Starting phenix.real_space_refine on Mon Sep 14 07:02:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5w9i_8784/09_2026/5w9i_8784.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 147 5.16 5 C 18252 2.51 5 N 4752 2.21 5 O 5745 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s 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: 28896 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "D" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "F" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "G" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "H" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "J" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "K" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "L" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 6.49, per 1000 atoms: 0.22 Number of scatterers: 28896 At special positions: 0 Unit cell: (155.04, 155.04, 183.6, 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 147 16.00 O 5745 8.00 N 4752 7.00 C 18252 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=43, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.04 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.04 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.99 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.07 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.09 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.14 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.09 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.28 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.01 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.02 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=1.89 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=2.02 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.09 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.03 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.09 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.12 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.08 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=1.92 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=1.88 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.03 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.01 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.04 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=2.01 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.04 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.09 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.13 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.06 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.20 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.14 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.01 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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=3, symmetry=0 Links applied BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG B1401 " - " ASN B 236 " " NAG B1402 " - " ASN B 155 " " NAG B1403 " - " ASN B 166 " " NAG B1404 " - " ASN B 719 " " NAG B1405 " - " ASN B 619 " " NAG B1406 " - " ASN B 104 " " NAG E1401 " - " ASN E 774 " " NAG F1401 " - " ASN F 236 " " NAG F1402 " - " ASN F 719 " " NAG F1403 " - " ASN F 166 " " NAG F1404 " - " ASN F 155 " " NAG F1405 " - " ASN F 619 " " NAG F1406 " - " ASN F 104 " " NAG I1401 " - " ASN I 774 " " NAG J1401 " - " ASN J 104 " " NAG J1402 " - " ASN J 155 " " NAG J1403 " - " ASN J 719 " " NAG J1410 " - " ASN J 236 " " NAG J1411 " - " ASN J 619 " " NAG J1412 " - " ASN J 166 " " NAG M 1 " - " ASN A 785 " " NAG N 1 " - " ASN A 870 " " NAG O 1 " - " ASN A1213 " " NAG P 1 " - " ASN A1176 " " NAG Q 1 " - " ASN B 66 " " NAG R 1 " - " ASN B 244 " " NAG S 1 " - " ASN B 125 " " NAG T 1 " - " ASN E 785 " " NAG U 1 " - " ASN E1176 " " NAG V 1 " - " ASN E 870 " " NAG W 1 " - " ASN E1213 " " NAG X 1 " - " ASN F 66 " " NAG Y 1 " - " ASN F 244 " " NAG Z 1 " - " ASN F 125 " " NAG a 1 " - " ASN I1213 " " NAG b 1 " - " ASN I 870 " " NAG c 1 " - " ASN I 785 " " NAG d 1 " - " ASN I1176 " " NAG e 1 " - " ASN J 244 " " NAG f 1 " - " ASN J 66 " " NAG g 1 " - " ASN J 125 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.2 seconds 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 69 sheets defined 23.6% alpha, 25.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.516A pdb=" N VAL A 810 " --> pdb=" O CYS A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.908A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 removed outlier: 4.070A pdb=" N ASP A 910 " --> pdb=" O GLN A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.502A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 955 removed outlier: 3.663A pdb=" N ILE A 955 " --> pdb=" O LEU A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.867A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1057 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.236A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.923A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 675 through 678 removed outlier: 4.387A pdb=" N ALA B 678 " --> pdb=" O GLY B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 675 through 678' Processing helix chain 'B' and resid 694 through 702 removed outlier: 3.560A pdb=" N LYS B 698 " --> pdb=" O ARG B 694 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.617A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 805 through 810 removed outlier: 3.814A pdb=" N VAL E 810 " --> pdb=" O CYS E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 824 through 854 removed outlier: 3.898A pdb=" N CYS E 828 " --> pdb=" O TYR E 824 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 852 " --> pdb=" O ASN E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 898 Processing helix chain 'E' and resid 908 through 912 Processing helix chain 'E' and resid 922 through 931 removed outlier: 4.722A pdb=" N TYR E 928 " --> pdb=" O ILE E 924 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL E 929 " --> pdb=" O CYS E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 940 through 953 Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 986 through 993 Processing helix chain 'E' and resid 993 through 1007 Processing helix chain 'E' and resid 1008 through 1010 No H-bonds generated for 'chain 'E' and resid 1008 through 1010' Processing helix chain 'E' and resid 1016 through 1040 removed outlier: 3.869A pdb=" N LEU E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU E1040 " --> pdb=" O LEU E1036 " (cutoff:3.500A) Processing helix chain 'E' and resid 1050 through 1057 Processing helix chain 'E' and resid 1059 through 1104 removed outlier: 4.267A pdb=" N ALA E1065 " --> pdb=" O PRO E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1200 No H-bonds generated for 'chain 'E' and resid 1198 through 1200' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.909A pdb=" N ARG F 307 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 675 through 678 removed outlier: 4.527A pdb=" N ALA F 678 " --> pdb=" O GLY F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 675 through 678' Processing helix chain 'F' and resid 694 through 702 removed outlier: 3.563A pdb=" N LYS F 698 " --> pdb=" O ARG F 694 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.615A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 Processing helix chain 'I' and resid 805 through 811 removed outlier: 3.524A pdb=" N VAL I 810 " --> pdb=" O CYS I 806 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 822 Processing helix chain 'I' and resid 824 through 854 removed outlier: 3.913A pdb=" N CYS I 828 " --> pdb=" O TYR I 824 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER I 852 " --> pdb=" O ASN I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 907 through 912 removed outlier: 4.015A pdb=" N ASP I 910 " --> pdb=" O GLN I 907 " (cutoff:3.500A) Processing helix chain 'I' and resid 922 through 931 removed outlier: 4.483A pdb=" N TYR I 928 " --> pdb=" O ILE I 924 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N VAL I 929 " --> pdb=" O CYS I 925 " (cutoff:3.500A) Processing helix chain 'I' and resid 940 through 955 removed outlier: 3.668A pdb=" N ILE I 955 " --> pdb=" O LEU I 951 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 993 Processing helix chain 'I' and resid 993 