B 458 LYS cc_start: 0.5652 (mptt) cc_final: 0.4176 (ptpt) REVERT: C 486 PHE cc_start: 0.6059 (t80) cc_final: 0.5557 (t80) REVERT: C 900 MET cc_start: 0.8461 (mpp) cc_final: 0.7762 (mpp) REVERT: E 94 MET cc_start: 0.0940 (tpp) cc_final: 0.0493 (tpp) REVERT: F 62 ILE cc_start: 0.6780 (mm) cc_final: 0.6394 (mm) REVERT: F 64 TYR cc_start: 0.5263 (m-10) cc_final: 0.4326 (m-80) REVERT: H 87 MET cc_start: 0.6094 (mpp) cc_final: 0.5823 (mpp) REVERT: D 87 MET cc_start: 0.2968 (ppp) cc_final: 0.2515 (ppp) REVERT: D 98 TYR cc_start: 0.5142 (m-10) cc_final: 0.4735 (m-10) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.5472 time to fit residues: 120.3272 Evaluate side-chains 98 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 4.264 ------------------------------------------------------------------------------- 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: 8.9990 chunk 383 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 250 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 426 optimal weight: 0.8980 chunk 354 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 370 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 487 ASN C 907 ASN ** C1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS G 204 GLN ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 35985 Z= 0.325 Angle : 0.624 10.700 48984 Z= 0.318 Chirality : 0.046 0.471 5724 Planarity : 0.005 0.055 6255 Dihedral : 6.307 59.588 5904 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.10 % Favored : 92.88 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.84 (0.13), residues: 4383 helix: 1.54 (0.20), residues: 679 sheet: 0.07 (0.16), residues: 1036 loop : -1.45 (0.12), residues: 2668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B1102 HIS 0.005 0.001 HIS B1064 PHE 0.027 0.002 PHE C 906 TYR 0.020 0.002 TYR A 266 ARG 0.008 0.001 ARG H 76 *********************** 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 127 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 4.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.7531 (tp) cc_final: 0.7226 (tt) REVERT: B 458 LYS cc_start: 0.6105 (mptt) cc_final: 0.4379 (ptpt) REVERT: C 486 PHE cc_start: 0.6549 (t80) cc_final: 0.5964 (t80) REVERT: C 900 MET cc_start: 0.8493 (mpp) cc_final: 0.7759 (mpp) REVERT: E 94 MET cc_start: 0.1419 (tpp) cc_final: 0.0850 (tpp) REVERT: F 62 ILE cc_start: 0.6900 (mm) cc_final: 0.6395 (mm) REVERT: F 64 TYR cc_start: 0.5718 (m-10) cc_final: 0.4559 (m-80) REVERT: H 87 MET cc_start: 0.6252 (mpp) cc_final: 0.5797 (mpp) REVERT: D 87 MET cc_start: 0.2643 (ppp) cc_final: 0.2074 (ppp) REVERT: D 98 TYR cc_start: 0.5142 (m-10) cc_final: 0.4853 (m-80) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.5490 time to fit residues: 113.1676 Evaluate side-chains 93 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 5.111 ------------------------------------------------------------------------------- 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: 7.9990 chunk 48 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 311 optimal weight: 20.0000 chunk 241 optimal weight: 10.0000 chunk 359 optimal weight: 7.9990 chunk 238 optimal weight: 0.0170 chunk 425 optimal weight: 9.9990 chunk 266 optimal weight: 7.9990 chunk 259 optimal weight: 6.9990 chunk 196 optimal weight: 0.9980 overall best weight: 2.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 370 ASN B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35985 Z= 0.193 Angle : 0.545 9.216 48984 Z= 0.276 Chirality : 0.045 0.463 5724 Planarity : 0.004 0.055 6255 Dihedral : 5.893 58.935 5904 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.22 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.69 (0.13), residues: 4383 helix: 1.84 (0.20), residues: 677 sheet: 0.16 (0.17), residues: 1021 loop : -1.39 (0.12), residues: 2685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 124 HIS 0.005 0.001 HIS A1064 PHE 0.020 0.001 PHE C 906 TYR 0.014 0.001 TYR A 266 ARG 0.007 0.000 ARG C 408 *********************** 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 135 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 3.