Starting phenix.real_space_refine on Mon Sep 14 13:14:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xo1_67066/09_2026/9xo1_67066.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xo1_67066/09_2026/9xo1_67066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9xo1_67066/09_2026/9xo1_67066.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xo1_67066/09_2026/9xo1_67066.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9xo1_67066/09_2026/9xo1_67066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xo1_67066/09_2026/9xo1_67066.map" } resolution = 2.42 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= -0.001 sd= 0.092 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 148 5.16 5 C 18997 2.51 5 N 4832 2.21 5 O 5931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29908 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 8719 Classifications: {'peptide': 1136} Link IDs: {'PTRANS': 42, 'TRANS': 1093} Chain breaks: 11 Chain: "B" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8489 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 40, 'TRANS': 1063} Chain breaks: 12 Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "C" Number of atoms: 8489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1104, 8489 Classifications: {'peptide': 1104} Link IDs: {'PTRANS': 40, 'TRANS': 1063} Chain breaks: 12 Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 881 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "E" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 743 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 8, 'TRANS': 93} Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 204 Unusual residues: {'NAG': 12, 'PAM': 2} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 6, 'PAM': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 120 Unusual residues: {'NAG': 6, 'PAM': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.32, per 1000 atoms: 0.21 Number of scatterers: 29908 At special positions: 0 Unit cell: (176.7, 204.6, 163.68, 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 148 16.00 O 5931 8.00 N 4832 7.00 C 18997 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=52, symmetry=0 Simple disulfide: pdb=" SG CYS A 26 " - pdb=" SG CYS A 67 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 234 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 307 " distance=2.03 Simple disulfide: pdb=" SG CYS A 349 " - pdb=" SG CYS A 373 " distance=2.03 Simple disulfide: pdb=" SG CYS A 464 " - pdb=" SG CYS A 473 " distance=2.02 Simple disulfide: pdb=" SG CYS A 543 " - pdb=" SG CYS A 589 " distance=2.03 Simple disulfide: pdb=" SG CYS A 572 " - pdb=" SG CYS A 599 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 700 " distance=2.04 Simple disulfide: pdb=" SG CYS A 744 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 830 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A 920 " - pdb=" SG CYS A 931 " distance=2.04 Simple disulfide: pdb=" SG CYS A1122 " - pdb=" SG CYS A1133 " distance=2.03 Simple disulfide: pdb=" SG CYS A1173 " - pdb=" SG CYS A1226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 67 " distance=2.03 Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS B 196 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 230 " - pdb=" SG CYS B 234 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 307 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 464 " - pdb=" SG CYS B 473 " distance=2.02 Simple disulfide: pdb=" SG CYS B 543 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 599 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 744 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 830 " distance=2.02 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 819 " distance=2.04 Simple disulfide: pdb=" SG CYS B 920 " - pdb=" SG CYS B 931 " distance=2.03 Simple disulfide: pdb=" SG CYS B1122 " - pdb=" SG CYS B1133 " distance=2.03 Simple disulfide: pdb=" SG CYS B1173 " - pdb=" SG CYS B1226 " distance=2.04 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 115 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 67 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 148 " distance=2.03 Simple disulfide: pdb=" SG CYS C 196 " - pdb=" SG CYS C 202 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 283 " - pdb=" SG CYS C 307 " distance=2.03 Simple disulfide: pdb=" SG CYS C 349 " - pdb=" SG CYS C 373 " distance=2.03 Simple disulfide: pdb=" SG CYS C 464 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 543 " - pdb=" SG CYS C 589 " distance=2.04 Simple disulfide: pdb=" SG CYS C 572 " - pdb=" SG CYS C 599 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 700 " distance=2.03 Simple disulfide: pdb=" SG CYS C 744 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 830 " distance=2.02 Simple disulfide: pdb=" SG CYS C 813 " - pdb=" SG CYS C 819 " distance=2.04 Simple disulfide: pdb=" SG CYS C 920 " - pdb=" SG CYS C 931 " distance=2.03 Simple disulfide: pdb=" SG CYS C1122 " - pdb=" SG CYS C1133 " distance=2.03 Simple disulfide: pdb=" SG CYS C1173 " - pdb=" SG CYS C1226 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 108 " distance=2.03 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 ALPHA1-3 " BMA H 3 " - " MAN H 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " " BMA P 3 " - " MAN P 5 " " BMA V 3 " - " MAN V 5 " BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 V 2 " - " BMA V 3 " NAG-ASN " NAG A1401 " - " ASN A 324 " " NAG A1402 " - " ASN A 216 " " NAG A1403 " - " ASN A 514 " " NAG A1404 " - " ASN A 726 " " NAG A1405 " - " ASN A 781 " " NAG A1406 " - " ASN A 743 " " NAG A1407 " - " ASN A 787 " " NAG A1408 " - " ASN A 873 " " NAG A1409 " - " ASN A1009 " " NAG A1410 " - " ASN A1232 " " NAG A1411 " - " ASN A 344 " " NAG A1412 " - " ASN A 351 " " NAG B1401 " - " ASN B 344 " " NAG B1402 " - " ASN B 726 " " NAG B1403 " - " ASN B 781 " " NAG B1404 " - " ASN B 743 " " NAG B1405 " - " ASN B 787 " " NAG B1406 " - " ASN B1009 " " NAG C1402 " - " ASN C 344 " " NAG C1403 " - " ASN C 726 " " NAG C1404 " - " ASN C 781 " " NAG C1405 " - " ASN C 743 " " NAG C1406 " - " ASN C 787 " " NAG C1407 " - " ASN C1009 " " NAG H 1 " - " ASN A 264 " " NAG I 1 " - " ASN A 688 " " NAG J 1 " - " ASN A 425 " " NAG K 1 " - " ASN B 216 " " NAG L 1 " - " ASN B 324 " " NAG M 1 " - " ASN B 688 " " NAG N 1 " - " ASN B 514 " " NAG O 1 " - " ASN B 873 " " NAG P 1 " - " ASN B 264 " " NAG Q 1 " - " ASN C 216 " " NAG R 1 " - " ASN C 324 " " NAG S 1 " - " ASN C 688 " " NAG T 1 " - " ASN C 514 " " NAG U 1 " - " ASN C 873 " " NAG V 1 " - " ASN C 264 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.6 seconds 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6940 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 56 sheets defined 19.8% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.682A pdb=" N GLY A 224 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 225 " --> pdb=" O GLU A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 225' Processing helix chain 'A' and resid 325 through 330 removed outlier: 3.558A pdb=" N VAL A 328 " --> pdb=" O ASP A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 577 through 581 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.573A pdb=" N ILE A 833 " --> pdb=" O ALA A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 855 through 860 Processing helix chain 'A' and resid 895 through 903 Processing helix chain 'A' and resid 928 through 935 Processing helix chain 'A' and resid 946 through 960 Processing helix chain 'A' and resid 973 through 986 removed outlier: 3.759A pdb=" N ALA A 977 " --> pdb=" O PRO A 973 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A 985 " --> pdb=" O ARG A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1016 removed outlier: 3.760A pdb=" N GLU A1001 " --> pdb=" O GLN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1030 through 1044 Processing helix chain 'A' and resid 1046 through 1054 Processing helix chain 'A' and resid 1055 through 1058 removed outlier: 3.619A pdb=" N HIS A1058 " --> pdb=" O GLN A1055 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1055 through 1058' Processing helix chain 'A' and resid 1066 through 1074 Processing helix chain 'A' and resid 1075 through 1123 removed outlier: 3.667A pdb=" N ARG A1085 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A1086 " --> pdb=" O GLN A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1216 through 1218 No H-bonds generated for 'chain 'A' and resid 1216 through 1218' Processing helix chain 'A' and resid 1234 through 1236 No H-bonds generated for 'chain 'A' and resid 1234 through 1236' Processing helix chain 'A' and resid 1237 through 1242 Processing helix chain 'B' and resid 31 through 38 Processing helix chain 'B' and resid 221 through 223 No H-bonds generated for 'chain 'B' and resid 221 through 223' Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 325 through 333 removed outlier: 3.677A pdb=" N ILE B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 577 through 581 removed outlier: 3.509A pdb=" N ASN B 580 " --> pdb=" O GLN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 812 Processing helix chain 'B' and resid 816 through 825 removed outlier: 4.156A pdb=" N GLN B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 852 Processing helix chain 'B' and resid 855 through 860 Processing helix chain 'B' and resid 895 through 903 Processing helix chain 'B' and resid 917 through 922 removed outlier: 3.646A pdb=" N SER B 921 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN B 922 " --> pdb=" O ARG B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 928 through 936 removed outlier: 3.530A pdb=" N SER B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 