through 1007 Processing helix chain 'I' and resid 1008 through 1010 No H-bonds generated for 'chain 'I' and resid 1008 through 1010' Processing helix chain 'I' and resid 1016 through 1040 removed outlier: 3.855A pdb=" N LEU I1036 " --> pdb=" O ALA I1032 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I1040 " --> pdb=" O LEU I1036 " (cutoff:3.500A) Processing helix chain 'I' and resid 1050 through 1057 Processing helix chain 'I' and resid 1059 through 1104 removed outlier: 4.255A pdb=" N ALA I1065 " --> pdb=" O PRO I1061 " (cutoff:3.500A) Processing helix chain 'I' and resid 1198 through 1200 No H-bonds generated for 'chain 'I' and resid 1198 through 1200' Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 removed outlier: 4.050A pdb=" N ARG J 307 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 675 through 678 removed outlier: 4.540A pdb=" N ALA J 678 " --> pdb=" O GLY J 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 675 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 3.618A pdb=" N LYS J 698 " --> pdb=" O ARG J 694 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.614A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 7.303A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLY B 732 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.728A pdb=" N ILE A 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.918A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 787 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.863A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.321A pdb=" N THR B 63 " --> pdb=" O TYR F 632 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 69 through 72 removed outlier: 3.695A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 75 through 76 Processing sheet with id=AB3, first strand: chain 'B' and resid 75 through 76 removed outlier: 6.582A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.400A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AB6, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.539A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE B 186 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS B 237 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU B 188 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG B 235 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.704A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.408A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.422A pdb=" N GLU B 605 " --> pdb=" O GLY B 372 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 615 " --> pdb=" O VAL B 604 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 617 through 619 removed outlier: 4.975A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AC4, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.573A pdb=" N SER C 44 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 34 " --> pdb=" O VAL C 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 96 through 99 removed outlier: 4.614A pdb=" N TYR C 98 " --> pdb=" O VAL C 100B" (cutoff:3.500A) removed outlier: 7.538A pdb=" N VAL C 100B" --> pdb=" O TYR C 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AC7, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.289A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N MET D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER D 49 " --> pdb=" O MET D 33 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 719 through 724 removed outlier: 7.331A pdb=" N LEU E 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU F 722 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY F 732 " --> pdb=" O LEU F 735 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ALA F 737 " --> pdb=" O PRO F 730 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 777 through 782 removed outlier: 5.928A pdb=" N VAL E1150 " --> pdb=" O LYS E1174 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 787 through 796 Processing sheet with id=AD2, first strand: chain 'E' and resid 802 through 804 Processing sheet with id=AD3, first strand: chain 'E' and resid 857 through 858 Processing sheet with id=AD4, first strand: chain 'E' and resid 1202 through 1205 removed outlier: 4.261A pdb=" N CYS E1164 " --> pdb=" O VAL E1205 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS E1156 " --> pdb=" O ILE E1214 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 33 through 35 Processing sheet with id=AD6, first strand: chain 'F' and resid 63 through 64 removed outlier: 6.288A pdb=" N THR F 63 " --> pdb=" O TYR J 632 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 68 through 72 removed outlier: 3.709A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'F' and resid 75 through 76 removed outlier: 6.627A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.400A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AE3, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.518A pdb=" N ALA F 146 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU F 180 " --> pdb=" O THR F 242 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR F 242 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA F 182 " --> pdb=" O MET F 240 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N MET F 240 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TYR F 184 " --> pdb=" O THR F 238 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE F 186 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ASN F 236 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N GLU F 188 " --> pdb=" O LEU F 234 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU F 234 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.723A pdb=" N SER F 126 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AE6, first strand: chain 'F' and resid 359 through 366 removed outlier: 4.392A pdb=" N VAL F 659 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER F 365 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL F 657 " --> pdb=" O SER F 365 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 371 through 376 removed outlier: 4.416A pdb=" N GLU F 605 " --> pdb=" O GLY F 372 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AE9, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.347A pdb=" N SER G 44 " --> pdb=" O SER G 40 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N VAL G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 96 through 99 removed outlier: 4.629A pdb=" N TYR G 98 " --> pdb=" O VAL G 100B" (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL G 100B" --> pdb=" O TYR G 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.288A pdb=" N LEU H 11 " --> pdb=" O GLU H 105 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N MET H 33 " --> pdb=" O SER H 49 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER H 49 " --> pdb=" O MET H 33 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.325A pdb=" N LEU I 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU J 722 " --> pdb=" O LEU I 759 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 777 through 782 removed outlier: 5.916A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 787 through 796 Processing sheet with id=AF7, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'I' and resid 1202 through 1204 removed outlier: 6.809A pdb=" N CYS I1156 " --> pdb=" O ILE I1214 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AG1, first strand: chain 'J' and resid 69 through 72 removed outlier: 3.699A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AG3, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.626A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.374A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AG6, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.510A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE J 186 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N CYS J 237 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLU J 188 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG J 235 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.710A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AG9, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.403A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.427A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AH3, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.362A pdb=" N SER K 44 " --> pdb=" O SER K 40 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 96 through 99 removed outlier: 4.630A pdb=" N TYR K 98 " --> pdb=" O VAL K 100B" (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL K 100B" --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AH6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.289A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N MET L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N SER L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 1100 hydrogen bonds defined for protein. 