Starting phenix.real_space_refine on Sat Feb 7 07:53:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ls3_63352/02_2026/9ls3_63352.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ls3_63352/02_2026/9ls3_63352.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ls3_63352/02_2026/9ls3_63352.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ls3_63352/02_2026/9ls3_63352.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ls3_63352/02_2026/9ls3_63352.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ls3_63352/02_2026/9ls3_63352.map" } resolution = 3.4 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= 0.003 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 135 5.16 5 C 19494 2.51 5 N 5127 2.21 5 O 5970 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30726 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8138 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain breaks: 7 Chain: "B" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8138 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain breaks: 7 Chain: "C" Number of atoms: 8138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8138 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 57, 'TRANS': 980} Chain breaks: 7 Chain: "D" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "E" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 890 Classifications: {'peptide': 114} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 105} Chain: "F" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "G" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 890 Classifications: {'peptide': 114} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 962 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 2, 'TRANS': 119} Chain: "I" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 890 Classifications: {'peptide': 114} Link IDs: {'PCIS': 3, 'PTRANS': 5, 'TRANS': 105} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.70, per 1000 atoms: 0.22 Number of scatterers: 30726 At special positions: 0 Unit cell: (189.138, 183.703, 168.485, 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 135 16.00 O 5970 8.00 N 5127 7.00 C 19494 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.05 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 93 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 93 " distance=2.04 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=0, symmetry=0 Links applied BETA1-4 " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 331 " " NAG A1304 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG J 1 " - " ASN A 122 " " NAG K 1 " - " ASN A 234 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 122 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1074 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " Time building additional restraints: 2.55 Conformation dependent library (CDL) restraints added in 1.0 seconds 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 58 sheets defined 20.2% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.575A pdb=" N GLU A 340 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.367A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.714A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.595A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.592A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.530A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.541A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.212A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.720A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.536A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.818A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.534A pdb=" N GLU B 340 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.267A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.563A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.615A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.598A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.612A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (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: 3.850A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.536A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.696A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.872A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.554A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.249A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.570A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 4.008A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.838A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.514A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 941 removed outlier: 4.035A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.300A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.421A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.809A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 44 removed outlier: 6.287A pdb=" N ASP C 568 " --> pdb=" O THR C 573 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N THR C 573 " --> pdb=" O ASP C 568 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.502A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.082A 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 Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 319 removed outlier: 5.496A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 539 through 543 removed outlier: 5.679A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 653 through 655 removed outlier: 6.624A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.999A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.624A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.624A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.533A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.629A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.809A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.503A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.082A 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 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 316 removed outlier: 6.119A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 5.580A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.768A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.067A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.630A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.567A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.777A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.777A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.593A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.808A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.503A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.109A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.051A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.588A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.459A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.039A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.710A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.710A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.613A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE8, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'D' and