961 removed outlier: 3.611A pdb=" N MET B 961 " --> pdb=" O LEU B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 986 removed outlier: 3.864A pdb=" N ALA B 977 " --> pdb=" O PRO B 973 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 985 " --> pdb=" O ARG B 981 " (cutoff:3.500A) Processing helix chain 'B' and resid 997 through 1014 Processing helix chain 'B' and resid 1030 through 1045 Processing helix chain 'B' and resid 1046 through 1055 Processing helix chain 'B' and resid 1056 through 1058 No H-bonds generated for 'chain 'B' and resid 1056 through 1058' Processing helix chain 'B' and resid 1066 through 1074 Processing helix chain 'B' and resid 1075 through 1123 Processing helix chain 'B' and resid 1216 through 1218 No H-bonds generated for 'chain 'B' and resid 1216 through 1218' Processing helix chain 'F' and resid 106 through 110 removed outlier: 3.843A pdb=" N ALA F 110 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'C' and resid 31 through 38 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 233 through 241 removed outlier: 3.531A pdb=" N SER C 238 " --> pdb=" O CYS C 234 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 333 removed outlier: 3.563A pdb=" N ILE C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 807 through 812 Processing helix chain 'C' and resid 816 through 825 removed outlier: 4.171A pdb=" N GLN C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 852 Processing helix chain 'C' and resid 855 through 861 removed outlier: 3.675A pdb=" N LEU C 861 " --> pdb=" O GLU C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 903 Processing helix chain 'C' and resid 917 through 922 removed outlier: 3.852A pdb=" N SER C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN C 922 " --> pdb=" O LYS C 918 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 917 through 922' Processing helix chain 'C' and resid 928 through 935 Processing helix chain 'C' and resid 946 through 960 Processing helix chain 'C' and resid 973 through 986 removed outlier: 3.811A pdb=" N ALA C 977 " --> pdb=" O PRO C 973 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU C 985 " --> pdb=" O ARG C 981 " (cutoff:3.500A) Processing helix chain 'C' and resid 997 through 1014 Processing helix chain 'C' and resid 1030 through 1045 Processing helix chain 'C' and resid 1046 through 1055 Processing helix chain 'C' and resid 1056 through 1058 No H-bonds generated for 'chain 'C' and resid 1056 through 1058' Processing helix chain 'C' and resid 1066 through 1074 Processing helix chain 'C' and resid 1078 through 1123 removed outlier: 3.975A pdb=" N GLN C1082 " --> pdb=" O SER C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1216 through 1218 No H-bonds generated for 'chain 'C' and resid 1216 through 1218' Processing helix chain 'E' and resid 48 through 52 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 49 removed outlier: 3.510A pdb=" N VAL A 47 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR A 213 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 70 removed outlier: 3.853A pdb=" N PHE A 91 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 123 " --> pdb=" O LYS A 152 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 152 " --> pdb=" O LEU A 123 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 184 removed outlier: 3.543A pdb=" N PHE A 81 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 271 through 288 removed outlier: 7.504A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 414 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 408 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLY A 412 " --> pdb=" O VAL A 408 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 288 removed outlier: 7.504A pdb=" N VAL A 273 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 453 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N SER A 275 " --> pdb=" O ILE A 451 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE A 451 " --> pdb=" O SER A 275 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN A 277 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ALA A 449 " --> pdb=" O GLN A 277 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N LEU A 279 " --> pdb=" O VAL A 447 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL A 447 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL A 281 " --> pdb=" O ASN A 445 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A 445 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS A 283 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP A 448 " --> pdb=" O TYR A 463 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N TYR A 463 " --> pdb=" O ASP A 448 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU A 450 " --> pdb=" O ILE A 461 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ILE A 461 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU A 452 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 293 through 298 removed outlier: 6.939A pdb=" N HIS A 338 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL A 422 " --> pdb=" O VAL A 336 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 336 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ILE A 335 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N CYS A 373 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 382 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 483 through 488 removed outlier: 3.704A pdb=" N GLY A 715 " --> pdb=" O ALA A 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 499 through 502 removed outlier: 4.844A pdb=" N LEU A 684 " --> pdb=" O VAL A 697 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR A 676 " --> pdb=" O LEU A 684 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 529 through 536 removed outlier: 4.414A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 10.673A pdb=" N PHE A 622 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 11.938A pdb=" N SER A 591 " --> pdb=" O PHE A 622 " (cutoff:3.500A) removed outlier: 11.604A pdb=" N LYS A 624 " --> pdb=" O CYS A 589 " (cutoff:3.500A) removed outlier: 11.928A pdb=" N CYS A 589 " --> pdb=" O LYS A 624 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLU A 626 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N LYS A 587 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU A 583 " --> pdb=" O GLY A 630 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 529 through 536 removed outlier: 4.414A pdb=" N ALA A 531 " --> pdb=" O SER A 520 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A 511 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER A 552 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 513 " --> pdb=" O SER A 552 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE A 554 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 515 " --> pdb=" O PHE A 554 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASN A 556 " --> pdb=" O ILE A 515 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL A 517 " --> pdb=" O ASN A 556 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N THR A 558 " --> pdb=" O VAL A 517 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 519 " --> pdb=" O THR A 558 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LEU A 603 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER A 617 " --> pdb=" O ILE A 601 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE A 601 " --> pdb=" O SER A 617 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR A 619 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS A 599 " --> pdb=" O TYR A 619 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB5, first strand: chain 'A' and resid 780 through 798 removed outlier: 6.523A pdb=" N ASN A 781 " --> pdb=" O ILE A1167 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE A1167 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER A 783 " --> pdb=" O ASP A1165 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP A1165 " --> pdb=" O SER A 783 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE A1163 " --> pdb=" O PRO A 785 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN A 787 " --> pdb=" O GLY A1161 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A1141 " --> pdb=" O THR A1156 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEU A1158 " --> pdb=" O HIS A1139 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N HIS A1139 " --> pdb=" O LEU A1158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 804 through 806 Processing sheet with id=AB7, first strand: chain 'A' and resid 1220 through 1223 removed outlier: 4.470A pdb=" N ALA A1179 " --> pdb=" O ILE A1223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1187 through 1190 Processing sheet with id=AB9, first strand: chain 'B' and resid 45 through 49 Processing sheet with id=AC1, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.630A pdb=" N GLY B 79 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 73 through 75 removed outlier: 3.770A pdb=" N PHE B 91 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 286 removed outlier: 7.747A pdb=" N VAL B 273 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 453 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER B 275 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 451 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN B 277 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA B 449 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU B 279 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 447 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 440 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP B 405 " --> pdb=" O THR B 401 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 414 