2841 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: 6.78 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5924 1.32 - 1.45: 8902 1.45 - 1.58: 14513 1.58 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 29544 Sorted by residual: bond pdb=" C1 NAG f 2 " pdb=" O5 NAG f 2 " ideal model delta sigma weight residual 1.406 1.521 -0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" CA PRO A1219 " pdb=" C PRO A1219 " ideal model delta sigma weight residual 1.517 1.567 -0.050 9.30e-03 1.16e+04 2.85e+01 bond pdb=" CA PRO E1219 " pdb=" C PRO E1219 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.81e+01 bond pdb=" CA PRO I1219 " pdb=" C PRO I1219 " ideal model delta sigma weight residual 1.517 1.566 -0.049 9.30e-03 1.16e+04 2.78e+01 bond pdb=" CA CYS I 817 " pdb=" C CYS I 817 " ideal model delta sigma weight residual 1.523 1.464 0.060 1.30e-02 5.92e+03 2.11e+01 ... (remaining 29539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 36359 2.80 - 5.59: 3292 5.59 - 8.39: 434 8.39 - 11.19: 48 11.19 - 13.99: 7 Bond angle restraints: 40140 Sorted by residual: angle pdb=" C GLN L 42 " pdb=" N PRO L 43 " pdb=" CA PRO L 43 " ideal model delta sigma weight residual 119.66 127.44 -7.78 7.20e-01 1.93e+00 1.17e+02 angle pdb=" C GLN H 42 " pdb=" N PRO H 43 " pdb=" CA PRO H 43 " ideal model delta sigma weight residual 119.66 127.39 -7.73 7.20e-01 1.93e+00 1.15e+02 angle pdb=" C LEU B 284 " pdb=" N PRO B 285 " pdb=" CA PRO B 285 " ideal model delta sigma weight residual 119.82 129.13 -9.31 9.80e-01 1.04e+00 9.02e+01 angle pdb=" C LEU F 284 " pdb=" N PRO F 285 " pdb=" CA PRO F 285 " ideal model delta sigma weight residual 119.56 129.24 -9.68 1.02e+00 9.61e-01 9.00e+01 angle pdb=" C LEU J 284 " pdb=" N PRO J 285 " pdb=" CA PRO J 285 " ideal model delta sigma weight residual 119.56 129.19 -9.63 1.02e+00 9.61e-01 8.91e+01 ... (remaining 40135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 16379 17.70 - 35.39: 447 35.39 - 53.09: 148 53.09 - 70.78: 62 70.78 - 88.48: 25 Dihedral angle restraints: 17061 sinusoidal: 6561 harmonic: 10500 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.28 -74.28 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.19 -74.19 1 1.00e+01 1.00e-02 6.98e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 166.95 -73.95 1 1.00e+01 1.00e-02 6.95e+01 ... (remaining 17058 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 4385 0.166 - 0.333: 210 0.333 - 0.499: 12 0.499 - 0.666: 4 0.666 - 0.832: 3 Chirality restraints: 4614 Sorted by residual: chirality pdb=" C1 NAG F1404 " pdb=" ND2 ASN F 155 " pdb=" C2 NAG F1404 " pdb=" O5 NAG F1404 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.73e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 66 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 619 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 -1.60 -0.80 2.00e-01 2.50e+01 1.62e+01 ... (remaining 4611 not shown) Planarity restraints: 5175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN J 66 " 0.015 2.00e-02 2.50e+03 7.12e-02 6.34e+01 pdb=" CG ASN J 66 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN J 66 " 0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN J 66 " -0.126 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " -0.077 2.00e-02 2.50e+03 3.88e-02 3.76e+01 pdb=" CG TRP C 47 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.046 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.055 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1401 " 0.043 2.00e-02 2.50e+03 5.26e-02 3.46e+01 pdb=" C7 NAG B1401 " 0.060 2.00e-02 2.50e+03 pdb=" C8 NAG B1401 " 0.012 2.00e-02 2.50e+03 pdb=" N2 NAG B1401 " -0.085 2.00e-02 2.50e+03 pdb=" O7 NAG B1401 " -0.030 2.00e-02 2.50e+03 ... (remaining 5172 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 23 2.33 - 2.97: 15164 2.97 - 3.61: 38910 3.61 - 4.26: 66882 4.26 - 4.90: 107515 Nonbonded interactions: 228494 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.682 3.470 nonbonded pdb=" OH TYR E 905 " pdb=" CA PRO E 936 " model vdw 1.700 3.470 nonbonded pdb=" OH TYR I 905 " pdb=" CA PRO I 936 " model vdw 1.754 3.470 nonbonded pdb=" OH TYR I 905 " pdb=" N PRO I 936 " model vdw 1.892 3.120 nonbonded pdb=" OH TYR A 905 " pdb=" N PRO A 936 " model vdw 1.926 3.120 ... (remaining 228489 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 27.410 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.140 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 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 : 0.015 0.964 29653 Z= 0.883 Angle : 1.827 37.897 40415 Z= 1.178 Chirality : 0.087 0.832 4614 Planarity : 0.012 0.100 5133 Dihedral : 10.786 88.480 10242 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.87 % Allowed : 4.16 % Favored : 94.97 % Rotamer: Outliers : 0.16 % Allowed : 0.78 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.14), residues: 3582 helix: -0.16 (0.17), residues: 603 sheet: 0.92 (0.17), residues: 798 loop : 1.52 (0.14), residues: 2181 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 307 TYR 0.060 0.007 TYR A 909 PHE 0.032 0.005 PHE H 98 TRP 0.077 0.011 TRP C 47 HIS 0.005 0.002 HIS B 681 Details of bonding type rmsd/Z covalent geometry : bond 0.01348 / 0.83 (29544) covalent geometry : angle 1.71378 / 1.16 (40140) SS BOND : bond 0.16315 / 8.78 ( 43) SS BOND : angle 7.34365 / 4.83 ( 86) hydrogen bonds : bond 0.20996 / 13.95 ( 1094) hydrogen bonds : angle 7.35372 / 5.22 ( 2841) Misc. bond : bond 0.01182 / 0.61 ( 3) link_BETA1-4 : bond 0.01405 / 0.92 ( 21) link_BETA1-4 : angle 3.67575 / 2.83 ( 63) link_NAG-ASN : bond 0.01530 / 1.06 ( 42) link_NAG-ASN : angle 9.54365 / 6.02 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 646 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 799 ILE cc_start: 0.8336 (mm) cc_final: 0.8078 (pt) REVERT: A 816 LYS cc_start: 0.8721 (tppt) cc_final: 0.8352 (tppt) REVERT: B 65 SER cc_start: 0.8039 (t) cc_final: 0.7830 (m) REVERT: B 164 PHE cc_start: 0.7471 (m-80) cc_final: 0.6896 (m-10) REVERT: B 204 PHE cc_start: 0.7757 (t80) cc_final: 0.7486 (t80) REVERT: B 621 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8330 (m) REVERT: F 232 PHE cc_start: 0.7440 (m-80) cc_final: 0.7141 (m-80) REVERT: F 686 MET cc_start: 0.8361 (mmt) cc_final: 0.8014 (mmm) REVERT: F 696 MET cc_start: 0.7110 (mtm) cc_final: 0.6636 (ttt) REVERT: G 36 TRP cc_start: 0.8622 (m100) cc_final: 0.8397 (m-10) REVERT: H 86 TYR cc_start: 0.8377 (m-80) cc_final: 0.7960 (m-80) REVERT: I 799 ILE cc_start: 0.8442 (mm) cc_final: 0.8161 (pt) REVERT: I 932 TYR cc_start: 0.6621 (m-10) cc_final: 0.6353 (m-80) REVERT: I 988 GLN cc_start: 0.8051 (tp40) cc_final: 0.7763 (tm-30) REVERT: J 604 VAL cc_start: 0.8054 (m) cc_final: 0.7783 (m) REVERT: K 36 TRP cc_start: 0.8446 (m100) cc_final: 0.8162 (m-10) REVERT: K 82 LEU cc_start: 0.6350 (tp) cc_final: 0.6014 (tt) REVERT: L 86 TYR cc_start: 0.8461 (m-80) cc_final: 0.8217 (m-80) REVERT: L 102 THR cc_start: 0.8663 (p) cc_final: 0.8376 (m) outliers start: 5 outliers final: 0 residues processed: 650 average time/residue: 0.2075 time to fit residues: 210.0502 Evaluate side-chains 324 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 621 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1003 GLN A1023 GLN A1129 ASN A1201 ASN B 208 HIS ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS E 808 GLN E1023 GLN E1129 ASN F 208 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN H 38 GLN H 74 ASN H 76 HIS I 808 GLN ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1129 ASN I1163 ASN I1201 ASN J 208 HIS J 346 GLN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.130064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.100145 restraints weight = 63638.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.099914 restraints weight = 39741.