resid 58 through 60 removed outlier: 5.003A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AF2, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.947A pdb=" N LEU E 11 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN E 42 " --> pdb=" O ARG E 51 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ARG E 51 " --> pdb=" O GLN E 42 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 13 removed outlier: 5.947A pdb=" N LEU E 11 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR E 103 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'F' and resid 58 through 60 removed outlier: 5.003A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AF7, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.947A pdb=" N LEU G 11 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN G 42 " --> pdb=" O ARG G 51 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ARG G 51 " --> pdb=" O GLN G 42 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 13 removed outlier: 5.947A pdb=" N LEU G 11 " --> pdb=" O GLU G 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR G 103 " --> pdb=" O GLN G 95 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.002A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AG3, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.947A pdb=" N LEU I 11 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN I 42 " --> pdb=" O ARG I 51 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ARG I 51 " --> pdb=" O GLN I 42 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 13 removed outlier: 5.947A pdb=" N LEU I 11 " --> pdb=" O GLU I 111 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR I 103 " --> pdb=" O GLN I 95 " (cutoff:3.500A) 1175 hydrogen bonds defined for protein. 3108 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: 7.38 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9794 1.34 - 1.46: 7678 1.46 - 1.59: 13779 1.59 - 1.71: 0 1.71 - 1.84: 174 Bond restraints: 31425 Sorted by residual: bond pdb=" N CYS A 391 " pdb=" CA CYS A 391 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.94e+00 bond pdb=" N PHE C 306 " pdb=" CA PHE C 306 " ideal model delta sigma weight residual 1.458 1.486 -0.028 9.00e-03 1.23e+04 9.86e+00 bond pdb=" N VAL A 524 " pdb=" CA VAL A 524 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.19e-02 7.06e+03 9.64e+00 bond pdb=" N PHE A 306 " pdb=" CA PHE A 306 " ideal model delta sigma weight residual 1.458 1.486 -0.028 9.00e-03 1.23e+04 9.59e+00 bond pdb=" N VAL A 308 " pdb=" CA VAL A 308 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.36e+00 ... (remaining 31420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 41129 1.94 - 3.87: 1465 3.87 - 5.81: 121 5.81 - 7.75: 9 7.75 - 9.68: 5 Bond angle restraints: 42729 Sorted by residual: angle pdb=" CA HIS B 519 " pdb=" CB HIS B 519 " pdb=" CG HIS B 519 " ideal model delta sigma weight residual 113.80 109.27 4.53 1.00e+00 1.00e+00 2.05e+01 angle pdb=" CA HIS C 519 " pdb=" CB HIS C 519 " pdb=" CG HIS C 519 " ideal model delta sigma weight residual 113.80 109.43 4.37 1.00e+00 1.00e+00 1.91e+01 angle pdb=" C THR C 523 " pdb=" N VAL C 524 " pdb=" CA VAL C 524 " ideal model delta sigma weight residual 120.49 126.17 -5.68 1.38e+00 5.25e-01 1.70e+01 angle pdb=" N LYS A 378 " pdb=" CA LYS A 378 " pdb=" C LYS A 378 " ideal model delta sigma weight residual 108.90 115.60 -6.70 1.63e+00 3.76e-01 1.69e+01 angle pdb=" N SER A 316 " pdb=" CA SER A 316 " pdb=" C SER A 316 " ideal model delta sigma weight residual 108.38 113.75 -5.37 1.35e+00 5.49e-01 1.58e+01 ... (remaining 42724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 16953 18.00 - 35.99: 1898 35.99 - 53.99: 430 53.99 - 71.99: 106 71.99 - 89.98: 56 Dihedral angle restraints: 19443 sinusoidal: 8352 harmonic: 11091 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -0.05 -85.95 1 1.00e+01 1.00e-02 8.92e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 93 " pdb=" CB CYS I 93 " ideal model delta sinusoidal sigma weight residual 93.00 178.39 -85.39 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS G 23 " pdb=" SG CYS G 23 " pdb=" SG CYS G 93 " pdb=" CB CYS G 93 " ideal model delta sinusoidal sigma weight residual 93.00 178.36 -85.36 1 1.00e+01 1.00e-02 8.82e+01 ... (remaining 19440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 4902 0.167 - 0.333: 15 0.333 - 0.500: 7 0.500 - 0.667: 0 0.667 - 0.833: 2 Chirality restraints: 4926 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 4923 not shown) Planarity restraints: 5517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.074 2.00e-02 2.50e+03 1.50e-01 2.82e+02 pdb=" CG ASN C 331 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.270 2.00e-02 2.50e+03 pdb=" C1 NAG C1303 " -0.168 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 905 " -0.640 9.50e-02 1.11e+02 2.87e-01 5.03e+01 pdb=" NE ARG C 905 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 905 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 905 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 905 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " 0.013 2.00e-02 2.50e+03 3.34e-02 1.39e+01 pdb=" CG ASN A 331 " -0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG A1303 " 0.037 2.00e-02 2.50e+03 ... (remaining 5514 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 803 2.69 - 3.24: 29674 3.24 - 3.79: 45514 3.79 - 4.35: 60301 4.35 - 4.90: 102094 Nonbonded interactions: 238386 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.135 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.158 3.040 nonbonded pdb=" OG SER C 813 " pdb=" N LYS C 814 " model vdw 2.228 3.120 nonbonded pdb=" NH1 ARG B 567 " pdb=" OD1 ASP B 571 " model vdw 2.236 3.120 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.245 3.040 ... (remaining 238381 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = 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' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 28.230 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.005 0.076 31527 Z= 0.274 Angle : 0.858 52.675 42987 Z= 0.476 Chirality : 0.054 0.833 4926 Planarity : 0.006 0.287 5484 Dihedral : 16.215 89.982 12183 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.01 % Favored : 93.65 % Rotamer: Outliers : 2.03 % Allowed : 20.93 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.99 (0.13), residues: 3762 helix: 0.35 (0.21), residues: 681 sheet: 0.77 (0.17), residues: 858 loop : -1.66 (0.12), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 355 TYR 0.016 0.001 TYR C1067 PHE 