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8697 (tp) cc_final: 0.8042 (mt) REVERT: B 458 LYS cc_start: 0.5949 (mptt) cc_final: 0.4310 (ptpt) REVERT: C 486 PHE cc_start: 0.6478 (t80) cc_final: 0.5988 (t80) REVERT: C 900 MET cc_start: 0.8343 (mpp) cc_final: 0.7662 (mpp) REVERT: F 62 ILE cc_start: 0.6801 (mm) cc_final: 0.6300 (mm) REVERT: F 64 TYR cc_start: 0.5698 (m-10) cc_final: 0.4565 (m-80) REVERT: H 87 MET cc_start: 0.6185 (mpp) cc_final: 0.5910 (mpp) REVERT: D 98 TYR cc_start: 0.5207 (m-10) cc_final: 0.4877 (m-10) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.5437 time to fit residues: 118.0907 Evaluate side-chains 94 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 3.757 ------------------------------------------------------------------------------- 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: 9.9990 chunk 169 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 83 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 289 optimal weight: 3.9990 chunk 210 optimal weight: 0.0050 chunk 39 optimal weight: 30.0000 chunk 334 optimal weight: 9.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B 121 ASN B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 196 ASN C 907 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35985 Z= 0.220 Angle : 0.564 9.130 48984 Z= 0.285 Chirality : 0.045 0.456 5724 Planarity : 0.004 0.055 6255 Dihedral : 5.834 58.704 5904 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.25 % Favored : 93.73 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.13), residues: 4383 helix: 1.77 (0.20), residues: 684 sheet: 0.12 (0.17), residues: 1028 loop : -1.37 (0.12), residues: 2671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 124 HIS 0.005 0.001 HIS A1064 PHE 0.029 0.001 PHE B 329 TYR 0.016 0.001 TYR B 501 ARG 0.008 0.000 ARG C 408 *********************** 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 131 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8698 (tp) cc_final: 0.8033 (mt) REVERT: A 374 PHE cc_start: 0.7557 (t80) cc_final: 0.6628 (t80) REVERT: A 582 LEU cc_start: 0.7039 (tp) cc_final: 0.6601 (tt) REVERT: A 775 ASP cc_start: 0.7565 (t70) cc_final: 0.7347 (t0) REVERT: A 1050 MET cc_start: 0.7248 (ptm) cc_final: 0.7041 (ptm) REVERT: B 458 LYS cc_start: 0.5948 (mptt) cc_final: 0.4270 (ptpt) REVERT: B 731 MET cc_start: 0.8315 (pmm) cc_final: 0.7941 (pmm) REVERT: C 486 PHE cc_start: 0.6478 (t80) cc_final: 0.6003 (t80) REVERT: C 900 MET cc_start: 0.8353 (mpp) cc_final: 0.7662 (mpp) REVERT: F 62 ILE cc_start: 0.6825 (mm) cc_final: 0.6295 (mm) REVERT: F 64 TYR cc_start: 0.5833 (m-10) cc_final: 0.4658 (m-80) REVERT: L 59 ARG cc_start: 0.4467 (mmt-90) cc_final: 0.3263 (mmm-85) REVERT: G 110 GLU cc_start: 0.3096 (mp0) cc_final: 0.2894 (mp0) REVERT: H 87 MET cc_start: 0.6558 (mpp) cc_final: 0.6320 (mpp) REVERT: D 98 TYR cc_start: 0.5444 (m-10) cc_final: 0.4991 (m-80) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.5651 time to fit residues: 120.0774 Evaluate side-chains 97 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 4.086 ------------------------------------------------------------------------------- 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: 0.0870 chunk 407 optimal weight: 4.9990 chunk 371 optimal weight: 50.0000 chunk 396 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 121 optimal weight: 0.0060 chunk 357 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 chunk 394 optimal weight: 7.9990 overall best weight: 3.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35985 Z= 0.257 Angle : 0.583 9.840 48984 Z= 0.296 Chirality : 0.045 0.462 5724 Planarity : 0.004 0.055 6255 Dihedral : 5.912 59.780 5904 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.37 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.77 (0.13), residues: 4383 helix: 1.68 (0.20), residues: 683 sheet: 0.05 (0.16), residues: 1046 loop : -1.41 (0.12), residues: 2654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 124 HIS 0.006 0.001 HIS A1064 PHE 0.021 0.001 PHE C 275 TYR 0.021 0.001 TYR B 501 ARG 0.008 0.000 ARG C 190 *********************** 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 137 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 4.