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.101126 restraints weight = 35440.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.101407 restraints weight = 29283.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.101593 restraints weight = 27437.400| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 29653 Z= 0.168 Angle : 0.799 14.571 40415 Z= 0.413 Chirality : 0.049 0.456 4614 Planarity : 0.007 0.080 5133 Dihedral : 5.684 38.568 3940 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.45 % Allowed : 3.94 % Favored : 95.62 % Rotamer: Outliers : 2.05 % Allowed : 6.83 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.14), residues: 3582 helix: 1.75 (0.21), residues: 615 sheet: 0.78 (0.16), residues: 789 loop : 0.74 (0.14), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 269 TYR 0.022 0.001 TYR F 77 PHE 0.020 0.002 PHE I1116 TRP 0.021 0.002 TRP G 47 HIS 0.012 0.001 HIS I1122 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (29544) covalent geometry : angle 0.74858 / 0.40 (40140) SS BOND : bond 0.00947 / 0.70 ( 43) SS BOND : angle 2.54122 / 1.72 ( 86) hydrogen bonds : bond 0.06915 / 4.67 ( 1094) hydrogen bonds : angle 5.95664 / 4.21 ( 2841) Misc. bond : bond 0.00106 / 0.05 ( 3) link_BETA1-4 : bond 0.00764 / 0.54 ( 21) link_BETA1-4 : angle 2.04361 / 1.50 ( 63) link_NAG-ASN : bond 0.00515 / 0.31 ( 42) link_NAG-ASN : angle 4.44011 / 2.80 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 421 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.5979 (m-80) cc_final: 0.5711 (m-10) REVERT: B 181 ARG cc_start: 0.7132 (mtt-85) cc_final: 0.6900 (mtt-85) REVERT: B 621 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8576 (m) REVERT: C 43 LYS cc_start: 0.7783 (mttt) cc_final: 0.7444 (mtpp) REVERT: C 82 LEU cc_start: 0.7661 (tp) cc_final: 0.7226 (pt) REVERT: D 90 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7638 (tt0) REVERT: E 1182 ASP cc_start: 0.7029 (t0) cc_final: 0.6686 (t0) REVERT: F 318 LEU cc_start: 0.9123 (mt) cc_final: 0.8261 (mm) REVERT: F 696 MET cc_start: 0.7258 (mtm) cc_final: 0.6899 (ttt) REVERT: G 28 THR cc_start: 0.7921 (m) cc_final: 0.7675 (p) REVERT: G 36 TRP cc_start: 0.8813 (m100) cc_final: 0.8354 (m-10) REVERT: H 85 MET cc_start: 0.8679 (mmm) cc_final: 0.8235 (tpt) REVERT: H 90 GLN cc_start: 0.7711 (tt0) cc_final: 0.7355 (tt0) REVERT: H 105 GLU cc_start: 0.6572 (mp0) cc_final: 0.6357 (mp0) REVERT: I 1182 ASP cc_start: 0.7098 (t0) cc_final: 0.6824 (t0) REVERT: J 627 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7843 (pt0) REVERT: K 36 TRP cc_start: 0.8469 (m100) cc_final: 0.8022 (m-10) REVERT: K 66 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8155 (ttm-80) REVERT: K 82 LEU cc_start: 0.7868 (tp) cc_final: 0.7446 (pt) REVERT: L 85 MET cc_start: 0.8343 (tpt) cc_final: 0.8123 (mmm) REVERT: L 89 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7476 (tm-30) outliers start: 63 outliers final: 37 residues processed: 455 average time/residue: 0.1861 time to fit residues: 134.8415 Evaluate side-chains 358 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 318 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 216 ASP Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 621 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 806 CYS Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 1035 LYS Chi-restraints excluded: chain E residue 1201 ASN Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain J residue 86 VAL Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 231 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 8 optimal weight: 6.9990 chunk 335 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 836 HIS ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS B 280 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 836 HIS ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1201 ASN K 39 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.124264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094066 restraints weight = 63712.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.093492 restraints weight = 40326.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094387 restraints weight = 38399.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.094715 restraints weight = 30584.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094974 restraints weight = 28779.824| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 29653 Z= 0.245 Angle : 0.770 12.349 40415 Z= 0.398 Chirality : 0.048 0.399 4614 Planarity : 0.006 0.056 5133 Dihedral : 5.454 34.932 3940 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 4.36 % Favored : 95.20 % Rotamer: Outliers : 2.93 % Allowed : 8.91 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % 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: 0.83 (0.14), residues: 3582 helix: 1.83 (0.21), residues: 621 sheet: 0.69 (0.16), residues: 870 loop : 0.18 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 699 TYR 0.023 0.002 TYR I 777 PHE 0.023 0.002 PHE J 204 TRP 0.018 0.002 TRP G 47 HIS 0.010 0.002 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (29544) covalent geometry : angle 0.74093 / 0.39 (40140) SS BOND : bond 0.00719 / 0.45 ( 43) SS BOND : angle 1.70460 / 1.15 ( 86) hydrogen bonds : bond 0.06556 / 4.43 ( 1094) hydrogen bonds : angle 5.64940 / 3.98 ( 2841) Misc. bond : bond 0.00144 / 0.06 ( 3) link_BETA1-4 : bond 0.00706 / 0.52 ( 21) link_BETA1-4 : angle 1.90722 / 1.35 ( 63) link_NAG-ASN : bond 0.00402 / 0.25 ( 42) link_NAG-ASN : angle 3.37483 / 2.20 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 352 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.6337 (m-80) cc_final: 0.5953 (m-10) REVERT: A 1182 ASP cc_start: 0.7566 (t0) cc_final: 0.7223 (t0) REVERT: C 62 LYS cc_start: 0.8031 (ptpt) cc_final: 0.7818 (ptpp) REVERT: C 79 TYR cc_start: 0.7840 (m-80) cc_final: 0.7578 (m-80) REVERT: C 82 LEU cc_start: 0.7645 (tp) cc_final: 0.7420 (mm) REVERT: D 11 LEU cc_start: 0.8019 (mt) cc_final: 0.7811 (mt) REVERT: D 86 TYR cc_start: 0.8466 (m-80) cc_final: 0.8184 (m-80) REVERT: D 89 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 90 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: E 1084 GLN cc_start: 0.7989 (tt0) cc_final: 0.7781 (tt0) REVERT: F 696 MET cc_start: 0.7281 (mtm) cc_final: 0.6944 (ttt) REVERT: G 36 TRP cc_start: 0.8762 (m100) cc_final: 0.8308 (m-10) REVERT: H 102 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (t) REVERT: H 105 GLU cc_start: 0.6820 (mp0) cc_final: 0.6568 (mp0) REVERT: I 1182 ASP cc_start: 0.7407 (t0) cc_final: 0.6980 (t0) REVERT: J 270 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: J 627 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: J 696 MET cc_start: 0.7335 (mtt) cc_final: 0.6941 (mtp) REVERT: K 36 TRP cc_start: 0.8470 (m100) cc_final: 0.8064 (m-10) REVERT: L 89 GLN cc_start: 0.8411 (tm-30) cc_final: 0.7947 (tm-30) REVERT: L 90 GLN cc_start: 0.7991 (tt0) cc_final: 0.7715 (tt0) outliers start: 90 outliers final: 64 residues processed: 415 average time/residue: 0.1905 time to fit residues: 126.3809 Evaluate side-chains 363 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 295 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 798 THR Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 94 VAL Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 806 CYS Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1168 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 148 MET Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 604 VAL Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 TYR Chi-restraints excluded: chain L residue 94 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 208 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 154 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 283 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 178 optimal weight: 9.9990 chunk 156 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 138 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1104 ASN A1201 ASN A1212 GLN B 208 HIS F 208 HIS ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1023 GLN J 91 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.126575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096261 restraints weight = 63001.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.096940 restraints weight = 36711.