0.022 0.001 PHE A 559 TRP 0.022 0.001 TRP A 436 HIS 0.008 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00458 (31425) covalent geometry : angle 0.76801 (42729) SS BOND : bond 0.00678 ( 48) SS BOND : angle 2.21881 ( 96) hydrogen bonds : bond 0.15507 ( 1134) hydrogen bonds : angle 7.10725 ( 3108) link_BETA1-4 : bond 0.00656 ( 21) link_BETA1-4 : angle 2.61517 ( 63) link_NAG-ASN : bond 0.00549 ( 33) link_NAG-ASN : angle 7.50471 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 444 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.4453 (p-80) cc_final: 0.3902 (p90) REVERT: A 303 LEU cc_start: 0.8205 (mm) cc_final: 0.7910 (mt) REVERT: A 305 SER cc_start: 0.8884 (t) cc_final: 0.8614 (m) REVERT: B 21 ARG cc_start: 0.3805 (ttt90) cc_final: 0.2733 (mtm110) REVERT: B 133 PHE cc_start: 0.6707 (m-80) cc_final: 0.6158 (m-80) REVERT: B 237 ARG cc_start: 0.8119 (mtm180) cc_final: 0.7452 (mtm110) REVERT: C 81 ASN cc_start: 0.6825 (m-40) cc_final: 0.6215 (p0) REVERT: C 118 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7927 (mp) REVERT: C 200 TYR cc_start: 0.7005 (m-10) cc_final: 0.6697 (m-80) REVERT: C 869 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8263 (mtt) REVERT: C 905 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.8111 (mmt180) REVERT: D 31 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8469 (ttm-80) REVERT: D 34 MET cc_start: 0.8563 (mmm) cc_final: 0.8335 (mmt) REVERT: D 73 ASP cc_start: 0.6323 (t0) cc_final: 0.5464 (p0) REVERT: E 38 LEU cc_start: 0.6772 (tt) cc_final: 0.6504 (tp) REVERT: F 76 LYS cc_start: 0.8719 (mttp) cc_final: 0.8404 (mmtm) REVERT: F 83 MET cc_start: 0.7568 (mtp) cc_final: 0.7017 (mtt) REVERT: F 84 ASN cc_start: 0.7102 (m-40) cc_final: 0.6562 (p0) REVERT: G 13 VAL cc_start: 0.4613 (m) cc_final: 0.4007 (t) REVERT: H 76 LYS cc_start: 0.8492 (mttp) cc_final: 0.8255 (mtmm) REVERT: H 106 GLU cc_start: 0.8840 (tp30) cc_final: 0.8590 (tp30) REVERT: I 36 THR cc_start: 0.8067 (m) cc_final: 0.7609 (t) REVERT: I 60 ASP cc_start: 0.5613 (t70) cc_final: 0.5350 (t0) REVERT: I 80 ILE cc_start: 0.3226 (mp) cc_final: 0.2401 (tp) outliers start: 68 outliers final: 15 residues processed: 493 average time/residue: 0.1919 time to fit residues: 147.0942 Evaluate side-chains 271 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain B residue 69 HIS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 905 ARG Chi-restraints excluded: chain C residue 906 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 804 GLN B 935 GLN C 188 ASN C 935 GLN C1106 GLN D 13 GLN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 ASN I 42 GLN I 43 GLN I 47 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.114219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.076873 restraints weight = 80910.079| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.70 r_work: 0.3038 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 31527 Z= 0.142 Angle : 0.734 15.897 42987 Z= 0.351 Chirality : 0.048 0.539 4926 Planarity : 0.004 0.049 5484 Dihedral : 7.270 59.120 5302 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.77 % Favored : 94.13 % Rotamer: Outliers : 3.20 % Allowed : 19.76 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.72 (0.13), residues: 3762 helix: 0.94 (0.21), residues: 677 sheet: 0.85 (0.17), residues: 815 loop : -1.53 (0.12), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 466 TYR 0.028 0.001 TYR I 54 PHE 0.023 0.001 PHE B 135 TRP 0.020 0.001 TRP E 40 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00326 (31425) covalent geometry : angle 0.68518 (42729) SS BOND : bond 0.00565 ( 48) SS BOND : angle 1.85396 ( 96) hydrogen bonds : bond 0.04590 ( 1134) hydrogen bonds : angle 5.51965 ( 3108) link_BETA1-4 : bond 0.00697 ( 21) link_BETA1-4 : angle 2.10570 ( 63) link_NAG-ASN : bond 0.00691 ( 33) link_NAG-ASN : angle 5.00465 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 284 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8766 (pp) cc_final: 0.8158 (tp) REVERT: A 245 HIS cc_start: 0.4713 (p-80) cc_final: 0.4381 (p90) REVERT: A 305 SER cc_start: 0.9151 (t) cc_final: 0.8918 (m) REVERT: A 559 PHE cc_start: 0.8091 (OUTLIER) cc_final: 0.6926 (t80) REVERT: A 708 SER cc_start: 0.9006 (OUTLIER) cc_final: 0.8781 (t) REVERT: A 856 ASN cc_start: 0.8463 (p0) cc_final: 0.7951 (p0) REVERT: A 1029 MET cc_start: 0.9214 (tpp) cc_final: 0.8885 (ttm) REVERT: B 21 ARG cc_start: 0.4018 (ttp80) cc_final: 0.2347 (mtm180) REVERT: C 118 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7809 (mp) REVERT: C 133 PHE cc_start: 0.5616 (m-80) cc_final: 0.5239 (m-80) REVERT: C 200 TYR cc_start: 0.7432 (m-10) cc_final: 0.6888 (m-80) REVERT: C 524 VAL cc_start: 0.6786 (p) cc_final: 0.6543 (p) REVERT: D 31 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8554 (ttm-80) REVERT: D 34 MET cc_start: 0.9008 (mmm) cc_final: 0.8759 (mmt) REVERT: E 24 ARG cc_start: 0.8416 (mtp85) cc_final: 0.8135 (mtp-110) REVERT: E 75 ASP cc_start: 0.8606 (m-30) cc_final: 0.7735 (p0) REVERT: E 84 GLU cc_start: 0.6062 (mp0) cc_final: 0.5822 (mp0) REVERT: F 76 LYS cc_start: 0.8555 (mttp) cc_final: 0.8345 (mmtm) REVERT: F 84 ASN cc_start: 0.7193 (m-40) cc_final: 0.6483 (p0) REVERT: G 87 ASP cc_start: 0.6689 (t0) cc_final: 0.5886 (t0) REVERT: I 36 THR cc_start: 0.8504 (m) cc_final: 0.8021 (t) REVERT: I 47 GLN cc_start: 0.6803 (mt0) cc_final: 0.6427 (mp10) REVERT: I 76 PHE cc_start: 0.8615 (m-80) cc_final: 0.8274 (m-80) outliers start: 107 outliers final: 46 residues processed: 370 average time/residue: 0.1885 time to fit residues: 111.7117 Evaluate side-chains 285 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 236 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 86 PHE Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 906 PHE Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain G residue 63 VAL Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 162 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 371 optimal weight: 9.9990 chunk 304 optimal weight: 0.8980 chunk 367 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 178 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 chunk 263 optimal weight: 9.9990 chunk 325 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 239 GLN A 824 ASN A1002 GLN B 239 GLN B 271 GLN B 422 ASN B1071 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 271 GLN C 751 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.111310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072932 restraints weight = 80827.392| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.58 r_work: 0.2982 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31527 Z= 0.178 Angle : 0.721 15.654 42987 Z= 0.346 Chirality : 0.049 0.512 4926 Planarity : 0.004 0.050 5484 Dihedral : 7.023 59.243 5289 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.43 % Favored : 93.49 % Rotamer: Outliers : 3.53 % Allowed : 19.91 