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 270 through 286 removed outlier: 7.747A pdb=" N VAL B 273 " --> pdb=" O VAL B 453 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL B 453 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N SER B 275 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE B 451 " --> pdb=" O SER B 275 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N GLN B 277 " --> pdb=" O ALA B 449 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ALA B 449 " --> pdb=" O GLN B 277 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU B 279 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 447 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N VAL B 281 " --> pdb=" O ASN B 445 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 445 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ASP B 448 " --> pdb=" O TYR B 463 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR B 463 " --> pdb=" O ASP B 448 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU B 450 " --> pdb=" O ILE B 461 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ILE B 461 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLU B 452 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 295 through 298 removed outlier: 3.998A pdb=" N ILE B 335 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL B 348 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N CYS B 373 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 483 through 488 removed outlier: 3.680A pdb=" N GLY B 715 " --> pdb=" O ALA B 707 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 499 through 502 removed outlier: 4.517A pdb=" N VAL B 694 " --> pdb=" O THR B 666 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LEU B 684 " --> pdb=" O VAL B 697 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 531 through 536 removed outlier: 3.906A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 587 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY B 625 " --> pdb=" O PHE B 585 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 585 " --> pdb=" O GLY B 625 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 531 through 536 removed outlier: 3.906A pdb=" N ALA B 531 " --> pdb=" O SER B 520 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N LYS B 614 " --> pdb=" O GLY B 605 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLY B 605 " --> pdb=" O LYS B 614 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR B 616 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 749 through 751 Processing sheet with id=AD2, first strand: chain 'B' and resid 780 through 786 removed outlier: 3.731A pdb=" N GLY B 780 " --> pdb=" O ALA B1168 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE B1167 " --> pdb=" O THR B1191 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N THR B1191 " --> pdb=" O ILE B1167 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU B1189 " --> pdb=" O ILE B1169 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 789 through 798 removed outlier: 3.584A pdb=" N PHE B1141 " --> pdb=" O THR B1156 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B1158 " --> pdb=" O HIS B1139 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N HIS B1139 " --> pdb=" O LEU B1158 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 804 through 806 Processing sheet with id=AD5, first strand: chain 'B' and resid 1171 through 1174 Processing sheet with id=AD6, first strand: chain 'F' and resid 22 through 26 removed outlier: 3.528A pdb=" N LYS F 22 " --> pdb=" O SER F 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 77 through 79 removed outlier: 6.637A pdb=" N TRP F 55 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY F 69 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE F 53 " --> pdb=" O GLY F 69 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 116 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N CYS F 115 " --> pdb=" O GLY F 134 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 132 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 22 through 24 removed outlier: 3.653A pdb=" N ALA G 41 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 65 through 68 removed outlier: 6.574A pdb=" N TRP G 55 " --> pdb=" O LEU G 67 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER G 54 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS G 109 " --> pdb=" O SER G 54 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 105 " --> pdb=" O GLN G 58 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 45 through 49 Processing sheet with id=AE2, first strand: chain 'C' and resid 73 through 75 removed outlier: 3.515A pdb=" N VAL C 192 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'C' and resid 270 through 286 removed outlier: 6.278A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR C 440 " --> pdb=" O ASN C 322 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP C 405 " --> pdb=" O THR C 401 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU C 414 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 270 through 286 removed outlier: 6.278A pdb=" N ASN C 445 " --> pdb=" O LEU C 279 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N VAL C 281 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N SER C 443 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N CYS C 283 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE C 441 " --> pdb=" O CYS C 283 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 285 " --> pdb=" O TRP C 439 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N TRP C 439 " --> pdb=" O LEU C 285 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASP C 448 " --> pdb=" O TYR C 463 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR C 463 " --> pdb=" O ASP C 448 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU C 450 " --> pdb=" O ILE C 461 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C 461 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N GLU C 452 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 295 through 298 removed outlier: 4.015A pdb=" N ILE C 335 " --> pdb=" O PHE C 347 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 344 " --> pdb=" O ASP C 378 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 348 " --> pdb=" O PHE C 374 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TYR C 371 " --> pdb=" O VAL C 390 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL C 390 " --> pdb=" O TYR C 371 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N CYS C 373 " --> pdb=" O LEU C 388 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 483 through 488 removed outlier: 3.714A pdb=" N GLY C 715 " --> pdb=" O ALA C 707 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 499 through 502 removed outlier: 4.433A pdb=" N VAL C 694 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU C 684 " --> pdb=" O VAL C 697 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 529 through 536 removed outlier: 4.032A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR C 619 " --> pdb=" O VAL C 590 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 590 " --> pdb=" O TYR C 619 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLN C 621 " --> pdb=" O PHE C 588 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE C 588 " --> pdb=" O GLN C 621 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR C 623 " --> pdb=" O SER C 586 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY C 625 " --> pdb=" O SER C 584 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N SER C 584 " --> pdb=" O GLY C 625 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 529 through 536 removed outlier: 4.032A pdb=" N ALA C 531 " --> pdb=" O SER C 520 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N LYS C 614 " --> pdb=" O GLY C 605 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLY C 605 " --> pdb=" O LYS C 614 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR C 616 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 749 through 751 Processing sheet with id=AF3, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.830A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE C1141 " --> pdb=" O THR C1156 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N LEU C1158 " --> pdb=" O HIS C1139 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS C1139 " --> pdb=" O LEU C1158 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 780 through 798 removed outlier: 6.830A pdb=" N ASN C 781 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE C1167 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER C 783 " --> pdb=" O ASP C1165 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASP C1165 " --> pdb=" O SER C 783 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE C1163 " --> pdb=" O PRO C 785 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASN C 787 " --> pdb=" O GLY C1161 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE C1167 " --> pdb=" O THR C1191 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR C1191 " --> pdb=" O ILE C1167 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU C1189 " --> pdb=" O ILE C1169 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 804 through 806 Processing sheet with id=AF6, first strand: chain 'C' and resid 1171 through 1174 removed outlier: 3.866A pdb=" N ILE C1178 " --> pdb=" O VAL C1174 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 22 through 26 removed outlier: 3.502A pdb=" N LYS D 22 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU D 100 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 90 " --> pdb=" O TYR D 99 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR D 88 " --> pdb=" O GLN D 101 