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.097564 restraints weight = 33306.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.097844 restraints weight = 29542.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098053 restraints weight = 26781.335| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 29653 Z= 0.129 Angle : 0.665 11.472 40415 Z= 0.338 Chirality : 0.045 0.342 4614 Planarity : 0.005 0.052 5133 Dihedral : 5.016 29.527 3939 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.05 % Favored : 95.56 % Rotamer: Outliers : 2.05 % Allowed : 10.60 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % 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: 0.93 (0.14), residues: 3582 helix: 2.20 (0.21), residues: 621 sheet: 0.78 (0.17), residues: 774 loop : 0.16 (0.14), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 699 TYR 0.027 0.001 TYR I 777 PHE 0.029 0.001 PHE E 850 TRP 0.016 0.001 TRP C 47 HIS 0.006 0.001 HIS F 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (29544) covalent geometry : angle 0.64045 / 0.33 (40140) SS BOND : bond 0.00575 / 0.31 ( 43) SS BOND : angle 1.53480 / 1.02 ( 86) hydrogen bonds : bond 0.05247 / 3.52 ( 1094) hydrogen bonds : angle 5.23951 / 3.67 ( 2841) Misc. bond : bond 0.00078 / 0.03 ( 3) link_BETA1-4 : bond 0.00602 / 0.42 ( 21) link_BETA1-4 : angle 1.69223 / 1.22 ( 63) link_NAG-ASN : bond 0.00399 / 0.23 ( 42) link_NAG-ASN : angle 2.85171 / 1.84 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 344 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.6268 (m-80) cc_final: 0.5992 (m-10) REVERT: A 1182 ASP cc_start: 0.7443 (t0) cc_final: 0.7052 (t0) REVERT: B 696 MET cc_start: 0.7039 (mtt) cc_final: 0.6316 (ttt) REVERT: C 43 LYS cc_start: 0.7397 (mttp) cc_final: 0.6886 (mmmm) REVERT: D 86 TYR cc_start: 0.8344 (m-80) cc_final: 0.8011 (m-80) REVERT: D 89 GLN cc_start: 0.7894 (tm-30) cc_final: 0.7529 (tm-30) REVERT: D 90 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: F 696 MET cc_start: 0.7191 (mtm) cc_final: 0.6907 (ttt) REVERT: F 699 ARG cc_start: 0.6329 (ttm110) cc_final: 0.6102 (ttm110) REVERT: G 36 TRP cc_start: 0.8717 (m100) cc_final: 0.8203 (m-10) REVERT: H 61 ARG cc_start: 0.7500 (mtp180) cc_final: 0.7110 (ttm170) REVERT: H 89 GLN cc_start: 0.8117 (tm-30) cc_final: 0.7625 (tm-30) REVERT: H 105 GLU cc_start: 0.6879 (mp0) cc_final: 0.6612 (mp0) REVERT: I 913 MET cc_start: 0.6384 (ttp) cc_final: 0.6081 (ttp) REVERT: I 1084 GLN cc_start: 0.7938 (tt0) cc_final: 0.7690 (tt0) REVERT: I 1182 ASP cc_start: 0.7336 (t0) cc_final: 0.6872 (t0) REVERT: J 627 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7978 (pt0) REVERT: J 696 MET cc_start: 0.7218 (mtt) cc_final: 0.6729 (ttt) REVERT: K 36 TRP cc_start: 0.8428 (m100) cc_final: 0.7840 (m-10) REVERT: L 89 GLN cc_start: 0.8423 (tm-30) cc_final: 0.7822 (tm-30) REVERT: L 90 GLN cc_start: 0.7964 (tt0) cc_final: 0.7380 (tt0) outliers start: 63 outliers final: 42 residues processed: 380 average time/residue: 0.2016 time to fit residues: 121.4288 Evaluate side-chains 354 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 310 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 600 LEU Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 28 TYR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 806 CYS Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 69 MET Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 28 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 93 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 283 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 147 optimal weight: 0.0170 chunk 56 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 overall best weight: 2.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1085 GLN B 208 HIS B 258 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 76 HIS E 927 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.093578 restraints weight = 63270.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093831 restraints weight = 38031.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094532 restraints weight = 35417.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.094799 restraints weight = 29412.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.095066 restraints weight = 27595.157| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29653 Z= 0.179 Angle : 0.683 11.085 40415 Z= 0.344 Chirality : 0.046 0.348 4614 Planarity : 0.005 0.051 5133 Dihedral : 4.925 25.439 3939 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.80 % Favored : 94.89 % Rotamer: Outliers : 2.54 % Allowed : 11.38 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % 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: 0.70 (0.14), residues: 3582 helix: 2.18 (0.21), residues: 618 sheet: 0.44 (0.17), residues: 912 loop : 0.01 (0.15), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 699 TYR 0.028 0.001 TYR I 777 PHE 0.022 0.002 PHE J 239 TRP 0.016 0.001 TRP C 47 HIS 0.008 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.18 (29544) covalent geometry : angle 0.65961 / 0.34 (40140) SS BOND : bond 0.00771 / 0.52 ( 43) SS BOND : angle 1.50906 / 1.00 ( 86) hydrogen bonds : bond 0.05489 / 3.70 ( 1094) hydrogen bonds : angle 5.18184 / 3.65 ( 2841) Misc. bond : bond 0.00100 / 0.04 ( 3) link_BETA1-4 : bond 0.00533 / 0.37 ( 21) link_BETA1-4 : angle 1.68178 / 1.19 ( 63) link_NAG-ASN : bond 0.00371 / 0.24 ( 42) link_NAG-ASN : angle 2.80793 / 1.90 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 932 TYR cc_start: 0.6603 (m-80) cc_final: 0.6330 (m-10) REVERT: B 696 MET cc_start: 0.7076 (mtt) cc_final: 0.6417 (ttt) REVERT: C 43 LYS cc_start: 0.7476 (mttp) cc_final: 0.7155 (mtpp) REVERT: C 82 LEU cc_start: 0.7673 (tp) cc_final: 0.7049 (pt) REVERT: D 89 GLN cc_start: 0.8164 (tm-30) cc_final: 0.7797 (tm-30) REVERT: D 90 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: E 1182 ASP cc_start: 0.7051 (t0) cc_final: 0.6791 (t0) REVERT: F 269 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5772 (ptt90) REVERT: F 696 MET cc_start: 0.7269 (mtm) cc_final: 0.6918 (ttt) REVERT: G 36 TRP cc_start: 0.8699 (m100) cc_final: 0.8091 (m-10) REVERT: I 913 MET cc_start: 0.6390 (ttp) cc_final: 0.5576 (tmm) REVERT: I 1084 GLN cc_start: 0.7999 (tt0) cc_final: 0.7778 (tt0) REVERT: J 240 MET cc_start: 0.7411 (tpt) cc_final: 0.7179 (tpt) REVERT: J 270 TYR cc_start: 0.7748 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: J 627 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8073 (pt0) REVERT: J 686 MET cc_start: 0.8303 (mmp) cc_final: 0.8052 (mmm) REVERT: J 696 MET cc_start: 0.7196 (mtt) cc_final: 0.6746 (ttt) REVERT: K 36 TRP cc_start: 0.8496 (m100) cc_final: 0.7929 (m-10) REVERT: K 101 ASP cc_start: 0.8105 (t0) cc_final: 0.7886 (t0) REVERT: L 85 MET cc_start: 0.8238 (tpt) cc_final: 0.7654 (tpp) REVERT: L 89 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8158 (tm-30) outliers start: 78 outliers final: 58 residues processed: 380 average time/residue: 0.1987 time to fit residues: 120.3003 Evaluate side-chains 368 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 306 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 208 HIS Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 95 optimal weight: 5.9990 chunk 284 optimal weight: 30.0000 chunk 46 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 321 optimal weight: 8.9990 chunk 289 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 130 optimal weight: 0.0470 overall best weight: 2.5884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1129 ASN B 280 GLN D 76 HIS G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.123433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.093361 restraints weight = 63015.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092963 restraints weight = 38901.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093959 restraints weight = 36364.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094197 restraints weight = 29998.