Starting phenix.real_space_refine on Mon Sep 14 14:41:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cai_30332/09_2026/7cai_30332.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 126 5.16 5 C 19889 2.51 5 N 5094 2.21 5 O 6157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31266 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7993 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 7995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7995 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 8000 Classifications: {'peptide': 1023} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 50, 'TRANS': 972} Chain breaks: 7 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1635 Chain: "E" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 1611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 207, 1605 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 1635 Chain: "G" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1608 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 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 chiralities: 2 Chain: "L" 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 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 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "V" 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 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 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 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 chiralities: 10 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER D 114 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER D 114 " occ=0.48 residue: pdb=" N ASER F 114 " occ=0.52 ... (10 atoms not shown) pdb=" OG BSER F 114 " occ=0.48 Time building chain proxies: 8.02, per 1000 atoms: 0.26 Number of scatterers: 31266 At special positions: 0 Unit cell: (196.56, 171.6, 190.32, 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 126 16.00 O 6157 8.00 N 5094 7.00 C 19889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 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 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 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 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 203 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 147 " - pdb=" SG CYS G 203 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 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 V 1 " - " NAG V 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG H 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1098 " " NAG L 1 " - " ASN A1134 " " NAG M 1 " - " ASN B 234 " " 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 234 " " NAG S 1 " - " ASN C 717 " " NAG T 1 " - " ASN C 801 " " NAG U 1 " - " ASN C1098 " " NAG V 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 1.5 seconds 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7342 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 78 sheets defined 18.8% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.704A pdb=" N THR A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 383 through 388 removed outlier: 3.787A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 408 Processing helix chain 'A' and resid 746 through 757 removed outlier: 4.238A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 772 removed outlier: 3.577A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 783 removed outlier: 3.632A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.550A pdb=" N ASP A 820 " --> pdb=" O SER A 816 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.588A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 907 removed outlier: 4.032A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.526A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU A 918 " --> pdb=" O ASN A 914 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.568A pdb=" N GLN A 965 " --> pdb=" O THR A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.867A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.148A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A1004 " --> pdb=" O ARG A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.945A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.951A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.542A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.552A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.687A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.516A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.591A pdb=" N ASP B 820 " --> pdb=" O SER B 816 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 821 " --> pdb=" O PHE B 817 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 4.262A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY B 885 " --> pdb=" O THR B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.505A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 941 removed outlier: 3.631A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.587A pdb=" N ALA B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.573A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.655A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 994 " --> pdb=" O GLU B 990 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.116A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 4.077A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 370 removed outlier: 4.030A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 366 through 370' Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.584A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.514A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.518A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 4.265A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 782 removed outlier: 4.475A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.630A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.594A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 903 through 908 removed outlier: 3.810A pdb=" N GLY C 908 " --> pdb=" O TYR C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.932A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.633A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.489A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP C 994 " --> pdb=" O GLU C 990 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.344A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C1145 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1140 through 1146' Processing helix chain 'D' and resid 121 through 128 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 