Starting phenix.real_space_refine on Mon Jul 6 12:28:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v85_31790/07_2026/7v85_31790.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.040 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 169 5.16 5 C 22353 2.51 5 N 5738 2.21 5 O 6841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s 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: 35101 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "H" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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 Time building chain proxies: 7.70, per 1000 atoms: 0.22 Number of scatterers: 35101 At special positions: 0 Unit cell: (177.1, 158.4, 240.9, 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 169 16.00 O 6841 8.00 N 5738 7.00 C 22353 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS H 133 " - pdb=" SG CYS H 141 " distance=2.02 Simple disulfide: pdb=" SG CYS H 344 " - pdb=" SG CYS H 361 " distance=2.03 Simple disulfide: pdb=" SG CYS H 530 " - pdb=" SG CYS H 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 234 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 603 " " NAG B2004 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 234 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG G 1 " - " ASN A 282 " " NAG I 1 " - " ASN A 331 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 282 " " NAG T 1 " - " ASN B 331 " " NAG U 1 " - " ASN B 616 " " NAG V 1 " - " ASN B 709 " " NAG W 1 " - " ASN B 717 " " NAG X 1 " - " ASN B 801 " " NAG Y 1 " - " ASN B1074 " " NAG Z 1 " - " ASN B1098 " " NAG a 1 " - " ASN B1134 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 282 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Time building additional restraints: 3.30 Conformation dependent library (CDL) restraints added in 1.1 seconds 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8088 Finding SS restraints... Secondary structure from input PDB file: 115 helices and 52 sheets defined 34.8% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.750A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.520A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.983A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.604A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.550A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.808A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.611A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.952A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.244A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.590A pdb=" N ASN B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 383 through 387 removed outlier: 4.158A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.944A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.092A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 783 Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.501A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.205A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 removed outlier: 3.662A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.137A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.617A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.197A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.671A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 742 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.023A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.929A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.706A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.297A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.870A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.656A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TRP F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 101 removed outlier: 3.646A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 157 through 171 removed outlier: 3.573A pdb=" N ARG F 161 " --> pdb=" O ASP F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 Processing helix chain 'F' and resid 221 through 231 removed outlier: 3.749A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 removed outlier: 3.931A pdb=" N ASN F 250 " --> pdb=" O ALA F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 281 removed outlier: 4.199A pdb=" N SER F 280 " --> pdb=" O ASN F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.641A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.207A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 3.588A pdb=" N GLU F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.477A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.736A pdb=" N TRP F 477 " --> pdb=" O TRP F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 532 removed outlier: 4.549A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.596A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.948A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 4.018A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN F 599 " --> pdb=" O LEU F 595 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 53 removed outlier: 3.740A pdb=" N HIS H 34 " --> pdb=" O ASP H 30 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP H 38 " --> pdb=" O HIS H 34 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU H 39 " --> pdb=" O GLU H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 80 removed outlier: 3.556A pdb=" N VAL H 59 " --> pdb=" O THR H 55 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TRP H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER H 70 " --> pdb=" O GLY H 66 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 101 removed outlier: 4.004A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 129 Processing helix chain 'H' and resid 147 through 154 Processing helix chain 'H' and resid 157 through 172 removed outlier: 3.999A pdb=" N ARG H 161 " --> pdb=" O ASP H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 194 removed outlier: 4.517A pdb=" N LEU H 179 " --> pdb=" O GLN H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 205 Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'H' and resid 220 through 231 removed outlier: 3.939A pdb=" N GLU H 224 " --> pdb=" O GLY H 220 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 251 Processing helix chain 