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094448 restraints weight = 28215.870| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29653 Z= 0.183 Angle : 0.689 12.267 40415 Z= 0.345 Chirality : 0.045 0.338 4614 Planarity : 0.005 0.049 5133 Dihedral : 4.874 25.840 3939 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.03 % Favored : 94.67 % Rotamer: Outliers : 2.99 % Allowed : 11.67 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % 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: 0.58 (0.14), residues: 3582 helix: 2.19 (0.21), residues: 618 sheet: 0.48 (0.17), residues: 888 loop : -0.17 (0.14), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 699 TYR 0.027 0.001 TYR I 777 PHE 0.022 0.002 PHE J 239 TRP 0.014 0.001 TRP C 47 HIS 0.019 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (29544) covalent geometry : angle 0.66629 / 0.34 (40140) SS BOND : bond 0.00556 / 0.34 ( 43) SS BOND : angle 1.51843 / 0.99 ( 86) hydrogen bonds : bond 0.05379 / 3.62 ( 1094) hydrogen bonds : angle 5.11221 / 3.59 ( 2841) Misc. bond : bond 0.00106 / 0.04 ( 3) link_BETA1-4 : bond 0.00463 / 0.31 ( 21) link_BETA1-4 : angle 1.62312 / 1.16 ( 63) link_NAG-ASN : bond 0.00437 / 0.30 ( 42) link_NAG-ASN : angle 2.81708 / 1.93 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 319 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8367 (ttmm) REVERT: A 932 TYR cc_start: 0.6709 (m-80) cc_final: 0.6302 (m-10) REVERT: A 1182 ASP cc_start: 0.7402 (t0) cc_final: 0.7077 (t0) REVERT: B 261 GLN cc_start: 0.8040 (mp10) cc_final: 0.7810 (mp10) REVERT: B 696 MET cc_start: 0.7092 (mtt) cc_final: 0.6366 (ttt) REVERT: B 699 ARG cc_start: 0.6289 (ttm110) cc_final: 0.6017 (ttm110) REVERT: C 43 LYS cc_start: 0.7590 (mttp) cc_final: 0.7076 (mmmm) REVERT: D 89 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7843 (tm-30) REVERT: D 90 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7407 (tt0) REVERT: F 269 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.5807 (ptt90) REVERT: F 696 MET cc_start: 0.7267 (mtm) cc_final: 0.6924 (ttt) REVERT: F 699 ARG cc_start: 0.6415 (ttm110) cc_final: 0.6151 (ttm110) REVERT: G 36 TRP cc_start: 0.8705 (m100) cc_final: 0.8014 (m-10) REVERT: G 43 LYS cc_start: 0.7831 (mmtt) cc_final: 0.7347 (mmmm) REVERT: H 61 ARG cc_start: 0.7516 (ttm170) cc_final: 0.7077 (ttm170) REVERT: H 85 MET cc_start: 0.8542 (mmm) cc_final: 0.8128 (tpt) REVERT: I 913 MET cc_start: 0.6441 (ttp) cc_final: 0.5804 (ttp) REVERT: I 1084 GLN cc_start: 0.8026 (tt0) cc_final: 0.7788 (tt0) REVERT: I 1182 ASP cc_start: 0.7219 (t0) cc_final: 0.6902 (t0) REVERT: J 270 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: J 627 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.8059 (pt0) REVERT: J 696 MET cc_start: 0.7233 (mtt) cc_final: 0.6705 (ttt) REVERT: K 36 TRP cc_start: 0.8503 (m100) cc_final: 0.7978 (m-10) REVERT: K 101 ASP cc_start: 0.8316 (t0) cc_final: 0.7971 (t70) REVERT: L 76 HIS cc_start: 0.7042 (m-70) cc_final: 0.6831 (m-70) REVERT: L 89 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8076 (tm-30) REVERT: L 90 GLN cc_start: 0.7812 (tm130) cc_final: 0.7363 (pp30) outliers start: 92 outliers final: 70 residues processed: 385 average time/residue: 0.1907 time to fit residues: 118.7681 Evaluate side-chains 378 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 847 ARG Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1095 SER Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 925 CYS Chi-restraints excluded: chain I residue 1168 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 264 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 HIS F 111 GLN G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1212 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.125099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094811 restraints weight = 63088.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094780 restraints weight = 37386.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.095650 restraints weight = 33724.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.095876 restraints weight = 28030.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096149 restraints weight = 26291.542| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29653 Z= 0.125 Angle : 0.643 10.575 40415 Z= 0.320 Chirality : 0.044 0.333 4614 Planarity : 0.004 0.046 5133 Dihedral : 4.656 28.471 3939 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.11 % Favored : 94.64 % Rotamer: Outliers : 2.70 % Allowed : 12.33 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % 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: 0.69 (0.14), residues: 3582 helix: 2.34 (0.21), residues: 636 sheet: 0.64 (0.17), residues: 861 loop : -0.18 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 699 TYR 0.025 0.001 TYR I 777 PHE 0.021 0.001 PHE B 204 TRP 0.013 0.001 TRP C 47 HIS 0.007 0.001 HIS B 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (29544) covalent geometry : angle 0.62164 / 0.32 (40140) SS BOND : bond 0.00451 / 0.27 ( 43) SS BOND : angle 1.35172 / 0.85 ( 86) hydrogen bonds : bond 0.04695 / 3.15 ( 1094) hydrogen bonds : angle 4.86550 / 3.41 ( 2841) Misc. bond : bond 0.00078 / 0.03 ( 3) link_BETA1-4 : bond 0.00538 / 0.38 ( 21) link_BETA1-4 : angle 1.61655 / 1.15 ( 63) link_NAG-ASN : bond 0.00405 / 0.25 ( 42) link_NAG-ASN : angle 2.60389 / 1.77 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 335 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8203 (ttmm) REVERT: A 932 TYR cc_start: 0.6757 (m-80) cc_final: 0.6515 (m-80) REVERT: A 1182 ASP cc_start: 0.7311 (t0) cc_final: 0.6869 (t0) REVERT: B 696 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6301 (ttt) REVERT: B 699 ARG cc_start: 0.6469 (ttm110) cc_final: 0.6243 (ttm110) REVERT: C 43 LYS cc_start: 0.7566 (mttp) cc_final: 0.7006 (mmmm) REVERT: D 42 GLN cc_start: 0.7726 (mt0) cc_final: 0.7404 (mp10) REVERT: D 89 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7768 (tm-30) REVERT: D 90 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7329 (tt0) REVERT: E 1182 ASP cc_start: 0.6881 (t0) cc_final: 0.6587 (t0) REVERT: F 240 MET cc_start: 0.7536 (mmm) cc_final: 0.7217 (mmm) REVERT: F 269 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.5909 (ptt90) REVERT: F 686 MET cc_start: 0.8169 (mmp) cc_final: 0.7845 (mmm) REVERT: F 696 MET cc_start: 0.7267 (mtm) cc_final: 0.6886 (ttt) REVERT: F 699 ARG cc_start: 0.6385 (ttm110) cc_final: 0.6132 (ttm110) REVERT: G 36 TRP cc_start: 0.8693 (m100) cc_final: 0.8321 (m100) REVERT: G 43 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7462 (mmmm) REVERT: I 757 MET cc_start: 0.8127 (mmt) cc_final: 0.7671 (mmt) REVERT: I 913 MET cc_start: 0.6453 (ttp) cc_final: 0.5763 (ttp) REVERT: I 1084 GLN cc_start: 0.8035 (tt0) cc_final: 0.7833 (tt0) REVERT: I 1182 ASP cc_start: 0.7345 (t0) cc_final: 0.6974 (t0) REVERT: J 183 PHE cc_start: 0.6968 (OUTLIER) cc_final: 0.6749 (m-80) REVERT: J 270 TYR cc_start: 0.7752 (OUTLIER) cc_final: 0.7364 (m-80) REVERT: J 627 GLN cc_start: 0.8331 (OUTLIER) cc_final: 0.8016 (pt0) REVERT: J 696 MET cc_start: 0.7166 (mtt) cc_final: 0.6698 (ttt) REVERT: K 36 TRP cc_start: 0.8472 (m100) cc_final: 0.7902 (m-10) REVERT: L 89 GLN cc_start: 0.8541 (tm-30) cc_final: 0.8064 (tm-30) REVERT: L 90 GLN cc_start: 0.7994 (tm130) cc_final: 0.7358 (pp30) outliers start: 83 outliers final: 60 residues processed: 390 average time/residue: 0.1876 time to fit residues: 118.1036 Evaluate side-chains 377 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 696 MET Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 925 CYS Chi-restraints excluded: chain I residue 1127 VAL Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 84 MET Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 183 PHE Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 347 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 337 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093333 restraints weight = 63318.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.093307 restraints weight = 38026.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.094096 restraints weight = 35929.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094355 restraints weight = 29415.