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7856 (t80) cc_final: 0.6995 (t80) REVERT: A 378 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7946 (pttm) REVERT: B 458 LYS cc_start: 0.6454 (mptt) cc_final: 0.4716 (ptpt) REVERT: B 775 ASP cc_start: 0.7300 (m-30) cc_final: 0.6980 (m-30) REVERT: C 486 PHE cc_start: 0.6499 (t80) cc_final: 0.6025 (t80) REVERT: C 900 MET cc_start: 0.8396 (mpp) cc_final: 0.7702 (mpp) REVERT: F 62 ILE cc_start: 0.6852 (mm) cc_final: 0.6302 (mm) REVERT: F 64 TYR cc_start: 0.6136 (m-10) cc_final: 0.4973 (m-80) REVERT: L 59 ARG cc_start: 0.4239 (mmt-90) cc_final: 0.3270 (mmm-85) REVERT: G 216 ARG cc_start: 0.6977 (tmt170) cc_final: 0.5554 (ttp80) REVERT: H 87 MET cc_start: 0.6607 (mpp) cc_final: 0.6199 (mpp) REVERT: D 98 TYR cc_start: 0.5518 (m-10) cc_final: 0.5102 (m-80) REVERT: D 119 ASP cc_start: 0.4159 (m-30) cc_final: 0.3957 (m-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.5691 time to fit residues: 125.6247 Evaluate side-chains 102 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 3.889 ------------------------------------------------------------------------------- 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: 20.0000 chunk 255 optimal weight: 0.9980 chunk 198 optimal weight: 0.8980 chunk 291 optimal weight: 7.9990 chunk 439 optimal weight: 30.0000 chunk 404 optimal weight: 10.0000 chunk 349 optimal weight: 0.3980 chunk 36 optimal weight: 0.3980 chunk 270 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 955 ASN B 370 ASN ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN B 955 ASN C 196 ASN C 907 ASN ** E 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 GLN H 185 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 35985 Z= 0.161 Angle : 0.541 9.257 48984 Z= 0.272 Chirality : 0.045 0.444 5724 Planarity : 0.004 0.055 6255 Dihedral : 5.506 59.801 5904 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.03 % 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: -0.61 (0.13), residues: 4383 helix: 2.00 (0.21), residues: 683 sheet: 0.06 (0.16), residues: 1054 loop : -1.32 (0.12), residues: 2646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 124 HIS 0.004 0.001 HIS A1064 PHE 0.019 0.001 PHE C 275 TYR 0.021 0.001 TYR B 501 ARG 0.009 0.000 ARG C 408 ********************** 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 137 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.8499 (tp) cc_final: 0.7906 (mt) REVERT: A 378 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7878 (pttm) REVERT: A 731 MET cc_start: 0.9171 (pmm) cc_final: 0.8649 (pmm) REVERT: B 458 LYS cc_start: 0.6307 (mptt) cc_final: 0.4960 (ptpt) REVERT: C 486 PHE cc_start: 0.6460 (t80) cc_final: 0.5975 (t80) REVERT: C 900 MET cc_start: 0.8116 (mpp) cc_final: 0.7602 (mpp) REVERT: F 62 ILE cc_start: 0.6517 (mm) cc_final: 0.5341 (tt) REVERT: F 64 TYR cc_start: 0.6066 (m-10) cc_final: 0.4575 (m-80) REVERT: G 216 ARG cc_start: 0.6696 (tmt170) cc_final: 0.6161 (mtp-110) REVERT: H 87 MET cc_start: 0.6508 (mpp) cc_final: 0.6294 (mpp) REVERT: D 98 TYR cc_start: 0.5475 (m-10) cc_final: 0.5024 (m-80) REVERT: D 119 ASP cc_start: 0.3694 (m-30) cc_final: 0.3412 (m-30) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.5641 time to fit residues: 126.2280 Evaluate side-chains 103 residues out of total 3891 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 4.213 ------------------------------------------------------------------------------- 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: 2.9990 chunk 372 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 322 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 350 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 359 optimal weight: 0.0670 chunk 44 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: