Starting phenix.real_space_refine on Sun Jul 5 04:39:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v7r_31779/07_2026/7v7r_31779.cif" } resolution = 2.9 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= -0.002 sd= 0.039 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 108 5.16 5 C 16108 2.51 5 N 4127 2.21 5 O 5019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25362 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8074 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 54, 'TRANS': 978} Chain breaks: 7 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.79, per 1000 atoms: 0.23 Number of scatterers: 25362 At special positions: 0 Unit cell: (139.7, 144.1, 196.9, 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 108 16.00 O 5019 8.00 N 4127 7.00 C 16108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.05 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG 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 h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 341 " " NAG J 1 " - " ASN A 614 " " NAG K 1 " - " ASN A 707 " " NAG L 1 " - " ASN A 715 " " NAG M 1 " - " ASN A 799 " " NAG N 1 " - " ASN A1072 " " NAG O 1 " - " ASN A1096 " " NAG P 1 " - " ASN A1132 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 163 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5800 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.1% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.542A pdb=" N GLU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.178A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.730A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.595A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 896 through 906 removed outlier: 3.787A pdb=" N TYR A 902 " --> pdb=" O MET A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.256A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.677A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.981A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.570A pdb=" N PHE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.139A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 388 removed outlier: 4.379A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 388 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.100A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.567A pdb=" N SER B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.806A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.536A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.530A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.054A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.569A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.589A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.363A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.957A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.666A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.640A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.983A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.593A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.557A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 4.106A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.154A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.856A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.731A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.091A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.229A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU A 132 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN A 134 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA A 161 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.489A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.681A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.079A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.065A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.613A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.565A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.547A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.995A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.185A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.429A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.308A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.197A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.576A pdb=" N LYS C 788 " --> pdb=" O ASN B 701 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 717 removed outlier: 6.043A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 717 removed outlier: 6.043A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.459A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1074 through 1076 removed outlier: 4.073A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.076A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 26 through 30 removed outlier: 8.045A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.007A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.994A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 317 removed outlier: 3.656A pdb=" N THR C 313 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE3, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.696A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.070A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.848A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C1057 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.848A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.573A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1120 1010 hydrogen bonds defined for protein. 