'H' and resid 279 through 283 removed outlier: 3.742A pdb=" N VAL H 283 " --> pdb=" O SER H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 301 Processing helix chain 'H' and resid 303 through 319 Processing helix chain 'H' and resid 326 through 331 removed outlier: 3.629A pdb=" N SER H 331 " --> pdb=" O PHE H 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 385 removed outlier: 3.558A pdb=" N TYR H 385 " --> pdb=" O TYR H 381 " (cutoff:3.500A) Processing helix chain 'H' and resid 389 through 393 removed outlier: 3.573A pdb=" N ARG H 393 " --> pdb=" O PHE H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 398 through 412 removed outlier: 4.514A pdb=" N GLU H 402 " --> pdb=" O GLU H 398 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N MET H 408 " --> pdb=" O VAL H 404 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER H 409 " --> pdb=" O GLY H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 421 removed outlier: 3.628A pdb=" N LEU H 418 " --> pdb=" O THR H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 447 removed outlier: 3.510A pdb=" N GLU H 435 " --> pdb=" O ASP H 431 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR H 445 " --> pdb=" O LYS H 441 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 466 Processing helix chain 'H' and resid 473 through 484 Processing helix chain 'H' and resid 503 through 508 Processing helix chain 'H' and resid 512 through 532 removed outlier: 3.809A pdb=" N TYR H 516 " --> pdb=" O PHE H 512 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU H 520 " --> pdb=" O TYR H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 538 through 542 Processing helix chain 'H' and resid 547 through 559 Processing helix chain 'H' and resid 560 through 564 removed outlier: 4.224A pdb=" N GLU H 564 " --> pdb=" O GLY H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 570 Processing helix chain 'H' and resid 581 through 588 removed outlier: 3.591A pdb=" N LEU H 585 " --> pdb=" O VAL H 581 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 588 " --> pdb=" O LEU H 584 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 599 removed outlier: 3.501A pdb=" N PHE H 592 " --> pdb=" O PHE H 588 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP H 597 " --> pdb=" O THR H 593 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASN H 599 " --> pdb=" O LEU H 595 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.205A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.917A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.523A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 105 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 9.238A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.552A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.685A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 removed outlier: 5.450A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 7.428A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.927A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 660 removed outlier: 5.994A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N VAL A 656 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.407A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 789 removed outlier: 5.662A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.912A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.896A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.848A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.885A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.711A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 143 through 144 removed outlier: 6.149A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.409A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 5.022A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.592A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.680A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.008A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.535A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.397A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.489A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.768A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.556A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.805A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.899A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.783A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.282A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 134 through 135 Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.291A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.922A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE8, first strand: chain 'C' and resid 566 through 567 removed outlier: 6.648A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 654 through 660 removed outlier: 6.123A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.549A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.487A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 3.557A pdb=" N SER C1123 " --> pdb=" O ALA C1087 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1094 through 1096 Processing sheet with id=AF5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 350 Processing sheet with id=AF7, first strand: chain 'H' and resid 347 through 349 1466 hydrogen bonds defined for protein. 4098 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: 8.28 Time building geometry restraints manager: 4.