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.703A pdb=" N TRP D 55 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY D 69 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE D 53 " --> pdb=" O GLY D 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 77 through 79 removed outlier: 6.703A pdb=" N TRP D 55 " --> pdb=" O LEU D 67 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLY D 69 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE D 53 " --> pdb=" O GLY D 69 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 54 " --> pdb=" O ALA D 116 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 22 through 24 Processing sheet with id=AG2, first strand: chain 'E' and resid 65 through 68 removed outlier: 5.863A pdb=" N LEU E 66 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN E 57 " --> pdb=" O LEU E 66 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET E 68 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 54 " --> pdb=" O LYS E 109 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS E 109 " --> pdb=" O SER E 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL E 105 " --> pdb=" O GLN E 58 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3372 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: 11.01 Time building geometry restraints manager: 3.80 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: 9425 1.34 - 1.47: 8074 1.47 - 1.59: 12844 1.59 - 1.72: 0 1.72 - 1.85: 192 Bond restraints: 30535 Sorted by residual: bond pdb=" CB CYS B 808 " pdb=" SG CYS B 808 " ideal model delta sigma weight residual 1.808 1.724 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CB CYS C 808 " pdb=" SG CYS C 808 " ideal model delta sigma weight residual 1.808 1.734 0.074 3.30e-02 9.18e+02 5.02e+00 bond pdb=" CB ARG A 981 " pdb=" CG ARG A 981 " ideal model delta sigma weight residual 1.520 1.471 0.049 3.00e-02 1.11e+03 2.66e+00 bond pdb=" CB THR C 631 " pdb=" CG2 THR C 631 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.22e+00 bond pdb=" CA THR A 456 " pdb=" C THR A 456 " ideal model delta sigma weight residual 1.526 1.551 -0.026 1.75e-02 3.27e+03 2.16e+00 ... (remaining 30530 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 40860 2.29 - 4.58: 562 4.58 - 6.87: 43 6.87 - 9.16: 8 9.16 - 11.46: 1 Bond angle restraints: 41474 Sorted by residual: angle pdb=" C2 NAG A1410 " pdb=" N2 NAG A1410 " pdb=" C7 NAG A1410 " ideal model delta sigma weight residual 124.56 136.02 -11.46 3.00e+00 1.11e-01 1.46e+01 angle pdb=" CA CYS B 808 " pdb=" CB CYS B 808 " pdb=" SG CYS B 808 " ideal model delta sigma weight residual 114.40 123.00 -8.60 2.30e+00 1.89e-01 1.40e+01 angle pdb=" N VAL A 638 " pdb=" CA VAL A 638 " pdb=" C VAL A 638 " ideal model delta sigma weight residual 112.96 109.55 3.41 1.00e+00 1.00e+00 1.16e+01 angle pdb=" CA CYS C 808 " pdb=" CB CYS C 808 " pdb=" SG CYS C 808 " ideal model delta sigma weight residual 114.40 122.22 -7.82 2.30e+00 1.89e-01 1.16e+01 angle pdb=" C GLY A 236 " pdb=" N TYR A 237 " pdb=" CA TYR A 237 " ideal model delta sigma weight residual 121.54 127.98 -6.44 1.91e+00 2.74e-01 1.14e+01 ... (remaining 41469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.02: 17834 21.02 - 42.04: 774 42.04 - 63.06: 120 63.06 - 84.09: 40 84.09 - 105.11: 4 Dihedral angle restraints: 18772 sinusoidal: 7905 harmonic: 10867 Sorted by residual: dihedral pdb=" CB CYS C 283 " pdb=" SG CYS C 283 " pdb=" SG CYS C 307 " pdb=" CB CYS C 307 " ideal model delta sinusoidal sigma weight residual 93.00 167.93 -74.93 1 1.00e+01 1.00e-02 7.10e+01 dihedral pdb=" CB CYS B 283 " pdb=" SG CYS B 283 " pdb=" SG CYS B 307 " pdb=" CB CYS B 307 " ideal model delta sinusoidal sigma weight residual 93.00 167.35 -74.35 1 1.00e+01 1.00e-02 7.01e+01 dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 700 " pdb=" CB CYS A 700 " ideal model delta sinusoidal sigma weight residual -86.00 -12.15 -73.85 1 1.00e+01 1.00e-02 6.93e+01 ... (remaining 18769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 4433 0.086 - 0.171: 449 0.171 - 0.257: 11 0.257 - 0.342: 3 0.342 - 0.428: 1 Chirality restraints: 4897 Sorted by residual: chirality pdb=" C1 NAG A1409 " pdb=" ND2 ASN A1009 " pdb=" C2 NAG A1409 " pdb=" O5 NAG A1409 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" C1 NAG A1404 " pdb=" ND2 ASN A 726 " pdb=" C2 NAG A1404 " pdb=" O5 NAG A1404 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" C2 NAG A1410 " pdb=" C1 NAG A1410 " pdb=" C3 NAG A1410 " pdb=" N2 NAG A1410 " both_signs ideal model delta sigma weight residual False -2.49 -2.19 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 4894 not shown) Planarity restraints: 5290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 411 " -0.020 2.00e-02 2.50e+03 1.71e-02 5.11e+00 pdb=" CG PHE C 411 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE C 411 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 411 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 411 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 411 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 411 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 74 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO E 75 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1009 " -0.019 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN A1009 " 0.021 2.00e-02 2.50e+03 pdb=" OD1 ASN A1009 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A1009 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.019 2.00e-02 2.50e+03 ... (remaining 5287 not shown) Histogram of nonbonded interaction distances: 2.49 - 2.97: 14044 2.97 - 3.45: 27562 3.45 - 3.94: 50842 3.94 - 4.42: 57148 4.42 - 4.90: 94817 Nonbonded interactions: 244413 Sorted by model distance: nonbonded pdb=" O2 MAN H 5 " pdb=" O3 MAN H 5 " model vdw 2.489 2.432 nonbonded pdb=" O5 NAG H 1 " pdb=" O6 NAG H 1 " model vdw 2.496 2.432 nonbonded pdb=" O5 NAG T 2 " pdb=" O6 NAG T 2 " model vdw 2.498 2.432 nonbonded pdb=" O4 NAG P 2 " pdb=" O2 BMA P 3 " model vdw 2.586 2.432 nonbonded pdb=" O ARG A1183 " pdb=" CA GLU A1184 " model vdw 2.593 2.776 ... (remaining 244408 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 57 or resid 64 through 112 or resid 119 through \ 128 or resid 147 through 356 or resid 370 through 426 or resid 435 through 880 \ or resid 894 through 904 or resid 915 through 970 or resid 972 through 989 or re \ sid 996 through 1014 or resid 1026 through 1231 or resid 1408 through 1412 or re \ sid 1414)) selection = (chain 'B' and (resid 26 through 57 or resid 64 through 83 or resid 87 through 1 \ 28 or resid 147 through 200 or resid 202 through 356 or resid 370 through 489 or \ resid 497 through 1231 or resid 1402 through 1406 or resid 1408)) selection = (chain 'C' and (resid 26 through 57 or resid 64 through 83 or resid 87 through 1 \ 28 or resid 147 through 200 or resid 202 through 356 or resid 370 through 489 or \ resid 497 through 1231 or resid 1402 through 1406 or resid 1408)) } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'P' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 9.110 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 33.880 Find NCS groups from input model: 0.880 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: 0.010 Load rotamer database and sin/cos tables:9.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 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 : 0.004 0.084 30650 Z= 0.185 Angle : 0.692 11.456 41767 Z= 0.353 Chirality : 0.049 0.428 4897 Planarity : 0.005 0.056 5251 Dihedral : 11.920 105.108 11676 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.65 (0.13), residues: 3698 helix: 0.56 (0.20), residues: 659 sheet: -0.03 (0.17), residues: 1004 loop : -0.95 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 460 TYR 0.031 0.002 TYR C 237 PHE 0.039 0.002 PHE C 411 TRP 0.012 0.002 TRP F 55 HIS 0.009 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (30535) covalent geometry : angle 0.66926 / 0.35 (41474) SS BOND : bond 0.00342 / 0.23 ( 52) SS BOND : angle 2.26975 / 1.49 ( 104) hydrogen bonds : bond 0.18102 / 12.55 ( 1134) hydrogen bonds : angle 8.68568 / 6.00 ( 3372) link_ALPHA1-3 : bond 0.00731 / 0.36 ( 3) link_ALPHA1-3 : angle 1.11313 / 0.70 ( 9) link_ALPHA1-6 : bond 0.01038 / 0.51 ( 3) link_ALPHA1-6 : angle 2.04548 / 1.46 ( 9) link_BETA1-4 : bond 0.00321 / 0.23 ( 18) link_BETA1-4 : angle 1.91958 / 1.27 ( 54) link_NAG-ASN : bond 0.00436 / 0.25 ( 39) link_NAG-ASN : angle 2.37960 / 1.66 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 VAL cc_start: 0.8481 (p) cc_final: 0.8262 (t) REVERT: A 158 MET cc_start: 0.5788 (mmt) cc_final: 0.5298 (tmm) REVERT: A 209 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6963 (mm-30) REVERT: A 301 GLN cc_start: 0.8112 (mt0) cc_final: 0.7778 (mm-40) REVERT: A 826 TYR cc_start: 0.7569 (m-80) cc_final: 0.7169 (m-80) REVERT: A 860 GLN cc_start: 0.8552 (pt0) cc_final: 0.8279 (mm-40) REVERT: B 35 PHE cc_start: 0.8341 (t80) cc_final: 0.8080 (t80) REVERT: B 82 VAL cc_start: 0.8401 (t) cc_final: 0.8182 (m) REVERT: B 222 GLU cc_start: 0.7091 (pt0) cc_final: 0.6236 (pm20) REVERT: B 371 TYR cc_start: 0.8001 (m-80) cc_final: 0.7564 (m-80) REVERT: F 125 TYR cc_start: 0.7637 (m-80) cc_final: 0.7423 (m-80) REVERT: C 109 LEU cc_start: 0.8266 (tt) cc_final: 0.7939 (tm) REVERT: C 208 TYR cc_start: 0.7409 (m-80) cc_final: 0.7051 (m-80) REVERT: C 270 HIS cc_start: 0.8482 (t-90) cc_final: 0.8239 (m90) REVERT: C 984 TYR cc_start: 0.8374 (t80) cc_final: 0.8133 (t80) REVERT: C 1178 ILE cc_start: 0.8135 (mp) cc_final: 0.7797 (tt) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.5710 time to fit residues: 323.0738 Evaluate side-chains 256 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 