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.47 (0.13), residues: 3762 helix: 1.25 (0.21), residues: 680 sheet: 1.06 (0.17), residues: 876 loop : -1.49 (0.12), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 24 TYR 0.024 0.001 TYR H 111 PHE 0.023 0.002 PHE A 559 TRP 0.017 0.001 TRP A 436 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00421 (31425) covalent geometry : angle 0.67311 (42729) SS BOND : bond 0.00499 ( 48) SS BOND : angle 2.18805 ( 96) hydrogen bonds : bond 0.04590 ( 1134) hydrogen bonds : angle 5.23647 ( 3108) link_BETA1-4 : bond 0.00668 ( 21) link_BETA1-4 : angle 2.03535 ( 63) link_NAG-ASN : bond 0.00584 ( 33) link_NAG-ASN : angle 4.76442 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 271 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 305 SER cc_start: 0.9348 (t) cc_final: 0.9125 (m) REVERT: A 559 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7255 (t80) REVERT: A 708 SER cc_start: 0.9010 (OUTLIER) cc_final: 0.8760 (t) REVERT: A 856 ASN cc_start: 0.8635 (p0) cc_final: 0.8111 (p0) REVERT: A 1029 MET cc_start: 0.9219 (tpp) cc_final: 0.8870 (ttm) REVERT: B 21 ARG cc_start: 0.3982 (ttp80) cc_final: 0.2478 (mtm180) REVERT: C 170 TYR cc_start: 0.7277 (t80) cc_final: 0.6724 (t80) REVERT: C 173 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7593 (tm-30) REVERT: C 524 VAL cc_start: 0.6905 (p) cc_final: 0.6667 (p) REVERT: D 20 LEU cc_start: 0.7433 (mt) cc_final: 0.7050 (tt) REVERT: D 31 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8555 (ttm-80) REVERT: D 34 MET cc_start: 0.8940 (mmm) cc_final: 0.8723 (mmt) REVERT: E 4 MET cc_start: 0.8415 (mmm) cc_final: 0.8078 (mmp) REVERT: E 75 ASP cc_start: 0.8568 (m-30) cc_final: 0.7594 (p0) REVERT: E 84 GLU cc_start: 0.6110 (mp0) cc_final: 0.5824 (mp0) REVERT: F 84 ASN cc_start: 0.7271 (m-40) cc_final: 0.6675 (p0) REVERT: G 24 ARG cc_start: 0.8482 (mtp-110) cc_final: 0.8236 (mtp-110) REVERT: H 36 TRP cc_start: 0.8049 (m100) cc_final: 0.7736 (m100) REVERT: I 47 GLN cc_start: 0.6849 (mt0) cc_final: 0.6502 (mp10) REVERT: I 56 VAL cc_start: 0.8379 (m) cc_final: 0.8051 (p) outliers start: 118 outliers final: 72 residues processed: 370 average time/residue: 0.1961 time to fit residues: 117.3701 Evaluate side-chains 304 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 285 optimal weight: 1.9990 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 246 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 271 GLN A1002 GLN B 321 GLN C 121 ASN C 125 ASN ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.111140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072009 restraints weight = 80369.047| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.22 r_work: 0.3008 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31527 Z= 0.140 Angle : 0.680 14.040 42987 Z= 0.325 Chirality : 0.047 0.493 4926 Planarity : 0.004 0.044 5484 Dihedral : 6.761 59.625 5279 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 3.23 % Allowed : 20.60 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.35 (0.13), residues: 3762 helix: 1.51 (0.21), residues: 671 sheet: 1.05 (0.17), residues: 908 loop : -1.45 (0.12), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1019 TYR 0.025 0.001 TYR D 111 PHE 0.018 0.001 PHE A 559 TRP 0.018 0.001 TRP A 436 HIS 0.006 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (31425) covalent geometry : angle 0.63704 (42729) SS BOND : bond 0.00507 ( 48) SS BOND : angle 1.75258 ( 96) hydrogen bonds : bond 0.04084 ( 1134) hydrogen bonds : angle 5.07188 ( 3108) link_BETA1-4 : bond 0.00637 ( 21) link_BETA1-4 : angle 1.93318 ( 63) link_NAG-ASN : bond 0.00625 ( 33) link_NAG-ASN : angle 4.52759 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 247 time to evaluate : 1.004 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 245 HIS cc_start: 0.4646 (p-80) cc_final: 0.4051 (p-80) REVERT: A 303 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8457 (mt) REVERT: A 305 SER cc_start: 0.9306 (t) cc_final: 0.9069 (m) REVERT: A 559 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7479 (t80) REVERT: A 708 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8743 (t) REVERT: A 856 ASN cc_start: 0.8587 (p0) cc_final: 0.8023 (p0) REVERT: A 1029 MET cc_start: 0.9152 (tpp) cc_final: 0.8844 (ttm) REVERT: B 21 ARG cc_start: 0.3836 (ttp80) cc_final: 0.2308 (mtm180) REVERT: B 617 CYS cc_start: 0.6360 (OUTLIER) cc_final: 0.6064 (m) REVERT: C 118 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 733 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.7984 (mtpp) REVERT: C 854 LYS cc_start: 0.4543 (OUTLIER) cc_final: 0.4215 (pttt) REVERT: D 31 ARG cc_start: 0.8829 (mtp85) cc_final: 0.8548 (ttm-80) REVERT: D 34 MET cc_start: 0.8899 (mmm) cc_final: 0.8676 (mmt) REVERT: E 4 MET cc_start: 0.8347 (mmm) cc_final: 0.8118 (mmp) REVERT: E 59 ARG cc_start: 0.7885 (mtm110) cc_final: 0.7662 (mtm110) REVERT: E 75 ASP cc_start: 0.8646 (m-30) cc_final: 0.7709 (p0) REVERT: E 84 GLU cc_start: 0.6311 (mp0) cc_final: 0.5983 (mp0) REVERT: F 19 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8294 (tpt-90) REVERT: F 76 LYS cc_start: 0.8877 (mppt) cc_final: 0.8539 (mmtm) REVERT: F 84 ASN cc_start: 0.7171 (m-40) cc_final: 0.6597 (p0) REVERT: F 87 ARG cc_start: 0.7254 (ptp-170) cc_final: 0.6581 (ptp-110) REVERT: F 105 TYR cc_start: 0.8499 (OUTLIER) cc_final: 0.7486 (t80) REVERT: F 106 GLU cc_start: 0.8771 (tp30) cc_final: 0.8493 (tp30) REVERT: F 107 GLU cc_start: 0.8919 (mp0) cc_final: 0.8571 (mp0) REVERT: G 18 PRO cc_start: 0.5915 (Cg_exo) cc_final: 0.5582 (Cg_endo) REVERT: G 39 ASN cc_start: 0.8421 (m-40) cc_final: 0.7887 (m-40) REVERT: G 75 ASP cc_start: 0.8554 (t70) cc_final: 0.8026 (p0) REVERT: G 94 MET cc_start: 0.6649 (tpp) cc_final: 0.6277 (tpp) REVERT: H 107 GLU cc_start: 0.8827 (mp0) cc_final: 0.8516 (mp0) REVERT: I 47 GLN cc_start: 0.6907 (mt0) cc_final: 0.6633 (mp10) REVERT: I 56 VAL cc_start: 0.8293 (m) cc_final: 0.7957 (p) REVERT: I 84 GLU cc_start: 0.6992 (mp0) cc_final: 0.6586 (mp0) outliers start: 108 outliers final: 76 residues processed: 338 average time/residue: 0.1876 time to fit residues: 102.4077 Evaluate side-chains 306 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 222 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 896 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 148 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 78 THR Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 155 optimal weight: 5.9990 chunk 224 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 368 optimal weight: 50.0000 chunk 236 optimal weight: 10.0000 chunk 245 optimal weight: 0.0870 chunk 235 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 359 optimal weight: 20.0000 chunk 112 optimal weight: 8.9990 overall best weight: 3.