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10922 1.34 - 1.46: 7345 1.46 - 1.58: 17427 1.58 - 1.70: 1 1.70 - 1.82: 238 Bond restraints: 35933 Sorted by residual: bond pdb=" CB PRO B 26 " pdb=" CG PRO B 26 " ideal model delta sigma weight residual 1.492 1.610 -0.118 5.00e-02 4.00e+02 5.55e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.361 0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C1 NAG h 1 " pdb=" O5 NAG h 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00 bond pdb=" C CYS B 617 " pdb=" N THR B 618 " ideal model delta sigma weight residual 1.332 1.304 0.029 1.40e-02 5.10e+03 4.24e+00 bond pdb=" C1 NAG Y 1 " pdb=" C2 NAG Y 1 " ideal model delta sigma weight residual 1.532 1.494 0.038 2.00e-02 2.50e+03 3.56e+00 ... (remaining 35928 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 48378 2.61 - 5.22: 459 5.22 - 7.83: 39 7.83 - 10.44: 5 10.44 - 13.05: 1 Bond angle restraints: 48882 Sorted by residual: angle pdb=" CA PRO B 26 " pdb=" N PRO B 26 " pdb=" CD PRO B 26 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" C GLN F 89 " pdb=" N ASN F 90 " pdb=" CA ASN F 90 " ideal model delta sigma weight residual 121.54 131.47 -9.93 1.91e+00 2.74e-01 2.70e+01 angle pdb=" N PRO B 26 " pdb=" CD PRO B 26 " pdb=" CG PRO B 26 " ideal model delta sigma weight residual 103.20 97.29 5.91 1.50e+00 4.44e-01 1.55e+01 angle pdb=" N GLN B1002 " pdb=" CA GLN B1002 " pdb=" CB GLN B1002 " ideal model delta sigma weight residual 110.12 115.62 -5.50 1.47e+00 4.63e-01 1.40e+01 angle pdb=" CA LEU A 560 " pdb=" CB LEU A 560 " pdb=" CG LEU A 560 " ideal model delta sigma weight residual 116.30 129.35 -13.05 3.50e+00 8.16e-02 1.39e+01 ... (remaining 48877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 18614 17.80 - 35.60: 1729 35.60 - 53.40: 287 53.40 - 71.19: 71 71.19 - 88.99: 42 Dihedral angle restraints: 20743 sinusoidal: 8178 harmonic: 12565 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual 93.00 179.77 -86.77 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 15 " pdb=" SG CYS B 15 " pdb=" SG CYS B 136 " pdb=" CB CYS B 136 " ideal model delta sinusoidal sigma weight residual 93.00 177.44 -84.44 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -168.16 82.16 1 1.00e+01 1.00e-02 8.29e+01 ... (remaining 20740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.214: 5634 0.214 - 0.427: 7 0.427 - 0.641: 1 0.641 - 0.854: 1 0.854 - 1.068: 2 Chirality restraints: 5645 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.85e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.39e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 165 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.36e+01 ... (remaining 5642 not shown) Planarity restraints: 6272 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 165 " -0.022 2.00e-02 2.50e+03 2.01e-02 5.06e+00 pdb=" CG ASN C 165 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN C 165 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN C 165 " 0.022 2.00e-02 2.50e+03 pdb=" C1 NAG C2002 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 89 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.27e+00 pdb=" C GLN F 89 " -0.036 2.00e-02 2.50e+03 pdb=" O GLN F 89 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN F 90 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.034 5.00e-02 4.00e+02 5.10e-02 4.16e+00 pdb=" N PRO A 986 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.028 5.00e-02 4.00e+02 ... (remaining 6269 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 816 2.67 - 3.23: 34785 3.23 - 3.78: 54627 3.78 - 4.34: 70860 4.34 - 4.90: 116349 Nonbonded interactions: 277437 Sorted by model distance: nonbonded pdb=" OE2 GLU B 725 " pdb=" NE2 HIS B1064 " model vdw 2.111 3.120 nonbonded pdb=" O GLU C 661 " pdb=" OH TYR C 695 " model vdw 2.135 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.136 3.040 nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.139 3.040 nonbonded pdb=" O TYR H 215 " pdb=" OG1 THR H 567 " model vdw 2.144 3.040 ... (remaining 277432 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' selection = (chain 'C' and resid 14 through 2004) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' 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' } ncs_group { reference = chain 'F' selection = chain 'H' } 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: 4.540 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: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 32.980 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 36052 Z= 0.233 Angle : 0.700 16.500 49195 Z= 0.349 Chirality : 0.052 1.068 5645 Planarity : 0.004 0.051 6228 Dihedral : 14.323 88.993 12523 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.75 % Favored : 93.16 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % 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: -0.87 (0.13), residues: 4254 helix: 1.12 (0.14), residues: 1334 sheet: -0.34 (0.19), residues: 728 loop : -1.82 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.016 0.001 TYR C1067 PHE 0.032 0.001 PHE B 906 TRP 0.033 0.001 TRP F 271 HIS 0.006 0.001 HIS F 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.23 (35933) covalent geometry : angle 0.66454 / 0.34 (48882) SS BOND : bond 0.00337 / 0.24 ( 44) SS BOND : angle 1.41137 / 1.04 ( 88) hydrogen bonds : bond 0.12954 / 8.34 ( 1450) hydrogen bonds : angle 6.11755 / 4.22 ( 4098) link_BETA1-4 : bond 0.00394 / 0.24 ( 31) link_BETA1-4 : angle 2.20657 / 1.43 ( 93) link_NAG-ASN : bond 0.00475 / 0.33 ( 44) link_NAG-ASN : angle 3.80830 / 2.45 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 323 MET cc_start: 0.2961 (ptm) cc_final: 0.2534 (ptt) REVERT: F 376 MET cc_start: -0.2848 (tpp) cc_final: -0.3384 (mmt) REVERT: H 190 MET cc_start: 0.0384 (mmp) cc_final: -0.0583 (tmm) REVERT: H 213 ASP cc_start: 0.6226 (m-30) cc_final: 0.5846 (t70) REVERT: H 360 MET cc_start: 0.0268 (tpp) cc_final: -0.0325 (mtp) REVERT: H 455 MET cc_start: 0.0396 (ppp) cc_final: 0.0103 (ttp) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1879 time to fit residues: 43.8831 Evaluate side-chains 93 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 0.2980 chunk 155 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 17 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 914 ASN C 919 ASN F 63 ASN F 98 GLN ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.115536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.073817 restraints weight = 164097.324| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 7.38 r_work: 0.2995 rms_B_bonded: 6.47 restraints_weight: 2.0000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 36052 Z= 0.121 Angle : 0.601 14.931 49195 Z= 0.300 Chirality : 0.046 0.529 5645 Planarity : 0.004 0.053 6228 Dihedral : 4.421 27.620 4621 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.62 % Favored : 94.31 % Rotamer: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % 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: -0.62 (0.13), residues: 4254 helix: 1.30 (0.14), residues: 1368 sheet: -0.09 (0.19), residues: 727 loop : -1.73 (0.13), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 457 TYR 0.022 0.001 TYR C 421 PHE 0.016 0.001 PHE C1121 TRP 0.017 0.001 TRP F 477 HIS 0.006 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (35933) covalent geometry : angle 0.57520 / 0.29 (48882) SS BOND : bond 0.00294 / 0.21 ( 44) SS BOND : angle 1.28393 / 0.91 ( 88) hydrogen bonds : bond 0.04588 / 3.04 ( 1450) hydrogen bonds : angle 5.05203 / 3.52 ( 4098) link_BETA1-4 : bond 0.00480 / 0.30 ( 31) link_BETA1-4 : angle 1.56813 / 1.04 ( 93) link_NAG-ASN : bond 0.00432 / 0.31 ( 44) link_NAG-ASN : angle 3.05164 / 1.99 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7598 (ppp) cc_final: 0.7394 (ppp) REVERT: A 775 ASP cc_start: 0.9218 (t0) cc_final: 0.8742 (m-30) REVERT: B 117 LEU cc_start: 0.9467 (mp) cc_final: 0.9209 (tp) REVERT: B 869 MET cc_start: 0.9132 (mtt) cc_final: 0.8813 (mtt) REVERT: B 1010 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9175 (mp10) REVERT: B 1111 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8503 (tm-30) REVERT: C 725 GLU cc_start: 0.8550 (tt0) cc_final: 0.8318 (tt0) REVERT: F 323 MET cc_start: 0.2627 (ptm) cc_final: 0.2229 (ptt) REVERT: F 376 MET cc_start: -0.2565 (tpp) cc_final: -0.3400 (tpt) REVERT: F 462 MET cc_start: 0.5349 (ptp) cc_final: 0.5101 (ptt) REVERT: H 152 MET cc_start: -0.4064 (ptm) cc_final: -0.4564 (ppp) REVERT: H 190 MET cc_start: 0.0734 (mmp) cc_final: -0.0158 (tmm) REVERT: H 213 ASP cc_start: 0.6313 (m-30) cc_final: 0.5941 (t70) REVERT: H 455 MET cc_start: 0.0436 (ppp) cc_final: -0.0052 (ttp) outliers start: 5 outliers final: 4 residues processed: 117 average time/residue: 0.1925 time to fit residues: 39.2936 Evaluate side-chains 99 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 491 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 159 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 206 optimal weight: 30.0000 chunk 129 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 chunk 112 optimal weight: 7.9990 chunk 229 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 345 optimal weight: 50.0000 chunk 287 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 607 GLN A1005 GLN A1036 GLN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN C 321 GLN C 487 ASN C 762 GLN C1048 HIS ** F 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.113631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.071480 restraints weight = 166850.781| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 9.93 r_work: 0.2927 rms_B_bonded: 5.84 restraints_weight: 2.0000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 36052 Z= 0.207 Angle : 0.635 14.139 49195 Z= 0.316 Chirality : 0.046 0.462 5645 Planarity : 0.004 0.055 6228 Dihedral : 4.484 28.353 4621 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 0.85 % Allowed : 9.09 % Favored : 90.06 % 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: -0.74 (0.13), residues: 4254 helix: 1.24 (0.14), residues: 1370 sheet: -0.25 (0.19), residues: 708 loop : -1.79 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.020 0.001 TYR C1067 PHE 0.029 0.002 PHE C1121 TRP 0.021 0.001 TRP H 610 HIS 0.008 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (35933) covalent geometry : angle 0.61035 / 0.31 (48882) SS BOND : bond 0.00315 / 0.24 ( 44) SS BOND : angle 1.41124 / 0.97 ( 88) hydrogen bonds : bond 0.04622 / 3.08 ( 1450) hydrogen bonds : angle 5.05781 / 3.52 ( 4098) link_BETA1-4 : bond 0.00310 / 0.19 ( 31) link_BETA1-4 : angle 1.46889 / 1.00 ( 93) link_NAG-ASN : bond 0.00378 / 0.26 ( 44) link_NAG-ASN : angle 3.04031 / 2.03 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 873 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.8477 (m-80) REVERT: B 117 LEU cc_start: 0.9482 (mp) cc_final: 0.9276 (tp) REVERT: B 869 MET cc_start: 0.9169 (mtt) cc_final: 0.8859 (mtt) REVERT: B 1010 GLN cc_start: 0.9436 (mm-40) cc_final: 0.9196 (mm-40) REVERT: B 1111 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 298 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: C 1029 MET cc_start: 0.9052 (tpp) cc_final: 0.8810 (tpp) REVERT: C 1050 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8638 (ptt) REVERT: F 323 MET cc_start: 0.3178 (ptm) cc_final: 0.2944 (ptt) REVERT: F 477 TRP cc_start: -0.4375 (OUTLIER) cc_final: -0.4660 (t-100) REVERT: H 152 MET cc_start: -0.5327 (ptm) cc_final: -0.5563 (ppp) REVERT: H 190 MET cc_start: 0.0264 (mmp) cc_final: -0.0765 (tmm) REVERT: H 213 ASP cc_start: 0.6114 (m-30) cc_final: 0.5684 (t70) REVERT: H 360 MET cc_start: -0.0831 (mtp) cc_final: -0.1284 (mtt) REVERT: H 455 MET cc_start: 0.0344 (ppp) cc_final: 0.0053 (ttp) outliers start: 32 outliers final: 15 residues processed: 124 average time/residue: 0.1745 time to fit residues: 38.5451 Evaluate side-chains 111 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 477 TRP Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 227 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 412 optimal weight: 20.0000 chunk 76 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 408 optimal weight: 0.4980 chunk 405 optimal weight: 50.0000 chunk 218 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 346 optimal weight: 40.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 751 ASN ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** F 540 HIS ** 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 = 0.4407 r_free = 0.4407 target = 0.114634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.072405 restraints weight = 162569.404| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 7.56 r_work: 0.3001 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 36052 Z= 0.119 Angle : 0.562 13.289 49195 Z= 0.279 Chirality : 0.044 0.450 5645 Planarity : 0.004 0.057 6228 Dihedral : 4.219 27.311 4621 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 1.09 % Allowed : 10.47 % Favored : 88.44 % 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: -0.53 (0.13), residues: 4254 helix: 1.44 (0.14), residues: 1364 sheet: -0.02 (0.19), residues: 720 loop : -1.73 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 408 TYR 0.017 0.001 TYR C1067 PHE 0.016 0.001 PHE C1121 TRP 0.022 0.001 TRP H 610 HIS 0.013 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (35933) covalent geometry : angle 0.53979 / 0.27 (48882) SS BOND : bond 0.00387 / 0.27 ( 44) SS BOND : angle 1.13201 / 0.78 ( 88) hydrogen bonds : bond 0.04032 / 2.68 ( 1450) hydrogen bonds : angle 4.78115 / 3.33 ( 4098) link_BETA1-4 : bond 0.00364 / 0.23 ( 31) link_BETA1-4 : angle 1.30707 / 0.88 ( 93) link_NAG-ASN : bond 0.00347 / 0.26 ( 44) link_NAG-ASN : angle 2.78735 / 1.87 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 100 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9490 (OUTLIER) cc_final: 0.9072 (pm20) REVERT: A 775 ASP cc_start: 0.9116 (t0) cc_final: 0.8660 (m-30) REVERT: B 117 LEU cc_start: 0.9485 (mp) cc_final: 0.9230 (tp) REVERT: B 120 VAL cc_start: 0.9177 (OUTLIER) cc_final: 0.8974 (p) REVERT: B 200 TYR cc_start: 0.9491 (m-80) cc_final: 0.9236 (t80) REVERT: B 229 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9154 (mm) REVERT: B 869 MET cc_start: 0.9208 (mtt) cc_final: 0.8828 (mtt) REVERT: B 1010 GLN cc_start: 0.9445 (mm-40) cc_final: 0.9214 (mm-40) REVERT: B 1111 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8556 (tm-30) REVERT: C 298 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: C 725 GLU cc_start: 0.8370 (tt0) cc_final: 0.8159 (tt0) REVERT: C 1005 GLN cc_start: 0.9313 (tp40) cc_final: 0.9049 (tp-100) REVERT: F 323 MET cc_start: 0.2473 (ptm) cc_final: 0.1890 (ptt) REVERT: F 376 MET cc_start: -0.3197 (tpp) cc_final: -0.4090 (tpt) REVERT: F 408 MET cc_start: 0.0697 (mtp) cc_final: 0.0232 (ppp) REVERT: H 190 MET cc_start: 0.0347 (mmp) cc_final: -0.0676 (tmm) REVERT: H 213 ASP cc_start: 0.6131 (m-30) cc_final: 0.5740 (t70) REVERT: H 360 MET cc_start: -0.0812 (mtp) cc_final: -0.1244 (mtt) REVERT: H 455 MET cc_start: 0.0449 (ppp) cc_final: 0.0174 (ttp) REVERT: H 480 MET cc_start: 0.2591 (ptt) cc_final: 0.2258 (ptt) outliers start: 41 outliers final: 22 residues processed: 132 average time/residue: 0.1783 time to fit residues: 42.2090 Evaluate side-chains 120 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 427 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 233 optimal weight: 4.9990 chunk 373 optimal weight: 20.0000 chunk 381 optimal weight: 50.0000 chunk 425 optimal weight: 30.0000 chunk 164 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 250 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN C 394 ASN F 137 ASN F 524 GLN H 340 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.113308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.073958 restraints weight = 166132.828| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 8.11 r_work: 0.2889 rms_B_bonded: 7.32 restraints_weight: 2.0000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36052 Z= 0.213 Angle : 0.625 13.438 49195 Z= 0.311 Chirality : 0.046 0.450 5645 Planarity : 0.004 0.058 6228 Dihedral : 4.349 27.964 4621 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.23 % Favored : 93.70 % Rotamer: Outliers : 1.86 % Allowed : 11.82 % Favored : 86.32 % 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: -0.69 (0.13), residues: 4254 helix: 1.32 (0.14), residues: 1364 sheet: -0.20 (0.19), residues: 699 loop : -1.78 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.021 0.001 TYR C1067 PHE 0.028 0.001 PHE C1121 TRP 0.027 0.001 TRP H 610 HIS 0.013 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.21 (35933) covalent geometry : angle 0.60335 / 0.31 (48882) SS BOND : bond 0.00326 / 0.24 ( 44) SS BOND : angle 1.43154 / 1.00 ( 88) hydrogen bonds : bond 0.04395 / 2.94 ( 1450) hydrogen bonds : angle 4.92551 / 3.43 ( 4098) link_BETA1-4 : bond 0.00316 / 0.20 ( 31) link_BETA1-4 : angle 1.40448 / 0.95 ( 93) link_NAG-ASN : bond 0.00362 / 0.25 ( 44) link_NAG-ASN : angle 2.86782 / 1.92 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 95 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9543 (OUTLIER) cc_final: 0.9125 (pm20) REVERT: A 873 TYR cc_start: 0.9053 (OUTLIER) cc_final: 0.8481 (m-80) REVERT: B 117 LEU cc_start: 0.9507 (mp) cc_final: 0.9224 (tp) REVERT: B 120 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8914 (p) REVERT: B 200 TYR cc_start: 0.9593 (m-80) cc_final: 0.9359 (t80) REVERT: B 229 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9192 (mm) REVERT: B 298 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7655 (pm20) REVERT: B 544 ASN cc_start: 0.9234 (OUTLIER) cc_final: 0.8736 (m110) REVERT: B 869 MET cc_start: 0.9230 (mtt) cc_final: 0.8874 (mtt) REVERT: B 1010 GLN cc_start: 0.9491 (mm-40) cc_final: 0.9261 (mm-40) REVERT: B 1111 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8612 (tm-30) REVERT: C 298 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: C 1029 MET cc_start: 0.9139 (tpp) cc_final: 0.8882 (tpp) REVERT: H 190 MET cc_start: 0.0093 (mmp) cc_final: -0.0874 (tmm) REVERT: H 213 ASP cc_start: 0.6133 (m-30) cc_final: 0.5745 (t70) REVERT: H 360 MET cc_start: -0.0072 (mtp) cc_final: -0.0596 (mtp) REVERT: H 455 MET cc_start: 0.0681 (ppp) cc_final: 0.0313 (ttp) REVERT: H 480 MET cc_start: 0.4040 (ptt) cc_final: 0.3570 (ptt) outliers start: 70 outliers final: 39 residues processed: 156 average time/residue: 0.1737 time to fit residues: 48.5992 Evaluate side-chains 138 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 92 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 283 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 169 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 151 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 35 optimal weight: 8.9990 chunk 325 optimal weight: 20.0000 chunk 297 optimal weight: 4.9990 chunk 281 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1048 HIS ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN C 804 GLN F 137 ASN H 96 GLN H 572 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.113012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070648 restraints weight = 165686.662| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 9.43 r_work: 0.2865 rms_B_bonded: 6.64 restraints_weight: 2.0000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 36052 Z= 0.221 Angle : 0.628 13.276 49195 Z= 0.313 Chirality : 0.046 0.457 5645 Planarity : 0.004 0.060 6228 Dihedral : 4.410 27.140 4621 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.28 % Favored : 93.65 % Rotamer: Outliers : 1.99 % Allowed : 12.72 % Favored : 85.29 % 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: -0.78 (0.13), residues: 4254 helix: 1.27 (0.14), residues: 1367 sheet: -0.50 (0.19), residues: 699 loop : -1.77 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 319 TYR 0.024 0.001 TYR F 243 PHE 0.027 0.001 PHE C1121 TRP 0.033 0.001 TRP H 610 HIS 0.014 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.22 (35933) covalent geometry : angle 0.60709 / 0.31 (48882) SS BOND : bond 0.00322 / 0.23 ( 44) SS BOND : angle 1.44899 / 1.02 ( 88) hydrogen bonds : bond 0.04389 / 2.94 ( 1450) hydrogen bonds : angle 4.94256 / 3.44 ( 4098) link_BETA1-4 : bond 0.00271 / 0.18 ( 31) link_BETA1-4 : angle 1.36829 / 0.91 ( 93) link_NAG-ASN : bond 0.00333 / 0.23 ( 44) link_NAG-ASN : angle 2.82734 / 1.91 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 92 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9566 (OUTLIER) cc_final: 0.9152 (pm20) REVERT: A 873 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8429 (m-80) REVERT: A 984 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8804 (tt) REVERT: B 117 LEU cc_start: 0.9500 (mp) cc_final: 0.9261 (tp) REVERT: B 200 TYR cc_start: 0.9680 (m-80) cc_final: 0.9439 (t80) REVERT: B 229 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9149 (mm) REVERT: B 298 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: B 869 MET cc_start: 0.9197 (mtt) cc_final: 0.8795 (mtt) REVERT: B 1010 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9252 (mm-40) REVERT: B 1111 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8562 (tm-30) REVERT: C 298 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8215 (mp0) REVERT: C 517 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8175 (mp) REVERT: C 788 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 1029 MET cc_start: 0.9118 (tpp) cc_final: 0.8850 (tpp) REVERT: C 1072 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8639 (mp0) REVERT: H 152 MET cc_start: -0.0350 (ppp) cc_final: -0.0739 (ppp) REVERT: H 190 MET cc_start: 0.0118 (mmp) cc_final: -0.0873 (tmm) REVERT: H 213 ASP cc_start: 0.6239 (m-30) cc_final: 0.5866 (t70) REVERT: H 360 MET cc_start: 0.0174 (mtp) cc_final: -0.0432 (mtt) REVERT: H 455 MET cc_start: 0.0696 (ppp) cc_final: 0.0265 (ttp) REVERT: H 480 MET cc_start: 0.3947 (ptt) cc_final: 0.3538 (ptt) outliers start: 75 outliers final: 45 residues processed: 160 average time/residue: 0.1801 time to fit residues: 51.9065 Evaluate side-chains 143 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 89 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 40.0000 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 255 optimal weight: 0.7980 chunk 45 optimal weight: 20.0000 chunk 331 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 254 optimal weight: 3.9990 chunk 426 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 380 optimal weight: 30.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN F 137 ASN H 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.114005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.071375 restraints weight = 165869.918| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 8.40 r_work: 0.2937 rms_B_bonded: 6.46 restraints_weight: 2.0000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36052 Z= 0.130 Angle : 0.570 12.809 49195 Z= 0.282 Chirality : 0.044 0.446 5645 Planarity : 0.004 0.063 6228 Dihedral : 4.200 26.914 4621 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 1.67 % Allowed : 13.60 % Favored : 84.73 % 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: -0.55 (0.13), residues: 4254 helix: 1.49 (0.14), residues: 1361 sheet: -0.20 (0.19), residues: 727 loop : -1.71 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 408 TYR 0.018 0.001 TYR C1067 PHE 0.017 0.001 PHE C1121 TRP 0.031 0.001 TRP H 610 HIS 0.016 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (35933) covalent geometry : angle 0.54963 / 0.28 (48882) SS BOND : bond 0.00256 / 0.18 ( 44) SS BOND : angle 1.27418 / 0.91 ( 88) hydrogen bonds : bond 0.03961 / 2.65 ( 1450) hydrogen bonds : angle 4.73126 / 3.29 ( 4098) link_BETA1-4 : bond 0.00327 / 0.21 ( 31) link_BETA1-4 : angle 1.26615 / 0.84 ( 93) link_NAG-ASN : bond 0.00330 / 0.24 ( 44) link_NAG-ASN : angle 2.66225 / 1.80 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 95 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9559 (OUTLIER) cc_final: 0.9074 (pm20) REVERT: A 775 ASP cc_start: 0.9186 (t0) cc_final: 0.8695 (m-30) REVERT: A 873 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8384 (m-80) REVERT: A 984 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8862 (tt) REVERT: B 117 LEU cc_start: 0.9482 (mp) cc_final: 0.9223 (tp) REVERT: B 200 TYR cc_start: 0.9641 (m-80) cc_final: 0.9387 (t80) REVERT: B 298 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7574 (pm20) REVERT: B 544 ASN cc_start: 0.9178 (OUTLIER) cc_final: 0.8909 (m-40) REVERT: B 869 MET cc_start: 0.9269 (mtt) cc_final: 0.8874 (mtt) REVERT: B 1010 GLN cc_start: 0.9445 (mm-40) cc_final: 0.9200 (mm-40) REVERT: B 1111 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8509 (tm-30) REVERT: C 298 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: C 1005 GLN cc_start: 0.9372 (tp40) cc_final: 0.9111 (tp-100) REVERT: C 1029 MET cc_start: 0.9015 (tpp) cc_final: 0.8776 (tpp) REVERT: C 1050 MET cc_start: 0.8776 (ptm) cc_final: 0.8328 (ptt) REVERT: F 474 MET cc_start: -0.1395 (tpp) cc_final: -0.1867 (mmp) REVERT: H 152 MET cc_start: -0.2185 (ppp) cc_final: -0.2597 (ppp) REVERT: H 190 MET cc_start: -0.0193 (mmp) cc_final: -0.1128 (tmm) REVERT: H 213 ASP cc_start: 0.6073 (m-30) cc_final: 0.5617 (t70) REVERT: H 360 MET cc_start: 0.0222 (mtp) cc_final: -0.0486 (mtp) REVERT: H 455 MET cc_start: 0.0386 (ppp) cc_final: -0.0116 (ttp) REVERT: H 480 MET cc_start: 0.3610 (ptt) cc_final: 0.3145 (ptt) outliers start: 63 outliers final: 40 residues processed: 152 average time/residue: 0.1935 time to fit residues: 52.3482 Evaluate side-chains 136 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 90 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 201 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 379 optimal weight: 50.0000 chunk 21 optimal weight: 5.9990 chunk 129 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 289 optimal weight: 0.0030 chunk 82 optimal weight: 3.9990 chunk 213 optimal weight: 0.0570 chunk 208 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 overall best weight: 1.