270 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN A 816 ASN A 821 GLN A 849 ASN A1051 GLN A1128 GLN A1175 ASN B 233 ASN B 295 GLN B 300 ASN B 301 GLN B 491 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 636 GLN B1059 ASN B1149 GLN G 51 ASN C 40 ASN C 425 ASN C 497 GLN C 556 ASN C 682 GLN C1045 GLN C1051 GLN C1059 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.172965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.123595 restraints weight = 37104.114| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.74 r_work: 0.3375 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 30650 Z= 0.115 Angle : 0.564 14.490 41767 Z= 0.288 Chirality : 0.045 0.654 4897 Planarity : 0.004 0.049 5251 Dihedral : 7.044 87.589 5422 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.43 % Allowed : 6.16 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.38 (0.14), residues: 3698 helix: 1.16 (0.20), residues: 671 sheet: -0.05 (0.16), residues: 1002 loop : -0.82 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 34 TYR 0.024 0.001 TYR A 237 PHE 0.015 0.001 PHE B 297 TRP 0.008 0.001 TRP D 55 HIS 0.005 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (30535) covalent geometry : angle 0.53740 / 0.28 (41474) SS BOND : bond 0.00347 / 0.25 ( 52) SS BOND : angle 1.93986 / 1.43 ( 104) hydrogen bonds : bond 0.04139 / 2.85 ( 1134) hydrogen bonds : angle 6.12608 / 4.19 ( 3372) link_ALPHA1-3 : bond 0.00845 / 0.42 ( 3) link_ALPHA1-3 : angle 1.15930 / 0.76 ( 9) link_ALPHA1-6 : bond 0.01069 / 0.54 ( 3) link_ALPHA1-6 : angle 1.87644 / 1.43 ( 9) link_BETA1-4 : bond 0.00261 / 0.18 ( 18) link_BETA1-4 : angle 1.65619 / 1.09 ( 54) link_NAG-ASN : bond 0.00317 / 0.17 ( 39) link_NAG-ASN : angle 2.52469 / 1.78 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 277 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5839 (mmt) cc_final: 0.5239 (tmm) REVERT: A 209 GLU cc_start: 0.7453 (mm-30) cc_final: 0.6997 (mm-30) REVERT: A 301 GLN cc_start: 0.8057 (mt0) cc_final: 0.7497 (mm-40) REVERT: A 418 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8256 (tt) REVERT: A 860 GLN cc_start: 0.8484 (pt0) cc_final: 0.7919 (mm-40) REVERT: A 989 THR cc_start: 0.7434 (m) cc_final: 0.6683 (p) REVERT: A 1104 LYS cc_start: 0.8730 (mtmm) cc_final: 0.8460 (mmtm) REVERT: A 1208 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8198 (mpp80) REVERT: B 35 PHE cc_start: 0.8283 (t80) cc_final: 0.7914 (t80) REVERT: B 82 VAL cc_start: 0.8242 (t) cc_final: 0.7856 (m) REVERT: B 222 GLU cc_start: 0.7147 (pt0) cc_final: 0.6070 (pm20) REVERT: B 371 TYR cc_start: 0.8019 (m-80) cc_final: 0.7526 (m-80) REVERT: B 587 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8267 (ptmm) REVERT: B 924 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7896 (mmt-90) REVERT: F 125 TYR cc_start: 0.7581 (m-80) cc_final: 0.7341 (m-80) REVERT: C 34 ARG cc_start: 0.7618 (ptp-110) cc_final: 0.7205 (ptp90) REVERT: C 109 LEU cc_start: 0.7785 (tt) cc_final: 0.7237 (tm) REVERT: C 270 HIS cc_start: 0.8355 (t-90) cc_final: 0.8038 (m90) REVERT: C 682 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7738 (pt0) REVERT: C 984 TYR cc_start: 0.8332 (t80) cc_final: 0.7985 (t80) REVERT: E 68 MET cc_start: 0.5325 (mmp) cc_final: 0.5018 (mmm) outliers start: 46 outliers final: 21 residues processed: 307 average time/residue: 0.5328 time to fit residues: 202.2703 Evaluate side-chains 258 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 232 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 650 THR Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 570 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 682 GLN Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 338 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 323 optimal weight: 5.9990 chunk 260 optimal weight: 2.9990 chunk 333 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 chunk 301 optimal weight: 2.9990 chunk 341 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 339 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1120 ASN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B 636 GLN B 838 GLN B1059 ASN B1149 GLN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 621 GLN C 838 GLN C1051 GLN C1059 ASN D 84 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.119909 restraints weight = 36938.918| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.68 r_work: 0.3324 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 30650 Z= 0.199 Angle : 0.629 11.433 41767 Z= 0.321 Chirality : 0.048 0.715 4897 Planarity : 0.005 0.053 5251 Dihedral : 7.512 82.340 5422 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.24 % Allowed : 7.07 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.14), residues: 3698 helix: 1.40 (0.20), residues: 665 sheet: 0.07 (0.16), residues: 995 loop : -0.74 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 460 TYR 0.022 0.002 TYR C 676 PHE 0.026 0.002 PHE C 411 TRP 0.009 0.001 TRP B 259 HIS 0.006 0.001 HIS A1033 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.20 (30535) covalent geometry : angle 0.60048 / 0.31 (41474) SS BOND : bond 0.00533 / 0.38 ( 52) SS BOND : angle 2.14958 / 1.49 ( 104) hydrogen bonds : bond 0.04609 / 3.15 ( 1134) hydrogen bonds : angle 5.85739 / 4.03 ( 3372) link_ALPHA1-3 : bond 0.00591 / 0.29 ( 3) link_ALPHA1-3 : angle 1.24832 / 0.76 ( 9) link_ALPHA1-6 : bond 0.01064 / 0.53 ( 3) link_ALPHA1-6 : angle 2.08964 / 1.62 ( 9) link_BETA1-4 : bond 0.00330 / 0.24 ( 18) link_BETA1-4 : angle 2.01239 / 1.32 ( 54) link_NAG-ASN : bond 0.00449 / 0.26 ( 39) link_NAG-ASN : angle 2.64840 / 1.87 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 257 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5833 (mmt) cc_final: 0.5303 (tmm) REVERT: A 209 GLU cc_start: 0.7440 (mm-30) cc_final: 0.6988 (mm-30) REVERT: A 301 GLN cc_start: 0.8107 (mt0) cc_final: 0.7497 (mm-40) REVERT: A 418 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8416 (tt) REVERT: A 533 ASP cc_start: 0.7462 (p0) cc_final: 0.7254 (p0) REVERT: A 860 GLN cc_start: 0.8459 (pt0) cc_final: 0.7946 (mm-40) REVERT: A 989 THR cc_start: 0.7602 (m) cc_final: 0.6950 (p) REVERT: A 998 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7755 (tp) REVERT: A 1104 LYS cc_start: 0.8779 (mtmm) cc_final: 0.8528 (mmtm) REVERT: A 1208 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7201 (ttp80) REVERT: B 35 PHE cc_start: 0.8305 (t80) cc_final: 0.7943 (t80) REVERT: B 82 VAL cc_start: 0.8240 (t) cc_final: 0.7829 (m) REVERT: B 222 GLU cc_start: 0.7372 (pt0) cc_final: 0.6221 (pm20) REVERT: B 245 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7884 (mm-30) REVERT: B 520 SER cc_start: 0.7057 (m) cc_final: 0.6802 (p) REVERT: B 587 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8096 (tmtm) REVERT: B 924 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7978 (mmt-90) REVERT: C 34 ARG cc_start: 0.7701 (ptp-110) cc_final: 0.7339 (ptp90) REVERT: C 270 HIS cc_start: 0.8462 (t-90) cc_final: 0.8087 (m90) REVERT: C 418 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8856 (mp) REVERT: C 860 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7883 (mp10) REVERT: C 984 TYR cc_start: 0.8391 (t80) cc_final: 0.8080 (t80) REVERT: E 68 MET cc_start: 0.5077 (mmp) cc_final: 0.4806 (mmm) outliers start: 72 outliers final: 36 residues processed: 304 average time/residue: 0.5364 time to fit residues: 200.4487 Evaluate side-chains 274 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 230 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 68 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 264 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 179 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 88 optimal weight: 6.9990 chunk 207 optimal weight: 0.0980 chunk 343 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1039 GLN B1059 ASN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 682 GLN C 825 GLN C1051 GLN C1059 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.167686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118465 restraints weight = 34952.426| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.97 r_work: 0.3225 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30650 Z= 0.127 Angle : 0.554 9.357 41767 Z= 0.282 Chirality : 0.045 0.653 4897 Planarity : 0.004 0.050 5251 Dihedral : 7.122 77.071 5422 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.87 % Allowed : 8.37 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.14), residues: 3698 helix: 1.65 (0.20), residues: 664 sheet: 0.17 (0.17), residues: 971 loop : -0.75 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.016 0.001 TYR B 676 PHE 0.016 0.001 PHE C 411 TRP 0.004 0.001 TRP F 66 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (30535) covalent geometry : angle 0.52810 / 0.27 (41474) SS BOND : bond 0.00363 / 0.26 ( 52) SS BOND : angle 1.99644 / 1.44 ( 104) hydrogen bonds : bond 0.03894 / 2.67 ( 1134) hydrogen bonds : angle 5.49625 / 3.78 ( 3372) link_ALPHA1-3 : bond 0.00786 / 0.39 ( 3) link_ALPHA1-3 : angle 1.12478 / 0.73 ( 9) link_ALPHA1-6 : bond 0.01315 / 0.66 ( 3) link_ALPHA1-6 : angle 2.08002 / 1.62 ( 9) link_BETA1-4 : bond 0.00279 / 0.19 ( 18) link_BETA1-4 : angle 1.75286 / 1.15 ( 54) link_NAG-ASN : bond 0.00308 / 0.20 ( 39) link_NAG-ASN : angle 2.34070 / 1.58 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 249 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5897 (mmt) cc_final: 0.5380 (tmm) REVERT: A 209 GLU cc_start: 0.7428 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 301 GLN cc_start: 0.8126 (mt0) cc_final: 0.7442 (mm-40) REVERT: A 317 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8112 (pt0) REVERT: A 418 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8325 (tt) REVERT: A 860 GLN cc_start: 0.8493 (pt0) cc_final: 0.7905 (mm-40) REVERT: A 989 THR cc_start: 0.7561 (m) cc_final: 0.6925 (p) REVERT: A 998 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7781 (tp) REVERT: A 1001 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7493 (tp30) REVERT: A 1104 LYS cc_start: 0.8809 (mtmm) cc_final: 0.8536 (mmtm) REVERT: A 1208 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8113 (mpp80) REVERT: B 34 ARG cc_start: 0.7701 (ttm-80) cc_final: 0.7368 (ptm160) REVERT: B 35 PHE cc_start: 0.8280 (t80) cc_final: 0.7974 (t80) REVERT: B 82 VAL cc_start: 0.8206 (t) cc_final: 0.7801 (m) REVERT: B 222 GLU cc_start: 0.7389 (pt0) cc_final: 0.6241 (pm20) REVERT: B 245 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7855 (mm-30) REVERT: F 125 TYR cc_start: 0.7628 (m-80) cc_final: 0.7191 (m-80) REVERT: C 34 ARG cc_start: 0.7676 (ptp-110) cc_final: 0.7353 (ptp90) REVERT: C 109 LEU cc_start: 0.7757 (tt) cc_final: 0.7267 (tm) REVERT: C 270 HIS cc_start: 0.8387 (t-90) cc_final: 0.8013 (m90) REVERT: C 418 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8890 (mp) REVERT: C 860 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: C 984 TYR cc_start: 0.8433 (t80) cc_final: 0.8052 (t80) outliers start: 60 outliers final: 35 residues processed: 287 average time/residue: 0.5363 time to fit residues: 190.0886 Evaluate side-chains 270 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 229 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 217 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 362 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 275 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 232 optimal weight: 30.0000 chunk 59 optimal weight: 2.9990 chunk 340 optimal weight: 0.2980 chunk 289 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 89 HIS ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN A1116 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1045 GLN B1059 ASN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 568 GLN C 682 GLN C 771 GLN C 988 GLN C1059 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.165026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115128 restraints weight = 35027.763| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.95 r_work: 0.3181 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 30650 Z= 0.205 Angle : 0.630 9.359 41767 Z= 0.321 Chirality : 0.048 0.612 4897 Planarity : 0.004 0.052 5251 Dihedral : 7.624 77.156 5422 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.37 % Allowed : 8.81 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.14), residues: 3698 helix: 1.46 (0.20), residues: 670 sheet: 0.18 (0.16), residues: 988 loop : -0.73 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 460 TYR 0.022 0.002 TYR A 676 PHE 0.024 0.002 PHE C 411 TRP 0.009 0.001 TRP B 259 HIS 0.005 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (30535) covalent geometry : angle 0.60302 / 0.31 (41474) SS BOND : bond 0.00452 / 0.33 ( 52) SS BOND : angle 2.16355 / 1.53 ( 104) hydrogen bonds : bond 0.04483 / 3.06 ( 1134) hydrogen bonds : angle 5.59785 / 3.86 ( 3372) link_ALPHA1-3 : bond 0.00470 / 0.23 ( 3) link_ALPHA1-3 : angle 1.28465 / 0.79 ( 9) link_ALPHA1-6 : bond 0.00953 / 0.47 ( 3) link_ALPHA1-6 : angle 2.17978 / 1.71 ( 9) link_BETA1-4 : bond 0.00319 / 0.23 ( 18) link_BETA1-4 : angle 2.06572 / 1.35 ( 54) link_NAG-ASN : bond 0.00452 / 0.28 ( 39) link_NAG-ASN : angle 2.52197 / 1.75 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 239 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.5958 (mmt) cc_final: 0.5536 (tmm) REVERT: A 209 GLU cc_start: 0.7448 (mm-30) cc_final: 0.6991 (mm-30) REVERT: A 301 GLN cc_start: 0.8210 (mt0) cc_final: 0.7504 (mm-40) REVERT: A 418 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8399 (tt) REVERT: A 636 GLN cc_start: 0.8501 (mm110) cc_final: 0.8280 (mm110) REVERT: A 860 GLN cc_start: 0.8433 (pt0) cc_final: 0.7922 (mm-40) REVERT: A 1001 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7430 (tp30) REVERT: A 1104 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8556 (mmtm) REVERT: A 1208 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7262 (ttp80) REVERT: B 35 PHE cc_start: 0.8247 (t80) cc_final: 0.7877 (t80) REVERT: B 82 VAL cc_start: 0.8252 (t) cc_final: 0.7726 (m) REVERT: B 204 MET cc_start: 0.5910 (mtt) cc_final: 0.4683 (tmt) REVERT: B 222 GLU cc_start: 0.7410 (pt0) cc_final: 0.6405 (pm20) REVERT: B 245 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8320 (mt-10) REVERT: B 1208 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8182 (mtp85) REVERT: F 125 TYR cc_start: 0.7610 (m-80) cc_final: 0.7368 (m-80) REVERT: C 34 ARG cc_start: 0.7710 (ptp-110) cc_final: 0.7375 (ptp90) REVERT: C 109 LEU cc_start: 0.7748 (tt) cc_final: 0.7206 (tm) REVERT: C 270 HIS cc_start: 0.8513 (t-90) cc_final: 0.8121 (m90) REVERT: C 418 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8931 (mp) REVERT: C 825 GLN cc_start: 0.7805 (mm-40) cc_final: 0.7598 (mm110) REVERT: C 856 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8135 (tp30) REVERT: C 864 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8082 (mm) REVERT: C 984 TYR cc_start: 0.8458 (t80) cc_final: 0.8091 (t80) REVERT: E 68 MET cc_start: 0.4525 (mmm) cc_final: 0.4112 (mmp) outliers start: 76 outliers final: 43 residues processed: 288 average time/residue: 0.5790 time to fit residues: 203.3853 Evaluate side-chains 279 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 599 CYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 164 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 267 THR Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1208 ARG Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 769 SER Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 288 optimal weight: 0.0770 chunk 300 optimal weight: 0.0980 chunk 88 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 371 optimal weight: 20.0000 chunk 213 optimal weight: 3.9990 chunk 301 optimal weight: 0.9990 chunk 355 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1059 ASN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 682 GLN C 771 GLN C1059 ASN C1128 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.167022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.117804 restraints weight = 35002.910| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.95 r_work: 0.3214 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30650 Z= 0.126 Angle : 0.555 9.138 41767 Z= 0.284 Chirality : 0.045 0.496 4897 Planarity : 0.004 0.052 5251 Dihedral : 7.128 71.052 5422 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.09 % Allowed : 9.46 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.14), residues: 3698 helix: 1.73 (0.20), residues: 666 sheet: 0.26 (0.17), residues: 960 loop : -0.73 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.016 0.001 TYR B 676 PHE 0.016 0.001 PHE C 411 TRP 0.006 0.001 TRP B 168 HIS 0.002 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (30535) covalent geometry : angle 0.52724 / 0.28 (41474) SS BOND : bond 0.00337 / 0.24 ( 52) SS BOND : angle 2.17620 / 1.57 ( 104) hydrogen bonds : bond 0.03810 / 2.60 ( 1134) hydrogen bonds : angle 5.31085 / 3.66 ( 3372) link_ALPHA1-3 : bond 0.00776 / 0.39 ( 3) link_ALPHA1-3 : angle 1.13451 / 0.73 ( 9) link_ALPHA1-6 : bond 0.01175 / 0.59 ( 3) link_ALPHA1-6 : angle 2.02757 / 1.55 ( 9) link_BETA1-4 : bond 0.00252 / 0.18 ( 18) link_BETA1-4 : angle 1.77090 / 1.16 ( 54) link_NAG-ASN : bond 0.00341 / 0.19 ( 39) link_NAG-ASN : angle 2.28723 / 1.56 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 246 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6038 (mmt) cc_final: 0.5597 (tmm) REVERT: A 171 ASP cc_start: 0.7483 (m-30) cc_final: 0.7024 (t70) REVERT: A 209 GLU cc_start: 0.7425 (mm-30) cc_final: 0.6975 (mm-30) REVERT: A 301 GLN cc_start: 0.8177 (mt0) cc_final: 0.7468 (mm-40) REVERT: A 418 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8342 (tt) REVERT: A 636 GLN cc_start: 0.8475 (mm110) cc_final: 0.8262 (mm110) REVERT: A 758 LYS cc_start: 0.8303 (tptt) cc_final: 0.8038 (tptm) REVERT: A 860 GLN cc_start: 0.8410 (pt0) cc_final: 0.7911 (mm-40) REVERT: A 989 THR cc_start: 0.7681 (m) cc_final: 0.7059 (p) REVERT: A 1104 LYS cc_start: 0.8791 (mtmm) cc_final: 0.8542 (mmtm) REVERT: A 1208 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8218 (mpp80) REVERT: B 34 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7308 (ptm160) REVERT: B 35 PHE cc_start: 0.8180 (t80) cc_final: 0.7848 (t80) REVERT: B 82 VAL cc_start: 0.8236 (t) cc_final: 0.7702 (m) REVERT: B 204 MET cc_start: 0.6065 (mtt) cc_final: 0.4624 (tmt) REVERT: B 222 GLU cc_start: 0.7386 (pt0) cc_final: 0.6417 (pm20) REVERT: B 245 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.7881 (mm-30) REVERT: F 125 TYR cc_start: 0.7531 (m-80) cc_final: 0.7209 (m-80) REVERT: C 34 ARG cc_start: 0.7711 (ptp-110) cc_final: 0.7224 (ptp90) REVERT: C 109 LEU cc_start: 0.7711 (tt) cc_final: 0.7158 (tm) REVERT: C 158 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6663 (mtp) REVERT: C 270 HIS cc_start: 0.8426 (t-90) cc_final: 0.8035 (m90) REVERT: C 856 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: C 860 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.8025 (mp10) REVERT: C 984 TYR cc_start: 0.8437 (t80) cc_final: 0.8100 (t80) REVERT: E 68 MET cc_start: 0.4431 (mmm) cc_final: 0.3933 (mmp) outliers start: 67 outliers final: 38 residues processed: 289 average time/residue: 0.5489 time to fit residues: 194.5798 Evaluate side-chains 272 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 