2757 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: 6.36 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8001 1.35 - 1.48: 6833 1.48 - 1.60: 10947 1.60 - 1.73: 0 1.73 - 1.86: 132 Bond restraints: 25913 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 25908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 34321 1.70 - 3.39: 843 3.39 - 5.09: 75 5.09 - 6.79: 16 6.79 - 8.48: 7 Bond angle restraints: 35262 Sorted by residual: angle pdb=" C GLU B 482 " pdb=" CA GLU B 482 " pdb=" CB GLU B 482 " ideal model delta sigma weight residual 116.63 110.46 6.17 1.16e+00 7.43e-01 2.83e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 116.02 -5.32 1.22e+00 6.72e-01 1.90e+01 angle pdb=" CA CYS C 430 " pdb=" CB CYS C 430 " pdb=" SG CYS C 430 " ideal model delta sigma weight residual 114.40 122.84 -8.44 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CB LYS A 384 " pdb=" CG LYS A 384 " pdb=" CD LYS A 384 " ideal model delta sigma weight residual 111.30 118.55 -7.25 2.30e+00 1.89e-01 9.95e+00 angle pdb=" CA PRO B 984 " pdb=" C PRO B 984 " pdb=" N PRO B 985 " ideal model delta sigma weight residual 117.93 121.69 -3.76 1.20e+00 6.94e-01 9.80e+00 ... (remaining 35257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 13388 17.79 - 35.58: 1131 35.58 - 53.38: 193 53.38 - 71.17: 39 71.17 - 88.96: 27 Dihedral angle restraints: 14778 sinusoidal: 5769 harmonic: 9009 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 -7.26 -78.74 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -159.94 73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C1080 " pdb=" SG CYS C1080 " pdb=" SG CYS C1124 " pdb=" CB CYS C1124 " ideal model delta sinusoidal sigma weight residual -86.00 -12.26 -73.74 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 14775 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3571 0.065 - 0.130: 642 0.130 - 0.195: 31 0.195 - 0.260: 4 0.260 - 0.325: 1 Chirality restraints: 4249 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.35e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 707 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4246 not shown) Planarity restraints: 4503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1137 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A1138 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1138 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1138 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO C 984 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 518 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO C 519 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 519 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 519 " -0.022 5.00e-02 4.00e+02 ... (remaining 4500 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 880 2.71 - 3.26: 24575 3.26 - 3.81: 38501 3.81 - 4.35: 46674 4.35 - 4.90: 81575 Nonbonded interactions: 192205 Sorted by model distance: nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.163 3.040 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.210 3.040 ... (remaining 192200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 633 through 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' 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' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 25.110 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26037 Z= 0.190 Angle : 0.639 9.458 35594 Z= 0.308 Chirality : 0.047 0.325 4249 Planarity : 0.003 0.047 4455 Dihedral : 13.584 88.960 8858 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.15), residues: 3047 helix: 2.08 (0.21), residues: 675 sheet: 0.60 (0.19), residues: 731 loop : -1.16 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 981 TYR 0.014 0.001 TYR A1065 PHE 0.015 0.001 PHE C 140 TRP 0.012 0.001 TRP B 884 HIS 0.002 0.000 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (25913) covalent geometry : angle 0.61132 / 0.30 (35262) SS BOND : bond 0.00398 / 0.30 ( 40) SS BOND : angle 1.67209 / 1.16 ( 80) hydrogen bonds : bond 0.11912 / 8.07 ( 994) hydrogen bonds : angle 5.65829 / 3.87 ( 2757) link_BETA1-4 : bond 0.00409 / 0.29 ( 36) link_BETA1-4 : angle 2.20889 / 1.42 ( 108) link_NAG-ASN : bond 0.00235 / 0.17 ( 48) link_NAG-ASN : angle 2.02909 / 1.29 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.023 Fit side-chains REVERT: A 345 PHE cc_start: 0.7842 (m-10) cc_final: 0.7561 (m-10) REVERT: B 400 ILE cc_start: 0.8975 (mm) cc_final: 0.8764 (pp) REVERT: B 1027 MET cc_start: 0.8959 (tpp) cc_final: 0.8204 (tpp) outliers start: 0 outliers final: 2 residues processed: 83 average time/residue: 0.5235 time to fit residues: 52.7251 Evaluate side-chains 58 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 237 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.076892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045521 restraints weight = 86820.594| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 4.20 r_work: 0.2617 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 26037 Z= 0.318 Angle : 0.714 9.478 35594 Z= 0.358 Chirality : 0.048 0.233 4249 Planarity : 0.004 0.047 4455 Dihedral : 4.726 30.998 3323 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 0.70 % Allowed : 6.06 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3047 helix: 1.86 (0.21), residues: 675 sheet: 0.35 (0.19), residues: 713 loop : -1.22 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1037 TYR 0.017 0.001 TYR B 394 PHE 0.029 0.002 PHE C 904 TRP 0.016 0.002 TRP A 434 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.32 (25913) covalent geometry : angle 0.69093 / 0.35 (35262) SS BOND : bond 0.00562 / 0.42 ( 40) SS BOND : angle 2.08087 / 1.43 ( 80) hydrogen bonds : bond 0.07561 / 5.05 ( 994) hydrogen bonds : angle 5.32981 / 3.62 ( 2757) link_BETA1-4 : bond 0.00318 / 0.21 ( 36) link_BETA1-4 : angle 1.92733 / 1.24 ( 108) link_NAG-ASN : bond 0.00435 / 0.25 ( 48) link_NAG-ASN : angle 1.99895 / 1.31 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.836 Fit side-chains REVERT: B 400 ILE cc_start: 0.9072 (mm) cc_final: 0.8695 (pp) REVERT: C 1000 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8212 (tm-30) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.5243 time to fit residues: 44.1293 Evaluate side-chains 61 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 105 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 286 optimal weight: 0.8980 chunk 307 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 221 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 GLN B 953 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.079001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048094 