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 501 ASN B 501 ASN B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.114400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.071871 restraints weight = 163418.924| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 7.72 r_work: 0.2962 rms_B_bonded: 5.88 restraints_weight: 2.0000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 36052 Z= 0.107 Angle : 0.556 12.315 49195 Z= 0.274 Chirality : 0.044 0.432 5645 Planarity : 0.004 0.065 6228 Dihedral : 4.065 26.413 4621 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 1.46 % Allowed : 13.84 % Favored : 84.71 % 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: -0.41 (0.13), residues: 4254 helix: 1.58 (0.14), residues: 1361 sheet: -0.05 (0.19), residues: 717 loop : -1.64 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 408 TYR 0.016 0.001 TYR C1067 PHE 0.013 0.001 PHE C1121 TRP 0.035 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (35933) covalent geometry : angle 0.53681 / 0.27 (48882) SS BOND : bond 0.00237 / 0.17 ( 44) SS BOND : angle 1.15025 / 0.83 ( 88) hydrogen bonds : bond 0.03745 / 2.51 ( 1450) hydrogen bonds : angle 4.60518 / 3.21 ( 4098) link_BETA1-4 : bond 0.00350 / 0.22 ( 31) link_BETA1-4 : angle 1.23023 / 0.82 ( 93) link_NAG-ASN : bond 0.00358 / 0.26 ( 44) link_NAG-ASN : angle 2.55671 / 1.74 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 95 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9524 (OUTLIER) cc_final: 0.9019 (pm20) REVERT: A 775 ASP cc_start: 0.9148 (t0) cc_final: 0.8677 (m-30) REVERT: A 984 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8789 (tt) REVERT: B 200 TYR cc_start: 0.9651 (m-80) cc_final: 0.9400 (t80) REVERT: B 298 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: B 544 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8967 (m-40) REVERT: B 869 MET cc_start: 0.9244 (mtt) cc_final: 0.8886 (mtt) REVERT: B 900 MET cc_start: 0.8371 (mtt) cc_final: 0.8063 (mtp) REVERT: B 1010 GLN cc_start: 0.9441 (mm-40) cc_final: 0.9204 (mm-40) REVERT: B 1111 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8522 (tm-30) REVERT: C 298 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: C 517 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8069 (mp) REVERT: C 703 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8377 (p0) REVERT: C 1005 GLN cc_start: 0.9370 (tp40) cc_final: 0.9090 (tp-100) REVERT: C 1029 MET cc_start: 0.8998 (tpp) cc_final: 0.8763 (tpp) REVERT: C 1050 MET cc_start: 0.8708 (ptm) cc_final: 0.8329 (ptt) REVERT: F 474 MET cc_start: -0.1831 (tpp) cc_final: -0.2208 (mmp) REVERT: H 190 MET cc_start: -0.0102 (mmp) cc_final: -0.1076 (tmm) REVERT: H 213 ASP cc_start: 0.5953 (m-30) cc_final: 0.5474 (t70) REVERT: H 360 MET cc_start: 0.0157 (mtp) cc_final: -0.0542 (mtp) REVERT: H 455 MET cc_start: 0.0215 (ppp) cc_final: -0.0280 (ttp) REVERT: H 480 MET cc_start: 0.3299 (ptt) cc_final: 0.2865 (ptt) outliers start: 55 outliers final: 41 residues processed: 145 average time/residue: 0.1740 time to fit residues: 45.0278 Evaluate side-chains 142 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 315 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 402 optimal weight: 0.9980 chunk 266 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 363 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.113048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.071474 restraints weight = 165657.163| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 8.97 r_work: 0.2884 rms_B_bonded: 6.73 restraints_weight: 2.0000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 36052 Z= 0.212 Angle : 0.615 12.300 49195 Z= 0.305 Chirality : 0.045 0.434 5645 Planarity : 0.004 0.061 6228 Dihedral : 4.230 26.926 4621 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.18 % Favored : 93.75 % Rotamer: Outliers : 1.70 % Allowed : 13.91 % Favored : 84.39 % 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: -0.59 (0.13), residues: 4254 helix: 1.43 (0.14), residues: 1361 sheet: -0.24 (0.20), residues: 702 loop : -1.71 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.021 0.001 TYR C1067 PHE 0.027 0.001 PHE C1121 TRP 0.038 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (35933) covalent geometry : angle 0.59609 / 0.30 (48882) SS BOND : bond 0.00316 / 0.23 ( 44) SS BOND : angle 1.36496 / 0.96 ( 88) hydrogen bonds : bond 0.04197 / 2.81 ( 1450) hydrogen bonds : angle 4.79864 / 3.33 ( 4098) link_BETA1-4 : bond 0.00240 / 0.16 ( 31) link_BETA1-4 : angle 1.32958 / 0.89 ( 93) link_NAG-ASN : bond 0.00346 / 0.24 ( 44) link_NAG-ASN : angle 2.64576 / 1.80 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 90 time to evaluate : 1.372 Fit side-chains REVERT: A 762 GLN cc_start: 0.9570 (OUTLIER) cc_final: 0.9105 (pm20) REVERT: A 873 TYR cc_start: 0.9018 (OUTLIER) cc_final: 0.8459 (m-80) REVERT: A 984 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8848 (tt) REVERT: A 1029 MET cc_start: 0.9221 (tpp) cc_final: 0.8957 (tpp) REVERT: B 200 TYR cc_start: 0.9666 (m-80) cc_final: 0.9419 (t80) REVERT: B 298 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: B 869 MET cc_start: 0.9322 (mtt) cc_final: 0.8923 (mtt) REVERT: B 900 MET cc_start: 0.8453 (mtt) cc_final: 0.8175 (mtp) REVERT: B 936 ASP cc_start: 0.9667 (t0) cc_final: 0.9338 (m-30) REVERT: B 1010 GLN cc_start: 0.9517 (mm-40) cc_final: 0.9308 (mm-40) REVERT: B 1111 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8510 (tm-30) REVERT: C 298 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: C 517 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 1029 MET cc_start: 0.9116 (tpp) cc_final: 0.8841 (tpp) REVERT: F 474 MET cc_start: -0.1460 (tpp) cc_final: -0.1892 (mmp) REVERT: H 190 MET cc_start: -0.0471 (mmp) cc_final: -0.1447 (tmm) REVERT: H 360 MET cc_start: 0.0293 (mtp) cc_final: -0.0329 (mtt) REVERT: H 455 MET cc_start: 0.0228 (ppp) cc_final: -0.0149 (ttp) REVERT: H 480 MET cc_start: 0.3557 (ptt) cc_final: 0.3110 (ptt) outliers start: 64 outliers final: 50 residues processed: 146 average time/residue: 0.1890 time to fit residues: 49.5430 Evaluate side-chains 146 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 90 