163 through 165 No H-bonds generated for 'chain 'E' and resid 163 through 165' Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing helix chain 'G' and resid 163 through 165 No H-bonds generated for 'chain 'G' and resid 163 through 165' Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 192 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 194 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.893A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.798A 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: 3.916A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 129 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.682A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.697A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 4.184A pdb=" N LYS A 537 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LEU A 552 " --> pdb=" O LYS A 537 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.549A 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: 3.683A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 575 through 577 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.291A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB5, first strand: chain 'A' and resid 718 through 728 removed outlier: 3.540A pdb=" N THR A1066 " --> pdb=" O SER A 721 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.506A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 52 removed outlier: 3.843A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.566A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.566A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B 128 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 89 through 91 Processing sheet with id=AC5, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AC6, first strand: chain 'B' and resid 201 through 205 removed outlier: 3.851A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 313 through 317 removed outlier: 5.231A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 326 through 328 removed outlier: 3.597A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 334 through 335 removed outlier: 6.995A pdb=" N ASN B 334 " --> pdb=" O VAL B 362 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.225A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.225A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N ARG B 403 " --> pdb=" O ALA B 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU B 513 " --> pdb=" O CYS B 432 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 453 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD5, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AD6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.196A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 672 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722 Processing sheet with id=AD9, first strand: chain 'B' and resid 718 through 722 removed outlier: 7.165A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 734 through 735 removed outlier: 3.836A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 789 through 790 removed outlier: 3.566A pdb=" N LYS B 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.696A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE5, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.055A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE C 92 " --> pdb=" O PHE C 192 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE C 194 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.055A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.980A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.577A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.098A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 311 through 318 removed outlier: 4.422A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF3, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.210A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.210A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 9.729A pdb=" N ARG C 403 " --> pdb=" O ALA C 348 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF6, first strand: chain 'C' and resid 576 through 577 Processing sheet with id=AF7, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.570A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF9, first strand: chain 'C' and resid 718 through 720 removed outlier: 6.212A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 723 through 728 removed outlier: 3.703A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AG4, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AG5, first strand: chain 'D' and resid 3 through 6 removed outlier: 4.170A pdb=" N VAL D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.631A pdb=" N GLN D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU D 104 " --> pdb=" O GLN D 10 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 44 through 45 Processing sheet with id=AG8, first strand: chain 'D' and resid 47 through 48 Processing sheet with id=AG9, first strand: chain 'D' and resid 116 through 118 Processing sheet with id=AH1, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.921A pdb=" N TYR D 191 " --> pdb=" O PHE D 206 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE D 206 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 204 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.950A pdb=" N GLU E 82 " --> pdb=" O THR E 69 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.122A pdb=" N GLU E 10 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR E 50 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER E 59 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 130 through 131 removed outlier: 3.700A pdb=" N GLY E 146 " --> pdb=" O LEU E 131 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL E 191 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU E 145 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 189 " --> pdb=" O LEU E 145 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER E 184 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA E 175 " --> pdb=" O SER E 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER E 186 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL E 188 " --> pdb=" O HIS E 171 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 158 through 161 removed outlier: 3.947A pdb=" N THR E 158 " --> pdb=" O ASN E 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 206 " --> pdb=" O THR E 158 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR E 201 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS E 203 " --> pdb=" O LYS E 216 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS E 216 " --> pdb=" O CYS E 203 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL E 205 " --> pdb=" O VAL E 214 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL E 214 " --> pdb=" O VAL E 205 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 3 through 6 removed outlier: 4.170A pdb=" N VAL F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'F' and resid 9 through 12 removed outlier: 3.631A pdb=" N GLN F 10 " --> pdb=" O LYS F 102 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 104 " --> pdb=" O GLN F 10 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 44 through 45 Processing sheet with id=AH9, first strand: chain 'F' and resid 47 through 48 Processing sheet with id=AI1, first strand: chain 'F' and resid 116 through 118 Processing sheet with id=AI2, first strand: chain 'F' and resid 153 through 154 removed outlier: 3.920A pdb=" N TYR F 191 " --> pdb=" O PHE F 206 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE F 206 " --> pdb=" O TYR F 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS F 204 " --> pdb=" O CYS F 193 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.950A pdb=" N GLU G 82 " --> pdb=" O THR G 69 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N THR G 69 " --> pdb=" O GLU G 82 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.122A pdb=" N GLU G 10 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR G 50 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER G 59 " --> pdb=" O TYR G 50 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'G' and resid 130 through 131 removed outlier: 3.700A pdb=" N GLY G 146 " --> pdb=" O LEU G 131 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL G 191 " --> pdb=" O ALA G 143 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU G 145 " --> pdb=" O VAL G 189 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL G 189 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER G 184 " --> pdb=" O ALA G 175 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA G 175 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER G 186 " --> pdb=" O PHE G 173 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL G 188 " --> pdb=" O HIS G 171 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'G' and resid 158 through 161 removed outlier: 3.948A pdb=" N THR G 158 " --> pdb=" O ASN G 206 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN G 206 " --> pdb=" O THR G 158 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYR G 201 " --> pdb=" O VAL G 218 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS G 203 " --> pdb=" O LYS G 216 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS G 216 " --> pdb=" O CYS G 203 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VAL G 205 " --> pdb=" O VAL G 214 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL G 214 " --> pdb=" O VAL G 205 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2436 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: 9.39 Time building geometry restraints manager: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9360 1.33 - 1.46: 8328 1.46 - 1.59: 14136 1.59 - 1.71: 0 1.71 - 1.84: 157 Bond restraints: 31981 Sorted by residual: bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.580 -0.246 2.34e-02 1.83e+03 1.10e+02 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.331 1.441 -0.110 1.63e-02 3.76e+03 4.55e+01 bond pdb=" C ILE C 805 " pdb=" N LEU C 806 " ideal model delta sigma weight residual 1.331 1.234 0.097 2.07e-02 2.33e+03 2.21e+01 bond pdb=" C ILE A 805 " pdb=" N LEU A 806 " ideal model delta sigma weight residual 1.331 1.263 0.068 2.07e-02 2.33e+03 1.08e+01 bond pdb=" C ILE C 587 " pdb=" N THR C 588 " ideal model delta sigma weight residual 1.331 1.264 0.067 2.07e-02 2.33e+03 1.05e+01 ... (remaining 31976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 42680 3.15 - 6.30: 749 6.30 - 9.46: 82 9.46 - 12.61: 12 12.61 - 15.76: 6 Bond angle restraints: 43529 Sorted by residual: angle pdb=" C TRP B 152 " pdb=" CA TRP B 152 " pdb=" CB TRP B 152 " ideal model delta sigma weight residual 115.79 108.21 7.58 1.19e+00 7.06e-01 4.06e+01 angle pdb=" C VAL B 159 " pdb=" N TYR B 160 " pdb=" CA TYR B 160 " ideal model delta sigma weight residual 122.84 112.21 10.63 1.81e+00 3.05e-01 3.45e+01 angle pdb=" C LEU B 335 " pdb=" N CYS B 336 " pdb=" CA CYS B 336 " ideal model delta sigma weight residual 121.61 129.36 -7.75 1.39e+00 5.18e-01 3.11e+01 angle pdb=" N HIS B 66 " pdb=" CA HIS B 66 " pdb=" C HIS B 66 " ideal model delta sigma weight residual 108.24 115.45 -7.21 1.32e+00 5.74e-01 2.99e+01 angle pdb=" C VAL B 83 " pdb=" N LEU B 84 " pdb=" CA LEU B 84 " ideal model delta sigma weight residual 123.96 116.82 7.14 1.44e+00 4.82e-01 2.46e+01 ... (remaining 43524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 17776 17.51 - 35.02: 633 35.02 - 52.53: 86 52.53 - 70.03: 35 70.03 - 87.54: 15 Dihedral angle restraints: 18545 sinusoidal: 7136 harmonic: 11409 Sorted by residual: dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual -86.00 -173.16 87.16 1 1.00e+01 1.00e-02 9.12e+01 dihedral pdb=" CA VAL B 159 " pdb=" C VAL B 159 " pdb=" N TYR B 160 " pdb=" CA TYR B 160 " ideal model delta harmonic sigma weight residual -180.00 -133.49 -46.51 0 5.00e+00 4.00e-02 8.65e+01 dihedral pdb=" CA HIS B 66 " pdb=" C HIS B 66 " pdb=" N ALA B 67 " pdb=" CA ALA B 67 " ideal model delta harmonic sigma weight residual 180.00 135.58 44.42 0 5.00e+00 4.00e-02 7.89e+01 ... (remaining 18542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.175: 5076 0.175 - 0.349: 28 0.349 - 0.524: 4 0.524 - 0.699: 2 0.699 - 0.873: 1 Chirality restraints: 5111 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.91e+01 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.99e+00 ... (remaining 5108 not shown) Planarity restraints: 5575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 64 " 0.033 2.00e-02 2.50e+03 2.25e-02 1.27e+01 pdb=" CG TRP B 64 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TRP B 64 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP B 64 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 64 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 64 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 64 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 64 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 64 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 64 " 0.033 2.00e-02 2.50e+03 2.17e-02 1.17e+01 pdb=" CG TRP C 64 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP C 64 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP C 64 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 64 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 64 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 64 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 64 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 64 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 64 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 800 " 0.018 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE A 800 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 800 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 800 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 800 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 800 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 800 " -0.000 2.00e-02 2.50e+03 ... (remaining 5572 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 36 2.14 - 2.83: 10828 2.83 - 3.52: 44619 3.52 - 4.21: 77236 4.21 - 4.90: 129080 Nonbonded interactions: 261799 Sorted by model distance: nonbonded pdb=" CZ PHE B 559 " pdb=" O PHE B 565 " model vdw 1.448 3.340 nonbonded pdb=" CB PHE A 43 " pdb=" OE1 GLN B 563 " model vdw 1.528 3.440 nonbonded pdb=" CA PHE A 43 " pdb=" OE1 GLN B 563 " model vdw 1.602 3.470 nonbonded pdb=" CB LEU A 560 " pdb=" OE1 GLN A 563 " model vdw 1.739 3.440 nonbonded pdb=" O ASN A 856 " pdb=" N LEU A 858 " model vdw 1.739 3.120 ... (remaining 261794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 524 or (resid 525 and (name N o \ r name CA or name C or name O or name CB )) or resid 526 through 1310)) selection = (chain 'B' and (resid 25 through 527 or (resid 528 and (name N or name CA or nam \ e C or name O or name CB )) or resid 529 through 1310)) selection = (chain 'C' and (resid 25 through 390 or (resid 391 and (name N or name CA or nam \ e C or name O or name CB )) or resid 392 through 524 or (resid 525 and (name N o \ r name CA or name C or name O or name CB )) or resid 526 through 527 or (resid 5 \ 28 and (name N or name CA or name C or name O or name CB )) or resid 529 through \ 698 or (resid 699 and (name N or name CA or name C or name O or name CB )) or r \ esid 700 through 1310)) } ncs_group { reference = (chain 'D' and (resid 2 through 113 or resid 115 through 208)) selection = (chain 'F' and (resid 2 through 113 or resid 115 through 208)) } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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' selection = chain 'V' } 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=0.48 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.300 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.180 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 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 : 0.012 0.246 32083 Z= 0.533 Angle : 1.120 20.248 43791 Z= 0.591 Chirality : 0.063 0.873 5111 Planarity : 0.006 0.072 5530 Dihedral : 10.114 87.542 11080 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.27 % Favored : 90.55 % Rotamer: Outliers : 0.70 % Allowed : 1.03 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.52 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.10), residues: 3857 helix: -4.35 (0.10), residues: 661 sheet: -2.76 (0.13), residues: 922 loop : -2.56 (0.10), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B 815 TYR 0.038 0.003 TYR B 873 PHE 0.054 0.004 PHE A 800 TRP 0.059 0.003 TRP B 64 HIS 0.011 0.003 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.01177 / 0.53 (31981) covalent geometry : angle 1.08431 / 0.58 (43529) SS BOND : bond 0.00682 / 0.47 ( 41) SS BOND : angle 1.56991 / 1.11 ( 82) hydrogen bonds : bond 0.29907 / 19.83 ( 893) hydrogen bonds : angle 12.35822 / 8.49 ( 2436) Misc. bond : bond 0.00166 / 0.11 ( 1) link_BETA1-4 : bond 0.00440 / 0.31 ( 15) link_BETA1-4 : angle 2.62207 / 1.63 ( 45) link_NAG-ASN : bond 0.01147 / 0.78 ( 45) link_NAG-ASN : angle 4.86690 / 3.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 318 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 SER cc_start: 0.8310 (t) cc_final: 0.8037 (p) REVERT: B 854 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.7941 (ttpp) REVERT: B 904 TYR cc_start: 0.8000 (m-10) cc_final: 0.7686 (m-10) REVERT: C 190 ARG cc_start: 0.5093 (ttt180) cc_final: 0.4471 (ttt180) outliers start: 24 outliers final: 17 residues processed: 339 average time/residue: 0.2206 time to fit residues: 116.4190 Evaluate side-chains 168 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 PHE Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain C residue 556 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 437 ASN A 439 ASN A 580 GLN A 655 HIS A 901 GLN A 913 GLN A1088 HIS B 69 HIS B 81 ASN ** B 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 218 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS C 81 ASN C 137 ASN C 239 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN C 437 ASN C 580 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 913 GLN C1002 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN D 10 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN D 138 ASN D 188 HIS E 55 ASN F 10 GLN ** F 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 ASN F 188 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.136500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.097972 restraints weight = 141254.320| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 5.19 r_work: 0.3382 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 32083 Z= 0.197 Angle : 0.828 20.469 43791 Z= 0.425 Chirality : 0.051 0.486 5111 Planarity : 0.006 0.084 5530 Dihedral : 8.052 80.113 4219 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.91 % Favored : 94.94 % Rotamer: Outliers : 1.26 % Allowed : 4.84 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.11), residues: 3857 helix: -2.26 (0.15), residues: 689 sheet: -2.54 (0.14), residues: 928 loop : -2.03 (0.11), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 319 TYR 0.031 0.002 TYR A 904 PHE 0.031 0.002 PHE B 135 TRP 0.032 0.002 TRP B 64 HIS 0.009 0.002 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (31981) covalent geometry : angle 0.79727 / 0.42 (43529) SS BOND : bond 0.00924 / 0.52 ( 41) SS BOND : angle 1.83261 / 1.24 ( 82) hydrogen bonds : bond 0.05335 / 3.51 ( 893) hydrogen bonds : angle 7.77242 / 5.30 ( 2436) Misc. bond : bond 0.00400 / 0.27 ( 1) link_BETA1-4 : bond 0.00574 / 0.44 ( 15) link_BETA1-4 : angle 1.41299 / 0.83 ( 45) link_NAG-ASN : bond 0.00555 / 0.40 ( 45) link_NAG-ASN : angle 3.80812 / 2.97 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 187 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5733 (mtt) cc_final: 0.5525 (mtt) REVERT: A 436 TRP cc_start: 0.0905 (p90) cc_final: 0.0676 (p90) REVERT: A 565 PHE cc_start: 0.8427 (m-10) cc_final: 0.8217 (m-80) REVERT: A 854 LYS cc_start: 0.7445 (OUTLIER) cc_final: 0.7207 (ttpt) REVERT: B 129 LYS cc_start: 0.7811 (mtmm) cc_final: 0.7510 (mmtt) REVERT: B 796 ASP cc_start: 0.6576 (p0) cc_final: 0.6051 (p0) REVERT: B 854 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7726 (tmmm) REVERT: B 902 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8503 (mpp) REVERT: C 190 ARG cc_start: 0.5336 (ttt180) cc_final: 0.4391 (ttm170) REVERT: C 563 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7493 (mt0) REVERT: C 740 MET cc_start: 0.8294 (tmm) cc_final: 0.8017 (tmm) REVERT: F 57 ILE cc_start: 0.1569 (mm) cc_final: 0.1232 (tp) REVERT: G 107 MET cc_start: 0.0475 (ptp) cc_final: 0.0185 (ptp) outliers start: 43 outliers final: 19 residues processed: 220 average time/residue: 0.1868 time to fit residues: 67.8059 Evaluate side-chains 170 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 902 MET Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 564 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 51 optimal weight: 0.1980 chunk 29 optimal weight: 7.9990 chunk 354 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 255 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 146 optimal weight: 8.9990 chunk 339 optimal weight: 20.0000 chunk 333 optimal weight: 3.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 856 ASN B 81 ASN B 218 GLN B 239 GLN B 901 GLN B1023 ASN C 81 ASN C 207 HIS C 218 GLN C 239 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.133058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.097376 restraints weight = 164343.309| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 6.77 r_work: 0.3330 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 32083 Z= 0.222 Angle : 0.747 20.818 43791 Z= 0.381 Chirality : 0.049 0.410 5111 Planarity : 0.005 0.082 5530 Dihedral : 7.135 68.377 4199 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.82 % Favored : 93.98 % Rotamer: Outliers : 2.08 % Allowed : 5.96 % Favored : 91.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.12), residues: 3857 helix: -0.89 (0.19), residues: 691 sheet: -2.41 (0.15), residues: 954 loop : -1.76 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 995 TYR 0.022 0.002 TYR B 495 PHE 0.021 0.002 PHE C 643 TRP 0.050 0.002 TRP B 152 HIS 0.006 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (31981) covalent geometry : angle 0.71606 / 0.37 (43529) SS BOND : bond 0.00560 / 0.36 ( 41) SS BOND : angle 1.71195 / 1.16 ( 82) hydrogen bonds : bond 0.04566 / 2.97 ( 893) hydrogen bonds : angle 7.02831 / 4.79 ( 2436) Misc. bond : bond 0.00365 / 0.24 ( 1) link_BETA1-4 : bond 0.00322 / 0.24 ( 15) link_BETA1-4 : angle 1.38472 / 0.86 ( 45) link_NAG-ASN : bond 0.00612 / 0.43 ( 45) link_NAG-ASN : angle 3.65198 / 2.89 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 153 time to evaluate : 1.197 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 436 TRP cc_start: 0.1244 (p90) cc_final: 0.0935 (p90) REVERT: A 581 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8788 (p) REVERT: A 740 MET cc_start: 0.7455 (ttp) cc_final: 0.6980 (ttt) REVERT: A 854 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.7348 (ttpt) REVERT: A 990 GLU cc_start: 0.8241 (mm-30) cc_final: 0.8030 (mm-30) REVERT: B 116 SER cc_start: 0.3509 (t) cc_final: 0.3033 (p) REVERT: B 129 LYS cc_start: 0.7806 (mtmm) cc_final: 0.7590 (mmtt) REVERT: B 153 MET cc_start: 0.4075 (mtp) cc_final: 0.3147 (mtt) REVERT: B 904 TYR cc_start: 0.8304 (m-10) cc_final: 0.8081 (m-10) REVERT: C 190 ARG cc_start: 0.5399 (ttt180) cc_final: 0.3464 (ttm170) REVERT: C 207 HIS cc_start: 0.7788 (OUTLIER) cc_final: 0.6337 (m-70) REVERT: F 57 ILE cc_start: 0.2115 (mm) cc_final: 0.1847 (tp) outliers start: 71 outliers final: 25 residues processed: 208 average time/residue: 0.1854 time to fit residues: 64.5572 Evaluate side-chains 164 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 136 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 55 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 82 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 342 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 118 optimal weight: 0.0000 chunk 208 optimal weight: 0.5980 chunk 367 optimal weight: 30.0000 chunk 380 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 ASN A 935 GLN B 81 ASN B 239 GLN C 81 ASN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.134510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.097853 restraints weight = 159915.264| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 6.80 r_work: 0.3366 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 32083 Z= 0.150 Angle : 0.669 20.548 43791 Z= 0.340 Chirality : 0.047 0.379 5111 Planarity : 0.004 0.073 5530 Dihedral : 6.423 55.513 4192 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.68 % Rotamer: Outliers : 1.88 % Allowed : 6.57 % Favored : 91.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.13), residues: 3857 helix: -0.16 (0.20), residues: 691 sheet: -2.14 (0.15), residues: 930 loop : -1.59 (0.12), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1019 TYR 0.029 0.002 TYR A 904 PHE 0.016 0.001 PHE C 643 TRP 0.052 0.002 TRP B 152 HIS 0.020 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (31981) covalent geometry : angle 0.64038 / 0.33 (43529) SS BOND : bond 0.00315 / 0.21 ( 41) SS BOND : angle 1.29394 / 0.87 ( 82) hydrogen bonds : bond 0.03830 / 2.50 ( 893) hydrogen bonds : angle 6.50891 / 4.44 ( 2436) Misc. bond : bond 0.00373 / 0.25 ( 1) link_BETA1-4 : bond 0.00272 / 0.19 ( 15) link_BETA1-4 : angle 1.19433 / 0.73 ( 45) link_NAG-ASN : bond 0.00459 / 0.32 ( 45) link_NAG-ASN : angle 3.38549 / 2.74 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 151 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7924 (OUTLIER) cc_final: 0.6856 (m-70) REVERT: A 237 ARG cc_start: 0.7707 (ptp-170) cc_final: 0.7218 (ptp90) REVERT: A 436 TRP cc_start: 0.1462 (p90) cc_final: 0.1084 (p90) REVERT: A 581 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 854 LYS cc_start: 0.7469 (OUTLIER) cc_final: 0.7167 (ttpt) REVERT: A 855 PHE cc_start: 0.8011 (OUTLIER) cc_final: 0.7737 (p90) REVERT: B 153 MET cc_start: 0.3914 (mtp) cc_final: 0.3401 (mtt) REVERT: B 854 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7405 (tmmm) REVERT: C 190 ARG cc_start: 0.5105 (ttt180) cc_final: 0.4032 (ttm170) REVERT: C 315 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8687 (p) REVERT: C 556 ASN cc_start: 0.7432 (p0) cc_final: 0.7136 (p0) REVERT: F 57 ILE cc_start: 0.2299 (mm) cc_final: 0.2067 (tp) outliers start: 64 outliers final: 28 residues processed: 196 average time/residue: 0.1860 time to fit residues: 61.3244 Evaluate side-chains 166 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 349 optimal weight: 7.9990 chunk 384 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 329 optimal weight: 40.0000 chunk 77 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 0.9990 chunk 198 optimal weight: 0.7980 chunk 144 optimal weight: 0.2980 chunk 146 optimal weight: 20.0000 chunk 283 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 81 ASN B 239 GLN B 762 GLN C 81 ASN C 239 GLN ** C 245 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.135375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.094380 restraints weight = 139920.166| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 5.48 r_work: 0.3393 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 32083 Z= 0.129 Angle : 0.627 20.504 43791 Z= 0.320 Chirality : 0.045 0.349 5111 Planarity : 0.004 0.058 5530 Dihedral : 5.990 55.397 4190 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.22 % Favored : 94.60 % Rotamer: Outliers : 1.53 % Allowed : 7.46 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.13), residues: 3857 helix: 0.23 (0.20), residues: 690 sheet: -1.94 (0.16), residues: 932 loop : -1.45 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.022 0.001 TYR A 904 PHE 0.016 0.001 PHE B 592 TRP 0.045 0.002 TRP B 152 HIS 0.004 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (31981) covalent geometry : angle 0.59842 / 0.31 (43529) SS BOND : bond 0.00309 / 0.21 ( 41) SS BOND : angle 1.74074 / 1.15 ( 82) hydrogen bonds : bond 0.03578 / 2.35 ( 893) hydrogen bonds : angle 6.22773 / 4.26 ( 2436) Misc. bond : bond 0.00370 / 0.25 ( 1) link_BETA1-4 : bond 0.00309 / 0.21 ( 15) link_BETA1-4 : angle 1.12321 / 0.70 ( 45) link_NAG-ASN : bond 0.00506 / 0.38 ( 45) link_NAG-ASN : angle 3.15413 / 2.64 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.168 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 210 ILE cc_start: 0.6946 (pp) cc_final: 0.6677 (pp) REVERT: A 237 ARG cc_start: 0.7580 (ptp-170) cc_final: 0.7191 (ptp90) REVERT: A 581 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 855 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7677 (p90) REVERT: A 1002 GLN cc_start: 0.8088 (tt0) cc_final: 0.7841 (tm-30) REVERT: B 153 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3507 (mtt) REVERT: B 157 PHE cc_start: 0.6770 (OUTLIER) cc_final: 0.6121 (m-80) REVERT: B 902 MET cc_start: 0.8989 (mmp) cc_final: 0.8664 (mmp) REVERT: C 190 ARG cc_start: 0.4970 (ttt180) cc_final: 0.3971 (ttm170) REVERT: C 315 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8609 (p) REVERT: C 543 PHE cc_start: 0.7851 (m-10) cc_final: 0.7549 (m-10) REVERT: C 556 ASN cc_start: 0.7201 (p0) cc_final: 0.6889 (p0) REVERT: F 57 ILE cc_start: 0.2799 (mm) cc_final: 0.2549 (tp) outliers start: 52 outliers final: 26 residues processed: 189 average time/residue: 0.1890 time to fit residues: 59.4568 Evaluate side-chains 162 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 26 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 211 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 304 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 229 optimal weight: 0.0040 chunk 292 optimal weight: 1.9990 overall best weight: 1.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 121 ASN B 239 GLN C 81 ASN C 207 HIS C 481 ASN ** C 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.131729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.092036 restraints weight = 132371.241| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 4.59 r_work: 0.3404 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32083 Z= 0.154 Angle : 0.629 20.398 43791 Z= 0.318 Chirality : 0.045 0.322 5111 Planarity : 0.004 0.050 5530 Dihedral : 5.741 48.312 4184 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.38 % Favored : 94.44 % Rotamer: Outliers : 1.85 % Allowed : 7.66 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.13), residues: 3857 helix: 0.39 (0.20), residues: 691 sheet: -1.76 (0.16), residues: 952 loop : -1.41 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1019 TYR 0.019 0.002 TYR A 904 PHE 0.019 0.001 PHE B1052 TRP 0.057 0.002 TRP B 152 HIS 0.004 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (31981) covalent geometry : angle 0.60299 / 0.31 (43529) SS BOND : bond 0.00426 / 0.33 ( 41) SS BOND : angle 1.39447 / 0.93 ( 82) hydrogen bonds : bond 0.03494 / 2.28 ( 893) hydrogen bonds : angle 6.08494 / 4.18 ( 2436) Misc. bond : bond 0.00348 / 0.23 ( 1) link_BETA1-4 : bond 0.00249 / 0.15 ( 15) link_BETA1-4 : angle 1.14024 / 0.72 ( 45) link_NAG-ASN : bond 0.00483 / 0.34 ( 45) link_NAG-ASN : angle 3.06835 / 2.59 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 154 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7752 (t-90) REVERT: A 210 ILE cc_start: 0.6910 (pp) cc_final: 0.6646 (pp) REVERT: A 237 ARG cc_start: 0.7544 (ptp-170) cc_final: 0.7185 (ptp90) REVERT: A 855 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7519 (p90) REVERT: B 157 PHE cc_start: 0.6524 (OUTLIER) cc_final: 0.5861 (m-80) REVERT: C 190 ARG cc_start: 0.5272 (ttt180) cc_final: 0.4198 (ttm170) REVERT: C 556 ASN cc_start: 0.7202 (p0) cc_final: 0.6954 (p0) REVERT: C 571 ASP cc_start: 0.7441 (t70) cc_final: 0.7166 (t0) REVERT: C 902 MET cc_start: 0.8792 (mmt) cc_final: 0.8515 (mmt) REVERT: F 57 ILE cc_start: 0.3632 (mm) cc_final: 0.3407 (tp) REVERT: G 107 MET cc_start: 0.0632 (ptp) cc_final: 0.0171 (ptp) outliers start: 63 outliers final: 35 residues processed: 202 average time/residue: 0.1903 time to fit residues: 62.9284 Evaluate side-chains 174 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 81 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 342 optimal weight: 7.9990 chunk 381 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 306 optimal weight: 0.4980 chunk 254 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 119 optimal weight: 0.0470 chunk 355 optimal weight: 10.0000 chunk 297 optimal weight: 0.6980 chunk 238 optimal weight: 20.0000 overall best weight: 0.8280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 81 ASN B1023 ASN C 81 ASN C 762 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.134479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098124 