restraints weight = 85402.704| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 4.15 r_work: 0.2694 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26037 Z= 0.117 Angle : 0.579 9.342 35594 Z= 0.289 Chirality : 0.045 0.253 4249 Planarity : 0.004 0.052 4455 Dihedral : 4.240 23.839 3319 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.64 % Favored : 96.26 % Rotamer: Outliers : 0.96 % Allowed : 8.53 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3047 helix: 2.20 (0.21), residues: 667 sheet: 0.64 (0.19), residues: 717 loop : -1.09 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.015 0.001 TYR B 447 PHE 0.018 0.001 PHE C 140 TRP 0.009 0.001 TRP A 434 HIS 0.002 0.000 HIS C1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (25913) covalent geometry : angle 0.55837 / 0.28 (35262) SS BOND : bond 0.00404 / 0.30 ( 40) SS BOND : angle 1.51125 / 1.07 ( 80) hydrogen bonds : bond 0.05724 / 3.86 ( 994) hydrogen bonds : angle 4.91192 / 3.34 ( 2757) link_BETA1-4 : bond 0.00481 / 0.33 ( 36) link_BETA1-4 : angle 1.86924 / 1.20 ( 108) link_NAG-ASN : bond 0.00274 / 0.19 ( 48) link_NAG-ASN : angle 1.65946 / 1.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.821 Fit side-chains revert: symmetry clash REVERT: B 400 ILE cc_start: 0.8991 (mm) cc_final: 0.8628 (pp) REVERT: B 516 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6957 (tm) REVERT: C 1000 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7925 (tm-30) outliers start: 26 outliers final: 11 residues processed: 82 average time/residue: 0.4900 time to fit residues: 49.2110 Evaluate side-chains 68 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 154 optimal weight: 0.8980 chunk 237 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 167 optimal weight: 0.9990 chunk 96 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 31 optimal weight: 10.0000 chunk 199 optimal weight: 0.9990 chunk 159 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.079202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.048397 restraints weight = 85246.180| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 4.09 r_work: 0.2700 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26037 Z= 0.115 Angle : 0.559 9.516 35594 Z= 0.277 Chirality : 0.044 0.247 4249 Planarity : 0.004 0.053 4455 Dihedral : 4.057 23.556 3319 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.22 % Allowed : 10.38 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.15), residues: 3047 helix: 2.33 (0.21), residues: 666 sheet: 0.76 (0.19), residues: 692 loop : -1.05 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.015 0.001 TYR C1065 PHE 0.018 0.001 PHE A 390 TRP 0.008 0.001 TRP C 434 HIS 0.002 0.000 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (25913) covalent geometry : angle 0.53857 / 0.27 (35262) SS BOND : bond 0.00397 / 0.29 ( 40) SS BOND : angle 1.39412 / 0.98 ( 80) hydrogen bonds : bond 0.05328 / 3.59 ( 994) hydrogen bonds : angle 4.72749 / 3.21 ( 2757) link_BETA1-4 : bond 0.00393 / 0.27 ( 36) link_BETA1-4 : angle 1.82719 / 1.18 ( 108) link_NAG-ASN : bond 0.00209 / 0.14 ( 48) link_NAG-ASN : angle 1.64672 / 1.08 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.967 Fit side-chains REVERT: A 363 TYR cc_start: 0.7671 (m-80) cc_final: 0.7452 (m-80) REVERT: A 982 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8372 (pp) REVERT: B 400 ILE cc_start: 0.8991 (mm) cc_final: 0.8627 (pp) REVERT: C 1000 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7780 (tm-30) outliers start: 33 outliers final: 14 residues processed: 86 average time/residue: 0.4402 time to fit residues: 47.1572 Evaluate side-chains 69 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8212 > 50: distance: 30 - 32: 27.101 distance: 32 - 33: 36.326 distance: 33 - 34: 13.702 distance: 33 - 36: 49.809 distance: 34 - 35: 15.031 distance: 34 - 40: 23.776 distance: 36 - 37: 43.139 distance: 36 - 38: 22.631 distance: 37 - 39: 38.587 distance: 40 - 41: 51.445 distance: 41 - 42: 18.761 distance: 41 - 44: 28.083 distance: 42 - 43: 12.408 distance: 42 - 52: 42.839 distance: 44 - 45: 39.832 distance: 45 - 46: 38.832 distance: 45 - 47: 56.963 distance: 46 - 48: 38.784 distance: 47 - 49: 36.946 distance: 48 - 50: 37.187 distance: 49 - 50: 24.648 distance: 50 - 51: 21.892 distance: 52 - 53: 40.947 distance: 53 - 54: 34.066 distance: 54 - 55: 40.775 distance: 54 - 61: 35.408 distance: 57 - 58: 40.679 distance: 58 - 59: 6.910 distance: 58 - 60: 37.950 distance: 61 - 62: 18.471 distance: 62 - 63: 27.262 distance: 62 - 65: 40.946 distance: 63 - 64: 22.136 distance: 63 - 68: 50.070 distance: 65 - 66: 28.416 distance: 65 - 67: 27.409 distance: 68 - 69: 11.325 distance: 69 - 70: 19.360 distance: 69 - 72: 23.285 distance: 70 - 71: 11.397 distance: 70 - 74: 9.682 distance: 71 - 156: 19.571 distance: 72 - 73: 29.022 distance: 74 - 75: 20.178 distance: 75 - 76: 11.985 distance: 75 - 78: 12.304 distance: 76 - 77: 11.850 distance: 76 - 82: 12.935 distance: 78 - 79: 7.002 distance: 79 - 80: 16.139 distance: 79 - 81: 5.256 distance: 82 - 83: 9.262 distance: 82 - 151: 14.218 distance: 83 - 84: 24.091 distance: 83 - 86: 11.506 distance: 84 - 85: 12.660 distance: 84 - 93: 55.610 distance: 85 - 148: 34.579 distance: 86 - 87: 11.457 distance: 87 - 88: 12.536 distance: 87 - 89: 11.597 distance: 88 - 90: 11.114 distance: 89 - 91: 7.351 distance: 90 - 92: 5.005 distance: 93 - 94: 18.286 distance: 94 - 95: 9.885 distance: 94 - 97: 4.720 distance: 95 - 96: 8.931 distance: 95 - 104: 6.591 distance: 97 - 98: 12.912 distance: 98 - 99: 5.967 distance: 99 - 100: 3.778 distance: 100 - 101: 13.170 distance: 101 - 102: 15.298 distance: 101 - 103: 26.133 distance: 104 - 105: 23.243 distance: 105 - 106: 34.438 distance: 105 - 108: 39.938 distance: 106 - 107: 4.624 distance: 106 - 111: 37.018 distance: 111 - 112: 32.313 distance: 112 - 113: 34.661 distance: 112 - 115: 41.711 distance: 113 - 114: 40.916 distance: 113 - 120: 33.839 distance: 115 - 116: 9.117 distance: 116 - 117: 41.817 distance: 117 - 118: 26.972 distance: 117 - 119: 28.758