228 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain C residue 158 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 808 CYS Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 117 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 103 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 228 optimal weight: 0.6980 chunk 369 optimal weight: 5.9990 chunk 263 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 235 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1059 ASN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 556 ASN C 682 GLN C 771 GLN C 825 GLN C1059 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.165949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.116567 restraints weight = 35008.937| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.97 r_work: 0.3199 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 30650 Z= 0.162 Angle : 0.588 9.090 41767 Z= 0.300 Chirality : 0.046 0.638 4897 Planarity : 0.004 0.052 5251 Dihedral : 7.271 70.723 5422 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 1.99 % Allowed : 9.93 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.14), residues: 3698 helix: 1.67 (0.20), residues: 668 sheet: 0.25 (0.17), residues: 966 loop : -0.73 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 460 TYR 0.020 0.001 TYR A 676 PHE 0.020 0.001 PHE C 411 TRP 0.010 0.001 TRP B 168 HIS 0.004 0.001 HIS B 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (30535) covalent geometry : angle 0.56127 / 0.29 (41474) SS BOND : bond 0.00314 / 0.23 ( 52) SS BOND : angle 2.16517 / 1.67 ( 104) hydrogen bonds : bond 0.04094 / 2.80 ( 1134) hydrogen bonds : angle 5.33571 / 3.68 ( 3372) link_ALPHA1-3 : bond 0.00638 / 0.32 ( 3) link_ALPHA1-3 : angle 1.19710 / 0.76 ( 9) link_ALPHA1-6 : bond 0.01155 / 0.58 ( 3) link_ALPHA1-6 : angle 2.10888 / 1.63 ( 9) link_BETA1-4 : bond 0.00286 / 0.21 ( 18) link_BETA1-4 : angle 1.90593 / 1.25 ( 54) link_NAG-ASN : bond 0.00335 / 0.21 ( 39) link_NAG-ASN : angle 2.37786 / 1.63 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6015 (mmt) cc_final: 0.5642 (tmm) REVERT: A 171 ASP cc_start: 0.7434 (m-30) cc_final: 0.6949 (t0) REVERT: A 209 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7000 (mm-30) REVERT: A 301 GLN cc_start: 0.8233 (mt0) cc_final: 0.7582 (mm-40) REVERT: A 317 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8211 (pt0) REVERT: A 418 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 636 GLN cc_start: 0.8484 (mm110) cc_final: 0.8265 (mm110) REVERT: A 860 GLN cc_start: 0.8395 (pt0) cc_final: 0.7898 (mm-40) REVERT: A 989 THR cc_start: 0.7777 (m) cc_final: 0.7178 (p) REVERT: A 1104 LYS cc_start: 0.8796 (mtmm) cc_final: 0.8559 (mmtm) REVERT: A 1208 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7094 (ttp80) REVERT: B 35 PHE cc_start: 0.8214 (t80) cc_final: 0.7869 (t80) REVERT: B 82 VAL cc_start: 0.8254 (t) cc_final: 0.7842 (m) REVERT: B 222 GLU cc_start: 0.7402 (pt0) cc_final: 0.6488 (pm20) REVERT: B 245 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: B 371 TYR cc_start: 0.8251 (m-80) cc_final: 0.8016 (m-80) REVERT: F 125 TYR cc_start: 0.7555 (m-80) cc_final: 0.7331 (m-80) REVERT: C 34 ARG cc_start: 0.7718 (ptp-110) cc_final: 0.7212 (ptp90) REVERT: C 91 PHE cc_start: 0.7852 (p90) cc_final: 0.7642 (p90) REVERT: C 109 LEU cc_start: 0.7729 (tt) cc_final: 0.7172 (tm) REVERT: C 270 HIS cc_start: 0.8449 (t-90) cc_final: 0.8067 (m90) REVERT: C 418 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8812 (mp) REVERT: C 633 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.7878 (pptt) REVERT: C 856 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8159 (tp30) REVERT: C 984 TYR cc_start: 0.8463 (t80) cc_final: 0.8142 (t80) REVERT: E 68 MET cc_start: 0.4304 (mmm) cc_final: 0.3753 (mmp) outliers start: 64 outliers final: 43 residues processed: 280 average time/residue: 0.5652 time to fit residues: 193.7683 Evaluate side-chains 277 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1208 ARG Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 245 GLU Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1053 THR Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain G residue 113 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 689 VAL Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 128 optimal weight: 0.7980 chunk 182 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 319 optimal weight: 0.5980 chunk 276 optimal weight: 2.9990 chunk 162 optimal weight: 0.0870 chunk 240 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 GLN A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1059 ASN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 556 ASN C 682 GLN C 771 GLN C 825 GLN C1059 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.167536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118582 restraints weight = 35161.960| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.96 r_work: 0.3230 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30650 Z= 0.115 Angle : 0.545 9.173 41767 Z= 0.278 Chirality : 0.044 0.564 4897 Planarity : 0.004 0.052 5251 Dihedral : 6.846 64.177 5422 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.81 % Allowed : 10.33 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.02 (0.14), residues: 3698 helix: 1.84 (0.20), residues: 668 sheet: 0.25 (0.16), residues: 971 loop : -0.72 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 490 TYR 0.020 0.001 TYR G 69 PHE 0.014 0.001 PHE C 411 TRP 0.013 0.001 TRP B 168 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (30535) covalent geometry : angle 0.51987 / 0.27 (41474) SS BOND : bond 0.00292 / 0.22 ( 52) SS BOND : angle 1.99279 / 1.50 ( 104) hydrogen bonds : bond 0.03636 / 2.49 ( 1134) hydrogen bonds : angle 5.13073 / 3.53 ( 3372) link_ALPHA1-3 : bond 0.00881 / 0.44 ( 3) link_ALPHA1-3 : angle 1.11964 / 0.72 ( 9) link_ALPHA1-6 : bond 0.01212 / 0.61 ( 3) link_ALPHA1-6 : angle 1.97978 / 1.50 ( 9) link_BETA1-4 : bond 0.00237 / 0.17 ( 18) link_BETA1-4 : angle 1.70649 / 1.12 ( 54) link_NAG-ASN : bond 0.00342 / 0.18 ( 39) link_NAG-ASN : angle 2.24330 / 1.51 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 234 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6030 (mmt) cc_final: 0.5512 (tmm) REVERT: A 171 ASP cc_start: 0.7334 (m-30) cc_final: 0.6828 (t0) REVERT: A 209 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6925 (mm-30) REVERT: A 214 MET cc_start: 0.6548 (mtt) cc_final: 0.6332 (mmt) REVERT: A 301 GLN cc_start: 0.8225 (mt0) cc_final: 0.7486 (mm-40) REVERT: A 418 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8313 (tt) REVERT: A 636 GLN cc_start: 0.8460 (mm110) cc_final: 0.8248 (mm110) REVERT: A 860 GLN cc_start: 0.8398 (pt0) cc_final: 0.7904 (mm-40) REVERT: A 989 THR cc_start: 0.7710 (m) cc_final: 0.7122 (p) REVERT: A 1104 LYS cc_start: 0.8783 (mtmm) cc_final: 0.8540 (mmtm) REVERT: B 34 ARG cc_start: 0.7713 (ttm-80) cc_final: 0.7414 (ptm160) REVERT: B 35 PHE cc_start: 0.8170 (t80) cc_final: 0.7896 (t80) REVERT: B 82 VAL cc_start: 0.8252 (t) cc_final: 0.7851 (m) REVERT: B 222 GLU cc_start: 0.7427 (pt0) cc_final: 0.6455 (pm20) REVERT: B 490 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6603 (mmp-170) REVERT: F 125 TYR cc_start: 0.7605 (m-80) cc_final: 0.7260 (m-80) REVERT: G 68 MET cc_start: 0.2503 (mmm) cc_final: 0.2117 (tpp) REVERT: C 34 ARG cc_start: 0.7724 (ptp-110) cc_final: 0.7237 (ptp90) REVERT: C 91 PHE cc_start: 0.7850 (p90) cc_final: 0.7629 (p90) REVERT: C 109 LEU cc_start: 0.7773 (tt) cc_final: 0.7251 (tm) REVERT: C 270 HIS cc_start: 0.8375 (t-90) cc_final: 0.7982 (m90) REVERT: C 633 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7790 (pptt) REVERT: C 856 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: C 984 TYR cc_start: 0.8371 (t80) cc_final: 0.8038 (t80) REVERT: E 68 MET cc_start: 0.4105 (mmm) cc_final: 0.3493 (mmp) outliers start: 58 outliers final: 42 residues processed: 273 average time/residue: 0.5792 time to fit residues: 193.6559 Evaluate side-chains 270 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 300 ASN Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 543 CYS Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 633 LYS Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 365 optimal weight: 6.9990 chunk 356 optimal weight: 0.0770 chunk 287 optimal weight: 0.2980 chunk 321 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 357 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 302 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 298 optimal weight: 1.9990 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1059 ASN G 51 ASN C 40 ASN C 78 HIS C 425 ASN C 682 GLN C 825 GLN C1059 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.167463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.117512 restraints weight = 35055.038| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.97 r_work: 0.3219 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30650 Z= 0.120 Angle : 0.544 9.170 41767 Z= 0.278 Chirality : 0.044 0.485 4897 Planarity : 0.004 0.051 5251 Dihedral : 6.760 60.904 5422 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.81 % Allowed : 10.43 % Favored : 87.