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN A1135 ASN C 121 ASN C 481 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.108776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069478 restraints weight = 80584.299| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.24 r_work: 0.2957 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 31527 Z= 0.207 Angle : 0.715 12.927 42987 Z= 0.344 Chirality : 0.048 0.504 4926 Planarity : 0.004 0.057 5484 Dihedral : 6.910 58.742 5279 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 3.83 % Allowed : 20.84 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.40 (0.13), residues: 3762 helix: 1.51 (0.21), residues: 668 sheet: 1.04 (0.17), residues: 919 loop : -1.53 (0.12), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 66 TYR 0.045 0.001 TYR D 102 PHE 0.022 0.002 PHE A 559 TRP 0.018 0.001 TRP A 436 HIS 0.006 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00495 (31425) covalent geometry : angle 0.67107 (42729) SS BOND : bond 0.00490 ( 48) SS BOND : angle 2.12453 ( 96) hydrogen bonds : bond 0.04711 ( 1134) hydrogen bonds : angle 5.15913 ( 3108) link_BETA1-4 : bond 0.00576 ( 21) link_BETA1-4 : angle 2.06440 ( 63) link_NAG-ASN : bond 0.00575 ( 33) link_NAG-ASN : angle 4.55002 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 241 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8359 (t) cc_final: 0.8045 (p) REVERT: A 245 HIS cc_start: 0.4646 (p-80) cc_final: 0.4424 (p-80) REVERT: A 303 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8527 (mt) REVERT: A 305 SER cc_start: 0.9463 (t) cc_final: 0.9209 (m) REVERT: A 559 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.7625 (t80) REVERT: A 708 SER cc_start: 0.8941 (OUTLIER) cc_final: 0.8671 (t) REVERT: A 856 ASN cc_start: 0.8534 (p0) cc_final: 0.8106 (p0) REVERT: A 1029 MET cc_start: 0.9205 (tpp) cc_final: 0.8838 (ttm) REVERT: A 1130 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8660 (tp) REVERT: B 21 ARG cc_start: 0.3691 (ttp80) cc_final: 0.2224 (ptp-110) REVERT: C 118 LEU cc_start: 0.8537 (tt) cc_final: 0.8153 (mp) REVERT: C 133 PHE cc_start: 0.6130 (m-80) cc_final: 0.5641 (m-10) REVERT: C 733 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8200 (mtpp) REVERT: C 854 LYS cc_start: 0.5366 (OUTLIER) cc_final: 0.5010 (pttt) REVERT: D 31 ARG cc_start: 0.8717 (mtp85) cc_final: 0.8326 (mtp85) REVERT: D 43 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6982 (mpp80) REVERT: E 4 MET cc_start: 0.8169 (mmm) cc_final: 0.7770 (mmp) REVERT: E 75 ASP cc_start: 0.8609 (m-30) cc_final: 0.7685 (p0) REVERT: E 84 GLU cc_start: 0.6310 (mp0) cc_final: 0.5949 (mp0) REVERT: F 19 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8252 (tpt-90) REVERT: F 84 ASN cc_start: 0.7252 (m-40) cc_final: 0.6676 (p0) REVERT: F 87 ARG cc_start: 0.7168 (ptp-110) cc_final: 0.6959 (ptp-110) REVERT: F 105 TYR cc_start: 0.8539 (OUTLIER) cc_final: 0.7439 (t80) REVERT: F 106 GLU cc_start: 0.8797 (tp30) cc_final: 0.8514 (tp30) REVERT: F 107 GLU cc_start: 0.8949 (mp0) cc_final: 0.8601 (mp0) REVERT: G 39 ASN cc_start: 0.8443 (m-40) cc_final: 0.7689 (m-40) REVERT: G 75 ASP cc_start: 0.8466 (t70) cc_final: 0.7953 (p0) REVERT: G 79 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8175 (tmtt) REVERT: G 94 MET cc_start: 0.6641 (tpp) cc_final: 0.6087 (tpp) REVERT: H 57 ASN cc_start: 0.7629 (m-40) cc_final: 0.6644 (p0) REVERT: H 107 GLU cc_start: 0.8874 (mp0) cc_final: 0.8065 (pm20) REVERT: I 56 VAL cc_start: 0.8435 (m) cc_final: 0.8229 (p) outliers start: 128 outliers final: 84 residues processed: 351 average time/residue: 0.1846 time to fit residues: 105.1381 Evaluate side-chains 304 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 213 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 69 HIS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 69 HIS Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Chi-restraints excluded: chain I residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 305 optimal weight: 0.7980 chunk 139 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 334 optimal weight: 0.7980 chunk 248 optimal weight: 0.0570 chunk 136 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 210 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A1002 GLN C 121 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 17 GLN G 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.110861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071919 restraints weight = 80036.236| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.23 r_work: 0.3009 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31527 Z= 0.111 Angle : 0.665 12.880 42987 Z= 0.315 Chirality : 0.046 0.475 4926 Planarity : 0.004 0.041 5484 Dihedral : 6.679 59.946 5278 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 3.11 % Allowed : 21.41 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.23 (0.13), residues: 3762 helix: 1.77 (0.21), residues: 664 sheet: 1.00 (0.16), residues: 953 loop : -1.41 (0.12), residues: 2145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 59 TYR 0.023 0.001 TYR B 170 PHE 0.021 0.001 PHE I 76 TRP 0.020 0.001 TRP A 436 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00247 (31425) covalent geometry : angle 0.62442 (42729) SS BOND : bond 0.00447 ( 48) SS BOND : angle 1.62890 ( 96) hydrogen bonds : bond 0.03764 ( 1134) hydrogen bonds : angle 4.97265 ( 3108) link_BETA1-4 : bond 0.00649 ( 21) link_BETA1-4 : angle 1.87338 ( 63) link_NAG-ASN : bond 0.00667 ( 33) link_NAG-ASN : angle 4.33730 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 246 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8326 (t) cc_final: 0.8008 (p) REVERT: A 245 HIS cc_start: 0.4791 (p-80) cc_final: 0.4517 (p-80) REVERT: A 305 SER cc_start: 0.9354 (t) cc_final: 0.9125 (m) REVERT: A 559 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7559 (t80) REVERT: A 708 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8762 (t) REVERT: A 856 ASN cc_start: 0.8456 (p0) cc_final: 0.7958 (p0) REVERT: A 1029 MET cc_start: 0.9103 (tpp) cc_final: 0.8820 (ttm) REVERT: A 1130 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8726 (tp) REVERT: B 21 ARG cc_start: 0.3668 (ttp80) cc_final: 0.2311 (ptp-110) REVERT: B 938 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7515 (mm) REVERT: B 992 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.7991 (mm-40) REVERT: C 118 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7844 (mp) REVERT: C 121 ASN cc_start: 0.6931 (OUTLIER) cc_final: 0.6642 (t0) REVERT: C 133 PHE cc_start: 0.6091 (m-80) cc_final: 0.5575 (m-10) REVERT: C 733 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8075 (mtpp) REVERT: C 854 LYS cc_start: 0.4837 (OUTLIER) cc_final: 0.4465 (pttt) REVERT: D 13 GLN cc_start: 0.8204 (mm-40) cc_final: 0.7892 (mm110) REVERT: D 31 ARG cc_start: 0.8743 (mtp85) cc_final: 0.8285 (mtp85) REVERT: D 43 ARG cc_start: 0.7320 (mmm160) cc_final: 0.7089 (mpp80) REVERT: D 73 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6237 (p0) REVERT: E 75 ASP cc_start: 0.8593 (m-30) cc_final: 0.7663 (p0) REVERT: E 84 GLU cc_start: 0.6306 (mp0) cc_final: 0.5941 (mp0) REVERT: F 19 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8290 (tpt-90) REVERT: F 73 ASP cc_start: 0.8130 (t0) cc_final: 0.7498 (t0) REVERT: F 76 LYS cc_start: 0.8833 (mppt) cc_final: 0.8223 (mmtm) REVERT: F 84 ASN cc_start: 0.7202 (m-40) cc_final: 0.6636 (p0) REVERT: F 105 TYR cc_start: 0.8507 (OUTLIER) cc_final: 0.7366 (t80) REVERT: F 106 GLU cc_start: 0.8745 (tp30) cc_final: 0.8458 (tp30) REVERT: F 107 GLU cc_start: 0.8945 (mp0) cc_final: 0.8627 (mp0) REVERT: G 39 ASN cc_start: 0.8494 (m-40) cc_final: 0.7752 (m-40) REVERT: G 75 ASP cc_start: 0.8560 (t70) cc_final: 0.8029 (p0) REVERT: G 79 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8098 (tptp) REVERT: G 94 MET cc_start: 0.6607 (tpp) cc_final: 0.6242 (tpp) REVERT: H 31 ARG cc_start: 0.8987 (ttp-110) cc_final: 0.8662 (ttp80) REVERT: H 107 GLU cc_start: 0.8868 (mp0) cc_final: 0.8143 (pm20) outliers start: 104 outliers final: 68 residues processed: 336 average time/residue: 0.1881 time to fit residues: 102.9720 Evaluate side-chains 292 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 213 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 80 ILE Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 252 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 122 optimal weight: 0.0170 chunk 249 optimal weight: 20.0000 chunk 328 optimal weight: 10.0000 chunk 364 optimal weight: 20.0000 chunk 330 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 overall best weight: 2.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 422 ASN B1002 GLN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 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 = 0.3876 r_free = 0.3876 target = 0.109351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.070237 restraints weight = 80315.204| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.21 r_work: 0.2971 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31527 Z= 0.164 Angle : 0.681 12.687 42987 Z= 0.327 Chirality : 0.047 0.479 4926 Planarity : 0.004 0.042 5484 Dihedral : 6.722 57.568 5278 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 3.44 % Allowed : 21.29 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.30 (0.13), residues: 3762 helix: 1.74 (0.21), residues: 658 sheet: 0.92 (0.16), residues: 956 loop : -1.44 (0.12), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 87 TYR 0.021 0.001 TYR C1067 PHE 0.027 0.001 PHE B 759 TRP 0.021 0.001 TRP A 436 HIS 0.011 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00391 (31425) covalent geometry : angle 0.64077 (42729) SS BOND : bond 0.00435 ( 48) SS BOND : angle 1.81066 ( 96) hydrogen bonds : bond 0.04194 ( 1134) hydrogen bonds : angle 4.99728 ( 3108) link_BETA1-4 : bond 0.00575 ( 21) link_BETA1-4 : angle 1.93307 ( 63) link_NAG-ASN : bond 0.00568 ( 33) link_NAG-ASN : angle 4.34130 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 218 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8382 (t) cc_final: 0.8021 (p) REVERT: A 245 HIS cc_start: 0.4753 (p-80) cc_final: 0.4468 (p-80) REVERT: A 303 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 305 SER cc_start: 0.9458 (t) cc_final: 0.9204 (m) REVERT: A 559 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7602 (t80) REVERT: A 708 SER cc_start: 0.8919 (OUTLIER) cc_final: 0.8654 (t) REVERT: A 856 ASN cc_start: 0.8489 (p0) cc_final: 0.8004 (p0) REVERT: A 1029 MET cc_start: 0.9142 (tpp) cc_final: 0.8850 (ttm) REVERT: A 1130 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8701 (tp) REVERT: B 21 ARG cc_start: 0.3717 (ttp80) cc_final: 0.2178 (ptp-110) REVERT: B 960 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.9108 (t0) REVERT: B 992 GLN cc_start: 0.8956 (OUTLIER) cc_final: 0.8044 (mm-40) REVERT: C 118 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8078 (mp) REVERT: C 133 PHE cc_start: 0.6019 (m-80) cc_final: 0.5548 (m-10) REVERT: C 212 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8548 (mm) REVERT: C 733 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8093 (mtpp) REVERT: C 854 LYS cc_start: 0.5357 (OUTLIER) cc_final: 0.4912 (pttt) REVERT: D 31 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8249 (mtp85) REVERT: D 43 ARG cc_start: 0.7273 (mmm160) cc_final: 0.7069 (mpp80) REVERT: E 75 ASP cc_start: 0.8580 (m-30) cc_final: 0.7529 (p0) REVERT: E 84 GLU cc_start: 0.6324 (mp0) cc_final: 0.5928 (mp0) REVERT: F 19 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8261 (tpt-90) REVERT: F 73 ASP cc_start: 0.8210 (t0) cc_final: 0.7495 (t0) REVERT: F 76 LYS cc_start: 0.8841 (mppt) cc_final: 0.8175 (mmtm) REVERT: F 84 ASN cc_start: 0.7210 (m-40) cc_final: 0.6682 (p0) REVERT: F 105 TYR cc_start: 0.8503 (OUTLIER) cc_final: 0.7259 (t80) REVERT: F 106 GLU cc_start: 0.8768 (tp30) cc_final: 0.8528 (tp30) REVERT: F 107 GLU cc_start: 0.8909 (mp0) cc_final: 0.8604 (mp0) REVERT: G 39 ASN cc_start: 0.8430 (m-40) cc_final: 0.7544 (m-40) REVERT: G 75 ASP cc_start: 0.8499 (t70) cc_final: 0.7997 (p0) REVERT: G 79 LYS cc_start: 0.8552 (ttmt) cc_final: 0.8048 (tptp) REVERT: G 94 MET cc_start: 0.6540 (tpp) cc_final: 0.6134 (tpp) REVERT: H 31 ARG cc_start: 0.8994 (ttp-110) cc_final: 0.8680 (ttp80) REVERT: H 107 GLU cc_start: 0.8850 (mp0) cc_final: 0.8312 (pm20) outliers start: 115 outliers final: 81 residues processed: 319 average time/residue: 0.1919 time to fit residues: 99.0863 Evaluate side-chains 294 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 202 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 938 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 80 ILE Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 1 ASP Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 336 optimal weight: 20.0000 chunk 117 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 227 optimal weight: 10.0000 chunk 143 optimal weight: 20.0000 chunk 373 optimal weight: 7.9990 chunk 158 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 115 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 121 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.109734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.070762 restraints weight = 80407.148| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.21 r_work: 0.2985 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31527 Z= 0.136 Angle : 0.667 12.747 42987 Z= 0.319 Chirality : 0.046 0.472 4926 Planarity : 0.004 0.043 5484 Dihedral : 6.684 59.062 5278 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.19 % Favored : 93.75 % Rotamer: Outliers : 3.32 % Allowed : 21.26 % Favored : 75.