restraints weight = 163238.419| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 5.93 r_work: 0.3387 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3383 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 32083 Z= 0.126 Angle : 0.608 20.459 43791 Z= 0.305 Chirality : 0.045 0.321 5111 Planarity : 0.004 0.048 5530 Dihedral : 5.523 46.877 4184 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.01 % Favored : 94.81 % Rotamer: Outliers : 1.56 % Allowed : 8.72 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 3857 helix: 0.62 (0.20), residues: 691 sheet: -1.58 (0.16), residues: 901 loop : -1.35 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 646 TYR 0.018 0.001 TYR C 200 PHE 0.021 0.001 PHE B 592 TRP 0.053 0.002 TRP B 152 HIS 0.003 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (31981) covalent geometry : angle 0.58022 / 0.30 (43529) SS BOND : bond 0.00313 / 0.23 ( 41) SS BOND : angle 1.23209 / 0.75 ( 82) hydrogen bonds : bond 0.03363 / 2.21 ( 893) hydrogen bonds : angle 5.89915 / 4.05 ( 2436) Misc. bond : bond 0.00327 / 0.22 ( 1) link_BETA1-4 : bond 0.00321 / 0.21 ( 15) link_BETA1-4 : angle 1.07770 / 0.67 ( 45) link_NAG-ASN : bond 0.00601 / 0.47 ( 45) link_NAG-ASN : angle 3.16928 / 2.61 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 152 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.7922 (OUTLIER) cc_final: 0.7610 (t-90) REVERT: A 210 ILE cc_start: 0.6890 (pp) cc_final: 0.6623 (pp) REVERT: A 237 ARG cc_start: 0.7630 (ptp-170) cc_final: 0.7251 (ptp90) REVERT: A 855 PHE cc_start: 0.7844 (OUTLIER) cc_final: 0.7444 (p90) REVERT: B 153 MET cc_start: 0.3956 (mtt) cc_final: 0.3453 (mtt) REVERT: B 157 PHE cc_start: 0.6498 (OUTLIER) cc_final: 0.5786 (m-80) REVERT: C 190 ARG cc_start: 0.5075 (ttt180) cc_final: 0.4021 (ttm170) REVERT: C 556 ASN cc_start: 0.7150 (p0) cc_final: 0.6835 (p0) REVERT: C 571 ASP cc_start: 0.7546 (t70) cc_final: 0.7280 (t0) REVERT: C 902 MET cc_start: 0.8807 (mmt) cc_final: 0.8542 (mmt) REVERT: C 1050 MET cc_start: 0.8688 (ptt) cc_final: 0.8460 (ptt) outliers start: 53 outliers final: 37 residues processed: 192 average time/residue: 0.1885 time to fit residues: 60.4274 Evaluate side-chains 169 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 157 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 762 GLN Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 244 optimal weight: 0.3980 chunk 129 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 324 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 chunk 59 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 chunk 223 optimal weight: 5.9990 chunk 351 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN B 81 ASN C 81 ASN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.131695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.094976 restraints weight = 188374.584| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 6.92 r_work: 0.3342 rms_B_bonded: 5.12 restraints_weight: 2.0000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 32083 Z= 0.166 Angle : 0.632 20.419 43791 Z= 0.316 Chirality : 0.046 0.369 5111 Planarity : 0.004 0.047 5530 Dihedral : 5.473 46.700 4182 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.45 % Favored : 94.37 % Rotamer: Outliers : 1.38 % Allowed : 9.36 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.13), residues: 3857 helix: 0.66 (0.20), residues: 698 sheet: -1.61 (0.16), residues: 927 loop : -1.34 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 815 TYR 0.019 0.001 TYR A 904 PHE 0.018 0.001 PHE C 643 TRP 0.055 0.002 TRP B 152 HIS 0.004 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (31981) covalent geometry : angle 0.60491 / 0.31 (43529) SS BOND : bond 0.00325 / 0.24 ( 41) SS BOND : angle 1.10958 / 0.71 ( 82) hydrogen bonds : bond 0.03475 / 2.27 ( 893) hydrogen bonds : angle 5.92030 / 4.06 ( 2436) Misc. bond : bond 0.00303 / 0.20 ( 1) link_BETA1-4 : bond 0.00241 / 0.15 ( 15) link_BETA1-4 : angle 1.14324 / 0.73 ( 45) link_NAG-ASN : bond 0.00552 / 0.40 ( 45) link_NAG-ASN : angle 3.21945 / 2.64 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 132 time to evaluate : 1.063 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 66 HIS cc_start: 0.8043 (OUTLIER) cc_final: 0.7776 (t-90) REVERT: A 210 ILE cc_start: 0.6931 (pp) cc_final: 0.6675 (pp) REVERT: A 237 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7372 (ptp90) REVERT: A 855 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7396 (p90) REVERT: A 1141 LEU cc_start: 0.8509 (tp) cc_final: 0.8228 (tt) REVERT: B 153 MET cc_start: 0.3856 (mtt) cc_final: 0.3362 (mtt) REVERT: C 152 TRP cc_start: 0.7339 (m-10) cc_final: 0.6998 (p-90) REVERT: C 190 ARG cc_start: 0.5227 (ttt180) cc_final: 0.4162 (ttm170) REVERT: C 556 ASN cc_start: 0.7292 (p0) cc_final: 0.6913 (p0) REVERT: C 1050 MET cc_start: 0.8852 (ptt) cc_final: 0.8579 (ptt) REVERT: G 107 MET cc_start: 0.1216 (ptp) cc_final: 0.0918 (ptp) outliers start: 47 outliers final: 40 residues processed: 168 average time/residue: 0.1825 time to fit residues: 50.8051 Evaluate side-chains 166 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 124 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 559 PHE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 55 ASN Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 251 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 353 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 225 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 385 optimal weight: 20.0000 chunk 143 optimal weight: 5.9990 chunk 182 optimal weight: 0.4980 chunk 213 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.132505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.093719 restraints weight = 127967.164| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 4.33 r_work: 0.3419 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3414 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3414 r_free = 0.3414 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3414 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32083 Z= 0.132 Angle : 0.612 20.906 43791 Z= 0.308 Chirality : 0.045 0.338 5111 Planarity : 0.004 0.047 5530 Dihedral : 5.317 45.965 4182 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.99 % Favored : 94.83 % Rotamer: Outliers : 1.23 % Allowed : 9.72 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3857 helix: 0.80 (0.20), residues: 699 sheet: -1.51 (0.16), residues: 926 loop : -1.28 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1019 TYR 0.019 0.001 TYR A 904 PHE 0.016 0.001 PHE C 643 TRP 0.056 0.002 TRP