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094613 restraints weight = 27699.099| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 29653 Z= 0.228 Angle : 0.712 10.976 40415 Z= 0.357 Chirality : 0.046 0.337 4614 Planarity : 0.005 0.061 5133 Dihedral : 4.903 25.943 3939 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.42 % Favored : 94.33 % Rotamer: Outliers : 3.02 % Allowed : 12.65 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3582 helix: 2.16 (0.21), residues: 636 sheet: 0.56 (0.17), residues: 864 loop : -0.36 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 699 TYR 0.021 0.001 TYR I 777 PHE 0.019 0.002 PHE J 239 TRP 0.012 0.001 TRP C 47 HIS 0.005 0.001 HIS A1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (29544) covalent geometry : angle 0.69130 / 0.35 (40140) SS BOND : bond 0.00725 / 0.40 ( 43) SS BOND : angle 1.56129 / 1.01 ( 86) hydrogen bonds : bond 0.05602 / 3.80 ( 1094) hydrogen bonds : angle 5.08653 / 3.58 ( 2841) Misc. bond : bond 0.00131 / 0.05 ( 3) link_BETA1-4 : bond 0.00529 / 0.37 ( 21) link_BETA1-4 : angle 1.61201 / 1.14 ( 63) link_NAG-ASN : bond 0.00336 / 0.21 ( 42) link_NAG-ASN : angle 2.74695 / 1.89 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 316 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8364 (ttmm) REVERT: A 932 TYR cc_start: 0.6925 (m-80) cc_final: 0.6668 (m-80) REVERT: A 1182 ASP cc_start: 0.7438 (t0) cc_final: 0.7012 (t0) REVERT: B 696 MET cc_start: 0.7148 (mtt) cc_final: 0.6308 (ttt) REVERT: C 43 LYS cc_start: 0.7682 (mttp) cc_final: 0.7136 (mmmm) REVERT: D 42 GLN cc_start: 0.7765 (mt0) cc_final: 0.7402 (mp10) REVERT: D 61 ARG cc_start: 0.7062 (mtp-110) cc_final: 0.6747 (mmt180) REVERT: D 89 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7885 (tm-30) REVERT: D 90 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: F 269 ARG cc_start: 0.6795 (OUTLIER) cc_final: 0.5900 (ptt90) REVERT: F 686 MET cc_start: 0.8345 (mmp) cc_final: 0.8071 (mmm) REVERT: F 696 MET cc_start: 0.7234 (mtm) cc_final: 0.6874 (ttt) REVERT: F 699 ARG cc_start: 0.6462 (ttm110) cc_final: 0.6217 (ttm110) REVERT: G 36 TRP cc_start: 0.8683 (m100) cc_final: 0.8404 (m100) REVERT: G 43 LYS cc_start: 0.7781 (mmtt) cc_final: 0.7310 (mmmm) REVERT: H 61 ARG cc_start: 0.7463 (ttm170) cc_final: 0.7027 (ttm170) REVERT: H 85 MET cc_start: 0.8609 (mmm) cc_final: 0.8316 (mmm) REVERT: I 913 MET cc_start: 0.6883 (ttp) cc_final: 0.6096 (ttp) REVERT: I 1084 GLN cc_start: 0.8079 (tt0) cc_final: 0.7843 (tt0) REVERT: J 270 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: J 627 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8105 (pt0) REVERT: J 696 MET cc_start: 0.7215 (mtt) cc_final: 0.6766 (mtp) REVERT: K 36 TRP cc_start: 0.8461 (m100) cc_final: 0.7944 (m-10) REVERT: L 89 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8330 (tm-30) REVERT: L 90 GLN cc_start: 0.8286 (tm130) cc_final: 0.7684 (pp30) outliers start: 93 outliers final: 78 residues processed: 384 average time/residue: 0.1880 time to fit residues: 117.0273 Evaluate side-chains 390 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 307 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 852 SER Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 717 LEU Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain D residue 102 THR Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 853 VAL Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 932 TYR Chi-restraints excluded: chain E residue 1034 SER Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain E residue 1214 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 135 SER Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 625 VAL Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain G residue 110 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain H residue 102 THR Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 852 SER Chi-restraints excluded: chain I residue 853 VAL Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 925 CYS Chi-restraints excluded: chain I residue 1185 SER Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 709 THR Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 107 THR Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 99 optimal weight: 4.9990 chunk 142 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 343 optimal weight: 4.9990 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 chunk 222 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 8.9990 chunk 7 optimal weight: 0.0870 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.124296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093950 restraints weight = 62990.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094772 restraints weight = 36693.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.095333 restraints weight = 33448.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095703 restraints weight = 29214.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.096094 restraints weight = 25654.339| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29653 Z= 0.124 Angle : 0.664 12.008 40415 Z= 0.328 Chirality : 0.045 0.343 4614 Planarity : 0.005 0.063 5133 Dihedral : 4.681 26.666 3939 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.11 % Favored : 94.67 % Rotamer: Outliers : 2.44 % Allowed : 13.79 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % 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: 0.55 (0.14), residues: 3582 helix: 2.35 (0.21), residues: 636 sheet: 0.56 (0.17), residues: 876 loop : -0.33 (0.14), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 66 TYR 0.022 0.001 TYR I 777 PHE 0.020 0.001 PHE B 204 TRP 0.011 0.001 TRP G 47 HIS 0.004 0.001 HIS J 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (29544) covalent geometry : angle 0.64427 / 0.32 (40140) SS BOND : bond 0.00420 / 0.25 ( 43) SS BOND : angle 1.27571 / 0.81 ( 86) hydrogen bonds : bond 0.04725 / 3.18 ( 1094) hydrogen bonds : angle 4.82460 / 3.38 ( 2841) Misc. bond : bond 0.00048 / 0.02 ( 3) link_BETA1-4 : bond 0.00555 / 0.35 ( 21) link_BETA1-4 : angle 1.54811 / 1.12 ( 63) link_NAG-ASN : bond 0.00384 / 0.25 ( 42) link_NAG-ASN : angle 2.60932 / 1.83 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 323 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8239 (ttmm) REVERT: A 932 TYR cc_start: 0.6748 (m-80) cc_final: 0.6536 (m-10) REVERT: A 1050 SER cc_start: 0.8766 (t) cc_final: 0.8418 (p) REVERT: A 1182 ASP cc_start: 0.7356 (t0) cc_final: 0.6893 (t0) REVERT: B 696 MET cc_start: 0.6912 (mtt) cc_final: 0.6260 (ttt) REVERT: C 43 LYS cc_start: 0.7717 (mttp) cc_final: 0.7135 (mmmm) REVERT: D 42 GLN cc_start: 0.7705 (mt0) cc_final: 0.7410 (mp10) REVERT: D 61 ARG cc_start: 0.7017 (mtp-110) cc_final: 0.6738 (mmt180) REVERT: D 89 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7780 (tm-30) REVERT: D 90 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: F 240 MET cc_start: 0.7871 (mmm) cc_final: 0.7551 (mmm) REVERT: F 269 ARG cc_start: 0.6760 (OUTLIER) cc_final: 0.5879 (ptt90) REVERT: F 352 GLU cc_start: 0.7604 (mp0) cc_final: 0.7333 (mp0) REVERT: F 686 MET cc_start: 0.8185 (mmp) cc_final: 0.7890 (mmm) REVERT: F 696 MET cc_start: 0.7062 (mtm) cc_final: 0.6750 (ttt) REVERT: F 699 ARG cc_start: 0.6388 (ttm110) cc_final: 0.6161 (ttm110) REVERT: G 36 TRP cc_start: 0.8671 (m100) cc_final: 0.8345 (m100) REVERT: G 43 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7305 (mmmm) REVERT: H 42 GLN cc_start: 0.7711 (mt0) cc_final: 0.7329 (pm20) REVERT: H 61 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6959 (ttm170) REVERT: H 85 MET cc_start: 0.8538 (mmm) cc_final: 0.8209 (mmm) REVERT: I 757 MET cc_start: 0.8076 (mmt) cc_final: 0.7602 (mmt) REVERT: I 913 MET cc_start: 0.6844 (ttp) cc_final: 0.6445 (ttm) REVERT: J 77 TYR cc_start: 0.8106 (m-80) cc_final: 0.7821 (m-80) REVERT: J 270 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7466 (m-80) REVERT: J 627 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7976 (pt0) REVERT: J 686 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (mmm) REVERT: J 696 MET cc_start: 0.7124 (mtt) cc_final: 0.6473 (ttt) REVERT: K 36 TRP cc_start: 0.8408 (m100) cc_final: 0.7867 (m-10) REVERT: L 89 GLN cc_start: 0.8579 (tm-30) cc_final: 0.8129 (tm-30) REVERT: L 90 GLN cc_start: 0.8243 (tm130) cc_final: 0.7755 (pp30) outliers start: 75 outliers final: 58 residues processed: 372 average time/residue: 0.1850 time to fit residues: 111.3708 Evaluate side-chains 371 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 307 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 225 LEU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain I residue 798 THR Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 157 optimal weight: 0.0270 chunk 205 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 186 optimal weight: 2.9990 chunk 330 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 310 optimal weight: 0.5980 chunk 249 optimal weight: 0.4980 chunk 158 optimal weight: 5.9990 chunk 236 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.124692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094381 restraints weight = 62527.