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 440 LEU Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 557 MET Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 220 optimal weight: 9.9990 chunk 405 optimal weight: 40.0000 chunk 36 optimal weight: 40.0000 chunk 125 optimal weight: 0.9990 chunk 379 optimal weight: 50.0000 chunk 127 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 262 optimal weight: 6.9990 chunk 235 optimal weight: 40.0000 chunk 131 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.112751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.071354 restraints weight = 166521.357| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 8.92 r_work: 0.2910 rms_B_bonded: 6.41 restraints_weight: 2.0000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 36052 Z= 0.222 Angle : 0.632 12.315 49195 Z= 0.314 Chirality : 0.046 0.444 5645 Planarity : 0.004 0.062 6228 Dihedral : 4.371 26.241 4621 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.37 % Favored : 93.56 % Rotamer: Outliers : 1.64 % Allowed : 14.15 % Favored : 84.20 % 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: -0.68 (0.13), residues: 4254 helix: 1.34 (0.14), residues: 1367 sheet: -0.28 (0.19), residues: 724 loop : -1.78 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 408 TYR 0.022 0.001 TYR C1067 PHE 0.027 0.001 PHE C1121 TRP 0.035 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (35933) covalent geometry : angle 0.61158 / 0.31 (48882) SS BOND : bond 0.00355 / 0.24 ( 44) SS BOND : angle 1.59234 / 1.08 ( 88) hydrogen bonds : bond 0.04347 / 2.91 ( 1450) hydrogen bonds : angle 4.88524 / 3.39 ( 4098) link_BETA1-4 : bond 0.00281 / 0.18 ( 31) link_BETA1-4 : angle 1.34261 / 0.89 ( 93) link_NAG-ASN : bond 0.00347 / 0.24 ( 44) link_NAG-ASN : angle 2.68874 / 1.83 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8508 Ramachandran restraints generated. 4254 Oldfield, 0 Emsley, 4254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 89 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 762 GLN cc_start: 0.9556 (OUTLIER) cc_final: 0.9099 (pm20) REVERT: A 873 TYR cc_start: 0.9006 (OUTLIER) cc_final: 0.8404 (m-80) REVERT: A 984 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8764 (tt) REVERT: A 1029 MET cc_start: 0.9241 (tpp) cc_final: 0.8979 (tpp) REVERT: B 200 TYR cc_start: 0.9566 (m-80) cc_final: 0.9291 (t80) REVERT: B 298 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: B 544 ASN cc_start: 0.9268 (OUTLIER) cc_final: 0.8972 (m-40) REVERT: B 869 MET cc_start: 0.9214 (mtt) cc_final: 0.8828 (mtt) REVERT: B 900 MET cc_start: 0.8500 (mtt) cc_final: 0.8194 (mtp) REVERT: B 936 ASP cc_start: 0.9671 (t0) cc_final: 0.9337 (m-30) REVERT: B 1010 GLN cc_start: 0.9489 (mm-40) cc_final: 0.9284 (mm-40) REVERT: B 1111 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8534 (tm-30) REVERT: C 298 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8236 (mp0) REVERT: C 1029 MET cc_start: 0.9168 (tpp) cc_final: 0.8899 (tpp) REVERT: C 1050 MET cc_start: 0.8878 (ptm) cc_final: 0.8438 (ptt) REVERT: F 474 MET cc_start: -0.2093 (tpp) cc_final: -0.2459 (mmp) REVERT: H 190 MET cc_start: -0.0477 (mmp) cc_final: -0.1601 (tmm) REVERT: H 360 MET cc_start: -0.0264 (mtp) cc_final: -0.0827 (mtt) REVERT: H 455 MET cc_start: 0.0162 (ppp) cc_final: -0.0172 (ttp) REVERT: H 480 MET cc_start: 0.3340 (ptt) cc_final: 0.2831 (ptt) outliers start: 62 outliers final: 50 residues processed: 144 average time/residue: 0.1745 time to fit residues: 45.0726 Evaluate side-chains 145 residues out of total 3773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 89 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 866 THR Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 544 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1002 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 298 GLU Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 869 MET Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 141 CYS Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 361 CYS Chi-restraints excluded: chain F residue 491 VAL Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 332 MET Chi-restraints excluded: chain H residue 365 THR Chi-restraints excluded: chain H residue 427 ASP Chi-restraints excluded: chain H residue 611 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 420 optimal weight: 8.9990 chunk 352 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 425 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 245 optimal weight: 20.0000 chunk 34 optimal weight: 20.0000 chunk 376 optimal weight: 50.0000 chunk 299 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 327 optimal weight: 50.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 544 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1048 HIS C 957 GLN C1011 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.112227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.071081 restraints weight = 165763.747| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 8.88 r_work: 0.2931 rms_B_bonded: 6.56 restraints_weight: 2.0000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 36052 Z= 0.259 Angle : 0.672 12.381 49195 Z= 0.333 Chirality : 0.047 0.450 5645 Planarity : 0.004 0.060 6228 Dihedral : 4.514 27.019 4621 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.75 % Favored : 93.18 % Rotamer: Outliers : 1.59 % Allowed : 14.55 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.13), residues: 4254 helix: 1.29 (0.14), residues: 1365 sheet: -0.54 (0.20), residues: 690 loop : -1.83 (0.12), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 408 TYR 0.025 0.001 TYR C1067 PHE 0.029 0.002 PHE C1121 TRP 0.044 0.001 TRP H 610 HIS 0.015 0.001 HIS F 228 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.26 (35933) covalent geometry : angle 0.65185 / 0.33 (48882) SS BOND : bond 0.00399 / 0.27 ( 44) SS BOND : angle 1.67497 / 1.13 ( 88) hydrogen bonds : bond 0.04557 / 3.06 ( 1450) hydrogen bonds : angle 4.98750 / 3.45 ( 4098) link_BETA1-4 : bond 0.00241 / 0.15 ( 31) link_BETA1-4 : angle 1.39159 / 0.93 ( 93) link_NAG-ASN : bond 0.00417 / 0.28 ( 44) link_NAG-ASN : angle 2.76316 / 1.88 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15865.70 seconds wall clock time: 270 minutes 7.71 seconds (16207.71 seconds total)