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.04 (0.14), residues: 3698 helix: 1.88 (0.20), residues: 668 sheet: 0.23 (0.17), residues: 964 loop : -0.69 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 490 TYR 0.018 0.001 TYR A 984 PHE 0.017 0.001 PHE A 183 TRP 0.018 0.001 TRP B 168 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (30535) covalent geometry : angle 0.52071 / 0.27 (41474) SS BOND : bond 0.00290 / 0.22 ( 52) SS BOND : angle 1.86604 / 1.37 ( 104) hydrogen bonds : bond 0.03653 / 2.51 ( 1134) hydrogen bonds : angle 5.08705 / 3.50 ( 3372) link_ALPHA1-3 : bond 0.00850 / 0.42 ( 3) link_ALPHA1-3 : angle 1.14576 / 0.74 ( 9) link_ALPHA1-6 : bond 0.01233 / 0.62 ( 3) link_ALPHA1-6 : angle 1.98908 / 1.50 ( 9) link_BETA1-4 : bond 0.00256 / 0.18 ( 18) link_BETA1-4 : angle 1.72224 / 1.13 ( 54) link_NAG-ASN : bond 0.00304 / 0.17 ( 39) link_NAG-ASN : angle 2.17018 / 1.48 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6003 (mmt) cc_final: 0.5680 (tmm) REVERT: A 171 ASP cc_start: 0.7299 (m-30) cc_final: 0.6753 (t0) REVERT: A 209 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7146 (mp0) REVERT: A 301 GLN cc_start: 0.8228 (mt0) cc_final: 0.7500 (mm-40) REVERT: A 553 LEU cc_start: 0.9026 (mt) cc_final: 0.8299 (tt) REVERT: A 758 LYS cc_start: 0.8120 (tptt) cc_final: 0.7835 (tptp) REVERT: A 860 GLN cc_start: 0.8416 (pt0) cc_final: 0.7932 (mm-40) REVERT: A 989 THR cc_start: 0.7714 (m) cc_final: 0.7111 (p) REVERT: A 1104 LYS cc_start: 0.8799 (mtmm) cc_final: 0.8548 (mmtm) REVERT: B 34 ARG cc_start: 0.7675 (ttm-80) cc_final: 0.7370 (ptm160) REVERT: B 35 PHE cc_start: 0.8175 (t80) cc_final: 0.7896 (t80) REVERT: B 82 VAL cc_start: 0.8202 (t) cc_final: 0.7834 (m) REVERT: B 222 GLU cc_start: 0.7428 (pt0) cc_final: 0.6460 (pm20) REVERT: B 371 TYR cc_start: 0.8221 (m-80) cc_final: 0.8006 (m-80) REVERT: B 490 ARG cc_start: 0.7100 (OUTLIER) cc_final: 0.6725 (mmp-170) REVERT: F 125 TYR cc_start: 0.7549 (m-80) cc_final: 0.7230 (m-80) REVERT: G 68 MET cc_start: 0.2445 (mmm) cc_final: 0.2103 (tpp) REVERT: C 34 ARG cc_start: 0.7716 (ptp-110) cc_final: 0.7220 (ptp90) REVERT: C 91 PHE cc_start: 0.7833 (p90) cc_final: 0.7614 (p90) REVERT: C 109 LEU cc_start: 0.7706 (tt) cc_final: 0.7177 (tm) REVERT: C 270 HIS cc_start: 0.8400 (t-90) cc_final: 0.8008 (m90) REVERT: C 418 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8773 (mp) REVERT: C 856 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: C 860 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: C 984 TYR cc_start: 0.8357 (t80) cc_final: 0.8042 (t80) REVERT: E 68 MET cc_start: 0.3976 (mmm) cc_final: 0.3619 (mmp) outliers start: 58 outliers final: 39 residues processed: 267 average time/residue: 0.5482 time to fit residues: 180.2642 Evaluate side-chains 265 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 222 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 825 GLN Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 373 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 280 optimal weight: 0.9990 chunk 297 optimal weight: 0.0970 chunk 219 optimal weight: 0.5980 chunk 354 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1059 ASN G 51 ASN C 40 ASN C 425 ASN C 682 GLN C 825 GLN C1059 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.118348 restraints weight = 35005.040| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.94 r_work: 0.3231 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30650 Z= 0.118 Angle : 0.541 9.084 41767 Z= 0.276 Chirality : 0.044 0.470 4897 Planarity : 0.004 0.051 5251 Dihedral : 6.626 57.716 5422 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.65 % Allowed : 10.83 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.14), residues: 3698 helix: 1.91 (0.20), residues: 668 sheet: 0.25 (0.17), residues: 974 loop : -0.68 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1085 TYR 0.018 0.001 TYR A 984 PHE 0.014 0.001 PHE C 411 TRP 0.022 0.001 TRP B 168 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (30535) covalent geometry : angle 0.51828 / 0.27 (41474) SS BOND : bond 0.00295 / 0.22 ( 52) SS BOND : angle 1.84937 / 1.36 ( 104) hydrogen bonds : bond 0.03624 / 2.49 ( 1134) hydrogen bonds : angle 5.03393 / 3.46 ( 3372) link_ALPHA1-3 : bond 0.00876 / 0.44 ( 3) link_ALPHA1-3 : angle 1.13094 / 0.74 ( 9) link_ALPHA1-6 : bond 0.01271 / 0.64 ( 3) link_ALPHA1-6 : angle 1.96068 / 1.46 ( 9) link_BETA1-4 : bond 0.00255 / 0.18 ( 18) link_BETA1-4 : angle 1.70012 / 1.12 ( 54) link_NAG-ASN : bond 0.00302 / 0.17 ( 39) link_NAG-ASN : angle 2.13382 / 1.46 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7396 Ramachandran restraints generated. 3698 Oldfield, 0 Emsley, 3698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 228 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 MET cc_start: 0.6076 (mmt) cc_final: 0.5665 (tmm) REVERT: A 171 ASP cc_start: 0.7230 (m-30) cc_final: 0.6668 (t0) REVERT: A 214 MET cc_start: 0.6559 (mtt) cc_final: 0.6344 (mmt) REVERT: A 301 GLN cc_start: 0.8200 (mt0) cc_final: 0.7479 (mm-40) REVERT: A 553 LEU cc_start: 0.9003 (mt) cc_final: 0.8255 (tt) REVERT: A 758 LYS cc_start: 0.8098 (tptt) cc_final: 0.7877 (tptm) REVERT: A 860 GLN cc_start: 0.8388 (pt0) cc_final: 0.7913 (mm-40) REVERT: A 989 THR cc_start: 0.7715 (m) cc_final: 0.7117 (p) REVERT: A 1104 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8544 (mmtm) REVERT: B 34 ARG cc_start: 0.7626 (ttm-80) cc_final: 0.7332 (ptm160) REVERT: B 35 PHE cc_start: 0.8153 (t80) cc_final: 0.7857 (t80) REVERT: B 82 VAL cc_start: 0.8195 (t) cc_final: 0.7831 (m) REVERT: B 222 GLU cc_start: 0.7466 (pt0) cc_final: 0.6524 (pm20) REVERT: B 490 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6727 (mmp-170) REVERT: G 68 MET cc_start: 0.2542 (mmm) cc_final: 0.2034 (tpp) REVERT: C 34 ARG cc_start: 0.7702 (ptp-110) cc_final: 0.7207 (ptp90) REVERT: C 91 PHE cc_start: 0.7856 (p90) cc_final: 0.7602 (p90) REVERT: C 109 LEU cc_start: 0.7702 (tt) cc_final: 0.7160 (tm) REVERT: C 270 HIS cc_start: 0.8382 (t-90) cc_final: 0.7986 (m90) REVERT: C 418 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 856 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8078 (tp30) REVERT: C 860 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.8052 (mp10) REVERT: C 984 TYR cc_start: 0.8330 (t80) cc_final: 0.8033 (t80) REVERT: E 68 MET cc_start: 0.4039 (mmm) cc_final: 0.3543 (mmp) outliers start: 53 outliers final: 40 residues processed: 266 average time/residue: 0.5451 time to fit residues: 178.2736 Evaluate side-chains 262 residues out of total 3213 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 624 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 865 SER Chi-restraints excluded: chain A residue 1075 ASP Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 218 THR Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 599 CYS Chi-restraints excluded: chain B residue 638 VAL Chi-restraints excluded: chain B residue 671 LEU Chi-restraints excluded: chain B residue 808 CYS Chi-restraints excluded: chain B residue 825 GLN Chi-restraints excluded: chain B residue 924 ARG Chi-restraints excluded: chain B residue 1044 SER Chi-restraints excluded: chain B residue 1187 LEU Chi-restraints excluded: chain B residue 1221 VAL Chi-restraints excluded: chain G residue 108 CYS Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 219 SER Chi-restraints excluded: chain C residue 326 THR Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 418 LEU Chi-restraints excluded: chain C residue 579 VAL Chi-restraints excluded: chain C residue 617 SER Chi-restraints excluded: chain C residue 639 THR Chi-restraints excluded: chain C residue 660 GLU Chi-restraints excluded: chain C residue 677 THR Chi-restraints excluded: chain C residue 856 GLU Chi-restraints excluded: chain C residue 860 GLN Chi-restraints excluded: chain C residue 1076 ILE Chi-restraints excluded: chain C residue 1173 CYS Chi-restraints excluded: chain C residue 1184 GLU Chi-restraints excluded: chain C residue 1231 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain E residue 48 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 28 optimal weight: 0.9990 chunk 325 optimal weight: 2.9990 chunk 295 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 191 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 99 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 356 optimal weight: 1.9990 chunk 154 optimal weight: 0.5980 chunk 213 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1051 GLN ** B 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 300 ASN ** B 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 571 ASN B1059 ASN G 51 ASN C 40 ASN C 425 ASN C 682 GLN C 825 GLN C1059 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118044 restraints weight = 35242.292| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.90 r_work: 0.3230 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30650 Z= 0.119 Angle : 0.548 9.427 41767 Z= 0.278 Chirality : 0.046 0.852 4897 Planarity : 0.004 0.051 5251 Dihedral : 6.587 59.553 5422 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.74 % Allowed : 10.74 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.07 (0.14), residues: 3698 helix: 1.89 (0.20), residues: 668 sheet: 0.27 (0.17), residues: 966 loop : -0.67 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1085 TYR 0.017 0.001 TYR A 984 PHE 0.018 0.001 PHE A 183 TRP 0.021 0.001 TRP B 168 HIS 0.003 0.001 HIS C 161 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (30535) covalent geometry : angle 0.52209 / 0.27 (41474) SS BOND : bond 0.00295 / 0.22 ( 52) SS BOND : angle 1.75777 / 1.31 ( 104) hydrogen bonds : bond 0.03647 / 2.51 ( 1134) hydrogen bonds : angle 5.02510 / 3.46 ( 3372) link_ALPHA1-3 : bond 0.00873 / 0.44 ( 3) link_ALPHA1-3 : angle 1.13158 / 0.74 ( 9) link_ALPHA1-6 : bond 0.01256 / 0.63 ( 3) link_ALPHA1-6 : angle 1.90469 / 1.41 ( 9) link_BETA1-4 : bond 0.00256 / 0.18 ( 18) link_BETA1-4 : angle 1.69743 / 1.12 ( 54) link_NAG-ASN : bond 0.00506 / 0.35 ( 39) link_NAG-ASN : angle 2.49558 / 1.65 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14653.51 seconds wall clock time: 249 minutes 29.93 seconds (14969.93 seconds total)