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.094711 restraints weight = 36082.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095392 restraints weight = 32986.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.095651 restraints weight = 27656.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095917 restraints weight = 25954.395| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29653 Z= 0.124 Angle : 0.663 12.036 40415 Z= 0.329 Chirality : 0.044 0.333 4614 Planarity : 0.005 0.061 5133 Dihedral : 4.618 34.367 3939 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.30 % Favored : 94.47 % Rotamer: Outliers : 2.37 % Allowed : 14.21 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3582 helix: 2.41 (0.21), residues: 636 sheet: 0.60 (0.18), residues: 855 loop : -0.36 (0.14), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 66 TYR 0.022 0.001 TYR I 777 PHE 0.021 0.001 PHE J 165 TRP 0.010 0.001 TRP C 47 HIS 0.003 0.001 HIS J 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (29544) covalent geometry : angle 0.64419 / 0.32 (40140) SS BOND : bond 0.00415 / 0.25 ( 43) SS BOND : angle 1.23251 / 0.79 ( 86) hydrogen bonds : bond 0.04557 / 3.06 ( 1094) hydrogen bonds : angle 4.74675 / 3.33 ( 2841) Misc. bond : bond 0.00058 / 0.03 ( 3) link_BETA1-4 : bond 0.00528 / 0.36 ( 21) link_BETA1-4 : angle 1.56247 / 1.12 ( 63) link_NAG-ASN : bond 0.00344 / 0.21 ( 42) link_NAG-ASN : angle 2.52752 / 1.70 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 315 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8168 (ttmm) REVERT: A 1050 SER cc_start: 0.8777 (t) cc_final: 0.8427 (p) REVERT: A 1182 ASP cc_start: 0.7325 (t0) cc_final: 0.6884 (t0) REVERT: B 240 MET cc_start: 0.8267 (tpp) cc_final: 0.7904 (tpt) REVERT: B 696 MET cc_start: 0.6904 (mtt) cc_final: 0.6218 (ttt) REVERT: C 43 LYS cc_start: 0.7768 (mttp) cc_final: 0.7154 (mmmm) REVERT: D 42 GLN cc_start: 0.7887 (mt0) cc_final: 0.7616 (mp10) REVERT: D 61 ARG cc_start: 0.7161 (mtp-110) cc_final: 0.6828 (mmt180) REVERT: D 89 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7727 (tm-30) REVERT: D 90 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: F 240 MET cc_start: 0.7877 (mmm) cc_final: 0.7582 (mmm) REVERT: F 269 ARG cc_start: 0.6797 (OUTLIER) cc_final: 0.5909 (ptt90) REVERT: F 352 GLU cc_start: 0.7608 (mp0) cc_final: 0.7320 (mp0) REVERT: F 686 MET cc_start: 0.8246 (mmp) cc_final: 0.7941 (mmm) REVERT: F 696 MET cc_start: 0.7175 (mtm) cc_final: 0.6841 (ttt) REVERT: F 699 ARG cc_start: 0.6355 (ttm110) cc_final: 0.6117 (ttm110) REVERT: G 36 TRP cc_start: 0.8653 (m100) cc_final: 0.8291 (m100) REVERT: G 43 LYS cc_start: 0.7789 (mmtt) cc_final: 0.6870 (mmmm) REVERT: H 42 GLN cc_start: 0.7774 (mt0) cc_final: 0.7341 (pm20) REVERT: H 61 ARG cc_start: 0.7458 (ttm170) cc_final: 0.7038 (ttm170) REVERT: H 85 MET cc_start: 0.8498 (mmm) cc_final: 0.7776 (mmm) REVERT: I 757 MET cc_start: 0.8116 (mmt) cc_final: 0.7852 (mmt) REVERT: I 913 MET cc_start: 0.6868 (ttp) cc_final: 0.6446 (ttm) REVERT: I 924 ILE cc_start: 0.5235 (OUTLIER) cc_final: 0.4969 (pt) REVERT: J 270 TYR cc_start: 0.7785 (OUTLIER) cc_final: 0.7462 (m-80) REVERT: J 627 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: J 686 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7933 (mmm) REVERT: J 696 MET cc_start: 0.7105 (mtt) cc_final: 0.6485 (ttt) REVERT: K 36 TRP cc_start: 0.8405 (m100) cc_final: 0.7829 (m-10) REVERT: K 47 TRP cc_start: 0.8368 (t60) cc_final: 0.8116 (t60) REVERT: L 89 GLN cc_start: 0.8546 (tm-30) cc_final: 0.8071 (tm-30) outliers start: 73 outliers final: 57 residues processed: 362 average time/residue: 0.1895 time to fit residues: 110.6042 Evaluate side-chains 367 residues out of total 3075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 303 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 817 CYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 1201 ASN Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 293 TYR Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 356 VAL Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 681 HIS Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 844 ASP Chi-restraints excluded: chain E residue 862 ILE Chi-restraints excluded: chain E residue 872 THR Chi-restraints excluded: chain E residue 893 LEU Chi-restraints excluded: chain E residue 1127 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 269 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 293 TYR Chi-restraints excluded: chain F residue 313 PHE Chi-restraints excluded: chain F residue 651 LEU Chi-restraints excluded: chain F residue 681 HIS Chi-restraints excluded: chain F residue 709 THR Chi-restraints excluded: chain F residue 717 LEU Chi-restraints excluded: chain F residue 728 LYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 38 LYS Chi-restraints excluded: chain G residue 92 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain I residue 861 ILE Chi-restraints excluded: chain I residue 924 ILE Chi-restraints excluded: chain I residue 925 CYS Chi-restraints excluded: chain I residue 1195 GLU Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 176 CYS Chi-restraints excluded: chain J residue 208 HIS Chi-restraints excluded: chain J residue 270 TYR Chi-restraints excluded: chain J residue 286 VAL Chi-restraints excluded: chain J residue 293 TYR Chi-restraints excluded: chain J residue 313 PHE Chi-restraints excluded: chain J residue 627 GLN Chi-restraints excluded: chain J residue 651 LEU Chi-restraints excluded: chain J residue 681 HIS Chi-restraints excluded: chain J residue 686 MET Chi-restraints excluded: chain J residue 709 THR Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 61 GLN Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 110 THR Chi-restraints excluded: chain L residue 42 GLN Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 322 optimal weight: 5.9990 chunk 235 optimal weight: 20.0000 chunk 184 optimal weight: 20.0000 chunk 88 optimal weight: 0.7980 chunk 227 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 314 optimal weight: 1.9990 chunk 317 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1129 ASN D 76 HIS ** E1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 56 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.124436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.094201 restraints weight = 63231.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094158 restraints weight = 36946.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.094892 restraints weight = 33101.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095177 restraints weight = 27672.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095456 restraints weight = 25820.796| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29653 Z= 0.133 Angle : 0.669 13.792 40415 Z= 0.333 Chirality : 0.044 0.325 4614 Planarity : 0.005 0.058 5133 Dihedral : 4.589 29.694 3939 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.36 % Favored : 94.42 % Rotamer: Outliers : 2.37 % Allowed : 14.28 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.52 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3582 helix: 2.50 (0.21), residues: 618 sheet: 0.53 (0.17), residues: 861 loop : -0.40 (0.14), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 66 TYR 0.021 0.001 TYR I 777 PHE 0.020 0.001 PHE B 204 TRP 0.009 0.001 TRP G 47 HIS 0.002 0.001 HIS A1146 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (29544) covalent geometry : angle 0.64976 / 0.33 (40140) SS BOND : bond 0.00624 / 0.43 ( 43) SS BOND : angle 1.50165 / 0.95 ( 86) hydrogen bonds : bond 0.04557 / 3.06 ( 1094) hydrogen bonds : angle 4.70132 / 3.29 ( 2841) Misc. bond : bond 0.00057 / 0.03 ( 3) link_BETA1-4 : bond 0.00534 / 0.37 ( 21) link_BETA1-4 : angle 1.56887 / 1.10 ( 63) link_NAG-ASN : bond 0.00329 / 0.20 ( 42) link_NAG-ASN : angle 2.50180 / 1.73 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4615.75 seconds wall clock time: 80 minutes 57.45 seconds (4857.45 seconds total)