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.25 (0.13), residues: 3762 helix: 1.77 (0.21), residues: 659 sheet: 0.94 (0.16), residues: 959 loop : -1.40 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 59 TYR 0.020 0.001 TYR C1067 PHE 0.025 0.001 PHE A 133 TRP 0.024 0.001 TRP A 436 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00320 (31425) covalent geometry : angle 0.62815 (42729) SS BOND : bond 0.00443 ( 48) SS BOND : angle 1.58375 ( 96) hydrogen bonds : bond 0.03946 ( 1134) hydrogen bonds : angle 4.93862 ( 3108) link_BETA1-4 : bond 0.00572 ( 21) link_BETA1-4 : angle 1.90114 ( 63) link_NAG-ASN : bond 0.00585 ( 33) link_NAG-ASN : angle 4.24318 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 216 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 SER cc_start: 0.8370 (t) cc_final: 0.8004 (p) REVERT: A 245 HIS cc_start: 0.4626 (p-80) cc_final: 0.4341 (p-80) REVERT: A 303 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8472 (mt) REVERT: A 305 SER cc_start: 0.9454 (t) cc_final: 0.9200 (m) REVERT: A 519 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.5735 (t-90) REVERT: A 559 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7635 (t80) REVERT: A 708 SER cc_start: 0.8892 (OUTLIER) cc_final: 0.8651 (t) REVERT: A 856 ASN cc_start: 0.8404 (p0) cc_final: 0.7964 (p0) REVERT: A 1029 MET cc_start: 0.9123 (tpp) cc_final: 0.8850 (ttm) REVERT: A 1130 ILE cc_start: 0.9198 (OUTLIER) cc_final: 0.8709 (tp) REVERT: B 21 ARG cc_start: 0.3387 (ttp80) cc_final: 0.2011 (ptp-110) REVERT: B 960 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.9090 (t0) REVERT: B 992 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8041 (mm-40) REVERT: C 118 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8059 (mp) REVERT: C 133 PHE cc_start: 0.6030 (m-80) cc_final: 0.5576 (m-10) REVERT: C 212 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (mm) REVERT: C 733 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8133 (mtpp) REVERT: C 854 LYS cc_start: 0.5292 (OUTLIER) cc_final: 0.4845 (pttt) REVERT: D 31 ARG cc_start: 0.8739 (mtp85) cc_final: 0.8255 (mtp85) REVERT: D 107 GLU cc_start: 0.7041 (pp20) cc_final: 0.6678 (pp20) REVERT: E 39 ASN cc_start: 0.8242 (m-40) cc_final: 0.7998 (m-40) REVERT: E 75 ASP cc_start: 0.8569 (m-30) cc_final: 0.7534 (p0) REVERT: E 84 GLU cc_start: 0.6295 (mp0) cc_final: 0.5894 (mp0) REVERT: F 19 ARG cc_start: 0.8571 (tpp80) cc_final: 0.8292 (tpt-90) REVERT: F 73 ASP cc_start: 0.8190 (t0) cc_final: 0.7554 (t0) REVERT: F 76 LYS cc_start: 0.8860 (mppt) cc_final: 0.8296 (mmtm) REVERT: F 84 ASN cc_start: 0.7206 (m-40) cc_final: 0.6701 (p0) REVERT: F 106 GLU cc_start: 0.8763 (tp30) cc_final: 0.8531 (tp30) REVERT: F 107 GLU cc_start: 0.8905 (mp0) cc_final: 0.8602 (mp0) REVERT: G 75 ASP cc_start: 0.8539 (t70) cc_final: 0.8019 (p0) REVERT: G 79 LYS cc_start: 0.8535 (ttmt) cc_final: 0.8097 (tptp) REVERT: G 94 MET cc_start: 0.6519 (tpp) cc_final: 0.6151 (tpp) REVERT: H 31 ARG cc_start: 0.8942 (ttp-110) cc_final: 0.8628 (ttp80) REVERT: H 107 GLU cc_start: 0.8808 (mp0) cc_final: 0.8340 (pm20) REVERT: I 76 PHE cc_start: 0.8259 (m-80) cc_final: 0.7962 (m-80) outliers start: 111 outliers final: 80 residues processed: 315 average time/residue: 0.1892 time to fit residues: 97.7565 Evaluate side-chains 299 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 208 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 351 optimal weight: 7.9990 chunk 341 optimal weight: 3.9990 chunk 335 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 273 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 30.0000 chunk 282 optimal weight: 0.7980 chunk 214 optimal weight: 10.0000 chunk 40 optimal weight: 30.0000 chunk 180 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 GLN I 43 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.108379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.069457 restraints weight = 80455.750| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.19 r_work: 0.2959 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31527 Z= 0.180 Angle : 0.690 12.888 42987 Z= 0.332 Chirality : 0.047 0.487 4926 Planarity : 0.004 0.045 5484 Dihedral : 6.825 59.636 5278 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.17 % Rotamer: Outliers : 3.26 % Allowed : 21.49 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.31 (0.13), residues: 3762 helix: 1.74 (0.21), residues: 658 sheet: 0.85 (0.16), residues: 979 loop : -1.44 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 44 TYR 0.021 0.001 TYR C1067 PHE 0.021 0.001 PHE A 559 TRP 0.024 0.001 TRP A 436 HIS 0.005 0.001 HIS D 35 Details of bonding type rmsd covalent geometry : bond 0.00429 (31425) covalent geometry : angle 0.65049 (42729) SS BOND : bond 0.00431 ( 48) SS BOND : angle 1.76889 ( 96) hydrogen bonds : bond 0.04418 ( 1134) hydrogen bonds : angle 5.02889 ( 3108) link_BETA1-4 : bond 0.00540 ( 21) link_BETA1-4 : angle 1.97914 ( 63) link_NAG-ASN : bond 0.00543 ( 33) link_NAG-ASN : angle 4.29478 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 224 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.4534 (p-80) cc_final: 0.4201 (p-80) REVERT: A 303 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8459 (mt) REVERT: A 305 SER cc_start: 0.9444 (t) cc_final: 0.9201 (m) REVERT: A 519 HIS cc_start: 0.6137 (OUTLIER) cc_final: 0.5788 (t-90) REVERT: A 559 PHE cc_start: 0.8549 (OUTLIER) cc_final: 0.7744 (t80) REVERT: A 708 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (t) REVERT: A 856 ASN cc_start: 0.8477 (p0) cc_final: 0.8034 (p0) REVERT: A 1029 MET cc_start: 0.9182 (tpp) cc_final: 0.8845 (ttm) REVERT: A 1130 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8724 (tp) REVERT: B 21 ARG cc_start: 0.3706 (ttp80) cc_final: 0.2119 (ptp-110) REVERT: B 960 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.9109 (t0) REVERT: B 992 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8070 (mm-40) REVERT: C 118 LEU cc_start: 0.8485 (tt) cc_final: 0.8121 (mp) REVERT: C 133 PHE cc_start: 0.6447 (m-80) cc_final: 0.6029 (m-80) REVERT: C 212 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8323 (mt) REVERT: C 436 TRP cc_start: 0.7712 (p90) cc_final: 0.7503 (p90) REVERT: C 733 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8212 (mtpp) REVERT: C 854 LYS cc_start: 0.5463 (OUTLIER) cc_final: 0.5118 (pttt) REVERT: D 31 ARG cc_start: 0.8723 (mtp85) cc_final: 0.8298 (mtp85) REVERT: D 107 GLU cc_start: 0.7170 (pp20) cc_final: 0.6659 (pp20) REVERT: E 75 ASP cc_start: 0.8522 (m-30) cc_final: 0.7713 (p0) REVERT: E 84 GLU cc_start: 0.6378 (mp0) cc_final: 0.5964 (mp0) REVERT: F 19 ARG cc_start: 0.8522 (tpp80) cc_final: 0.8253 (tpt-90) REVERT: F 73 ASP cc_start: 0.8171 (t0) cc_final: 0.7710 (t0) REVERT: F 76 LYS cc_start: 0.8867 (mppt) cc_final: 0.8511 (mptt) REVERT: F 84 ASN cc_start: 0.7235 (m-40) cc_final: 0.6745 (p0) REVERT: F 106 GLU cc_start: 0.8764 (tp30) cc_final: 0.8546 (tp30) REVERT: F 107 GLU cc_start: 0.8909 (mp0) cc_final: 0.8578 (mp0) REVERT: G 39 ASN cc_start: 0.8663 (m-40) cc_final: 0.8439 (t0) REVERT: G 79 LYS cc_start: 0.8554 (ttmt) cc_final: 0.8106 (tptp) REVERT: G 94 MET cc_start: 0.6737 (tpp) cc_final: 0.6341 (tpp) REVERT: H 31 ARG cc_start: 0.8923 (ttp-110) cc_final: 0.8615 (ttp80) REVERT: H 107 GLU cc_start: 0.8814 (mp0) cc_final: 0.8393 (pm20) REVERT: I 76 PHE cc_start: 0.8423 (m-80) cc_final: 0.8074 (m-10) outliers start: 109 outliers final: 91 residues processed: 318 average time/residue: 0.1911 time to fit residues: 98.2637 Evaluate side-chains 308 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 207 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 21 ILE Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 226 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 55 optimal weight: 0.2980 chunk 142 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 368 optimal weight: 8.9990 chunk 193 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 245 optimal weight: 10.0000 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN C 121 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.107470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068684 restraints weight = 80363.367| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.19 r_work: 0.2933 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 31527 Z= 0.244 Angle : 0.734 13.264 42987 Z= 0.357 Chirality : 0.049 0.512 4926 Planarity : 0.004 0.052 5484 Dihedral : 7.077 59.798 5278 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.12 % Favored : 92.80 % Rotamer: Outliers : 3.17 % Allowed : 21.91 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.50 (0.13), residues: 3762 helix: 1.60 (0.21), residues: 660 sheet: 0.68 (0.17), residues: 921 loop : -1.49 (0.12), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 67 TYR 0.036 0.002 TYR D 102 PHE 0.026 0.002 PHE A 456 TRP 0.028 0.002 TRP A 886 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00585 (31425) covalent geometry : angle 0.69408 (42729) SS BOND : bond 0.00488 ( 48) SS BOND : angle 2.08982 ( 96) hydrogen bonds : bond 0.04832 ( 1134) hydrogen bonds : angle 5.18259 ( 3108) link_BETA1-4 : bond 0.00538 ( 21) link_BETA1-4 : angle 2.01301 ( 63) link_NAG-ASN : bond 0.00605 ( 33) link_NAG-ASN : angle 4.35950 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7524 Ramachandran restraints generated. 3762 Oldfield, 0 Emsley, 3762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 209 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 HIS cc_start: 0.4528 (p-80) cc_final: 0.4199 (p-80) REVERT: A 303 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8479 (mt) REVERT: A 305 SER cc_start: 0.9451 (t) cc_final: 0.9236 (m) REVERT: A 519 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5707 (t-90) REVERT: A 559 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.7851 (t80) REVERT: A 708 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8682 (t) REVERT: A 856 ASN cc_start: 0.8460 (p0) cc_final: 0.8012 (p0) REVERT: A 1029 MET cc_start: 0.9235 (tpp) cc_final: 0.8869 (ttm) REVERT: A 1130 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8769 (tp) REVERT: B 960 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.9111 (t0) REVERT: B 992 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.8113 (mm-40) REVERT: C 118 LEU cc_start: 0.8475 (tt) cc_final: 0.8082 (mp) REVERT: C 133 PHE cc_start: 0.6619 (m-80) cc_final: 0.6235 (m-80) REVERT: C 212 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 436 TRP cc_start: 0.7700 (p90) cc_final: 0.7479 (p90) REVERT: C 733 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8257 (mtpp) REVERT: C 854 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.4971 (ptmm) REVERT: D 31 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8313 (mtp85) REVERT: E 75 ASP cc_start: 0.8536 (m-30) cc_final: 0.7752 (p0) REVERT: F 19 ARG cc_start: 0.8575 (tpp80) cc_final: 0.8319 (tpt-90) REVERT: F 73 ASP cc_start: 0.8183 (t0) cc_final: 0.7721 (t0) REVERT: F 76 LYS cc_start: 0.8778 (mppt) cc_final: 0.8242 (mmtm) REVERT: F 84 ASN cc_start: 0.7219 (m-40) cc_final: 0.6677 (p0) REVERT: F 106 GLU cc_start: 0.8751 (tp30) cc_final: 0.8288 (tp30) REVERT: F 107 GLU cc_start: 0.8958 (mp0) cc_final: 0.8576 (mp0) REVERT: G 79 LYS cc_start: 0.8582 (ttmt) cc_final: 0.8090 (tptp) REVERT: G 94 MET cc_start: 0.6682 (tpp) cc_final: 0.6212 (tpp) REVERT: H 31 ARG cc_start: 0.8870 (ttp-110) cc_final: 0.8585 (ttp80) REVERT: H 107 GLU cc_start: 0.8814 (mp0) cc_final: 0.8340 (pm20) REVERT: I 76 PHE cc_start: 0.8437 (m-80) cc_final: 0.8096 (m-10) outliers start: 106 outliers final: 90 residues processed: 303 average time/residue: 0.1927 time to fit residues: 95.3401 Evaluate side-chains 299 residues out of total 3345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 199 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 142 ASP Chi-restraints excluded: chain B residue 247 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 992 GLN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 733 LYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 739 THR Chi-restraints excluded: chain C residue 854 LYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 105 TYR Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 105 TYR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain I residue 15 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 95 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 254 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 323 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 339 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 236 optimal weight: 0.5980 chunk 143 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN B 422 ASN ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN C 121 ASN ** C 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.108248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.069623 restraints weight = 80405.182| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 3.20 r_work: 0.2954 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31527 Z= 0.168 Angle : 0.694 13.091 42987 Z= 0.335 Chirality : 0.047 0.499 4926 Planarity : 0.004 0.051 5484 Dihedral : 6.984 59.766 5278 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.46 % Favored : 93.49 % Rotamer: Outliers : 3.14 % Allowed : 21.79 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.48 % 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: -0.40 (0.13), residues: 3762 helix: 1.62 (0.21), residues: 665 sheet: 0.75 (0.16), residues: 1008 loop : -1.50 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 67 TYR 0.021 0.001 TYR C1067 PHE 0.020 0.001 PHE A 133 TRP 0.026 0.001 TRP A 436 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00400 (31425) covalent geometry : angle 0.65360 (42729) SS BOND : bond 0.00430 ( 48) SS BOND : angle 1.95446 ( 96) hydrogen bonds : bond 0.04367 ( 1134) hydrogen bonds : angle 5.11014 ( 3108) link_BETA1-4 : bond 0.00547 ( 21) link_BETA1-4 : angle 1.95079 ( 63) link_NAG-ASN : bond 0.00578 ( 33) link_NAG-ASN : angle 4.33988 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8469.95 seconds wall clock time: 145 minutes 51.65 seconds (8751.65 seconds total)