B 152 HIS 0.003 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (31981) covalent geometry : angle 0.58571 / 0.30 (43529) SS BOND : bond 0.00274 / 0.20 ( 41) SS BOND : angle 1.06560 / 0.70 ( 82) hydrogen bonds : bond 0.03322 / 2.18 ( 893) hydrogen bonds : angle 5.80666 / 3.99 ( 2436) Misc. bond : bond 0.00297 / 0.20 ( 1) link_BETA1-4 : bond 0.00273 / 0.18 ( 15) link_BETA1-4 : angle 1.07618 / 0.67 ( 45) link_NAG-ASN : bond 0.00491 / 0.36 ( 45) link_NAG-ASN : angle 3.14262 / 2.62 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 1.165 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 66 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7764 (t-90) REVERT: A 210 ILE cc_start: 0.6796 (pp) cc_final: 0.6524 (pp) REVERT: A 237 ARG cc_start: 0.7522 (ptp-170) cc_final: 0.7143 (ptp90) REVERT: A 576 VAL cc_start: 0.8281 (OUTLIER) cc_final: 0.8067 (p) REVERT: A 855 PHE cc_start: 0.7781 (OUTLIER) cc_final: 0.7384 (p90) REVERT: C 190 ARG cc_start: 0.5057 (ttt180) cc_final: 0.3964 (ttm170) REVERT: C 556 ASN cc_start: 0.7323 (p0) cc_final: 0.6916 (p0) REVERT: C 1050 MET cc_start: 0.8789 (ptt) cc_final: 0.8495 (ptt) REVERT: C 1125 ASN cc_start: 0.8423 (p0) cc_final: 0.8205 (p0) REVERT: G 107 MET cc_start: 0.1008 (ptp) cc_final: 0.0747 (ptp) outliers start: 42 outliers final: 36 residues processed: 169 average time/residue: 0.1933 time to fit residues: 54.5356 Evaluate side-chains 166 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 127 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 592 PHE Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain G residue 145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 92 optimal weight: 2.9990 chunk 195 optimal weight: 4.9990 chunk 179 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 226 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 332 optimal weight: 10.0000 chunk 101 optimal weight: 0.0370 chunk 248 optimal weight: 7.9990 chunk 121 optimal weight: 0.0030 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN A 935 GLN B 81 ASN C 81 ASN C 245 HIS ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.136445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.100346 restraints weight = 150376.063| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 5.72 r_work: 0.3422 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 32083 Z= 0.109 Angle : 0.595 20.252 43791 Z= 0.299 Chirality : 0.044 0.343 5111 Planarity : 0.004 0.053 5530 Dihedral : 5.094 44.944 4182 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.67 % Favored : 95.14 % Rotamer: Outliers : 1.26 % Allowed : 10.01 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.13), residues: 3857 helix: 1.02 (0.20), residues: 697 sheet: -1.37 (0.16), residues: 917 loop : -1.21 (0.13), residues: 2243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 158 TYR 0.015 0.001 TYR B1067 PHE 0.014 0.001 PHE C 643 TRP 0.027 0.001 TRP B 152 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (31981) covalent geometry : angle 0.57002 / 0.29 (43529) SS BOND : bond 0.00266 / 0.20 ( 41) SS BOND : angle 0.94501 / 0.63 ( 82) hydrogen bonds : bond 0.03205 / 2.11 ( 893) hydrogen bonds : angle 5.64575 / 3.88 ( 2436) Misc. bond : bond 0.00292 / 0.19 ( 1) link_BETA1-4 : bond 0.00289 / 0.19 ( 15) link_BETA1-4 : angle 1.03341 / 0.66 ( 45) link_NAG-ASN : bond 0.00525 / 0.40 ( 45) link_NAG-ASN : angle 3.05887 / 2.56 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7714 Ramachandran restraints generated. 3857 Oldfield, 0 Emsley, 3857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7831 (t-90) REVERT: A 210 ILE cc_start: 0.6759 (pp) cc_final: 0.6476 (pp) REVERT: A 237 ARG cc_start: 0.7527 (ptp-170) cc_final: 0.7158 (ptp90) REVERT: A 855 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7308 (p90) REVERT: B 129 LYS cc_start: 0.7468 (mmtt) cc_final: 0.6368 (mtpp) REVERT: B 1029 MET cc_start: 0.8871 (tpp) cc_final: 0.8618 (ttm) REVERT: C 152 TRP cc_start: 0.7146 (m-10) cc_final: 0.6876 (p-90) REVERT: C 190 ARG cc_start: 0.5126 (ttt180) cc_final: 0.4060 (ttm170) REVERT: C 556 ASN cc_start: 0.7231 (p0) cc_final: 0.6846 (p0) REVERT: C 1050 MET cc_start: 0.8707 (ptt) cc_final: 0.8402 (ptt) REVERT: G 107 MET cc_start: 0.1426 (ptp) cc_final: 0.1162 (ptp) outliers start: 43 outliers final: 33 residues processed: 179 average time/residue: 0.1931 time to fit residues: 56.7905 Evaluate side-chains 164 residues out of total 3425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 854 LYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 611 LEU Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 28 ILE Chi-restraints excluded: chain D residue 107 LYS Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 81 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 388 random chunks: chunk 0 optimal weight: 5.9990 chunk 362 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 286 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 373 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 341 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 199 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.135599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.097428 restraints weight = 145894.282| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 5.43 r_work: 0.3426 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.4542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.216 32083 Z= 0.209 Angle : 0.814 59.200 43791 Z= 0.460 Chirality : 0.048 0.673 5111 Planarity : 0.004 0.084 5530 Dihedral : 5.110 45.013 4182 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.75 % Favored : 95.04 % Rotamer: Outliers : 1.03 % Allowed : 10.45 % Favored : 88.52 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 3857 helix: 0.96 (0.20), residues: 697 sheet: -1.35 (0.16), residues: 921 loop : -1.22 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 328 TYR 0.037 0.001 TYR E 32 PHE 0.022 0.001 PHE B1052 TRP 0.025 0.001 TRP B 152 HIS 0.003 0.001 HIS F 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (31981) covalent geometry : angle 0.78373 / 0.45 (43529) SS BOND : bond 0.01447 / 0.52 ( 41) SS BOND : angle 3.39350 / 2.15 ( 82) hydrogen bonds : bond 0.03229 / 2.13 ( 893) hydrogen bonds : angle 5.64419 / 3.87 ( 2436) Misc. bond : bond 0.00265 / 0.18 ( 1) link_BETA1-4 : bond 0.00488 / 0.35 ( 15) link_BETA1-4 : angle 1.10049 / 0.69 ( 45) link_NAG-ASN : bond 0.00517 / 0.38 ( 45) link_NAG-ASN : angle 3.05073 / 2.55 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9954.12 seconds wall clock time: 170 minutes 58.81 seconds (10258.81 seconds total)