Starting phenix.real_space_refine on Mon Feb 19 13:43:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb4_31051/02_2024/7eb4_31051.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb4_31051/02_2024/7eb4_31051.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb4_31051/02_2024/7eb4_31051.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb4_31051/02_2024/7eb4_31051.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb4_31051/02_2024/7eb4_31051.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb4_31051/02_2024/7eb4_31051.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.043 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 105 5.16 5 C 15794 2.51 5 N 4027 2.21 5 O 4906 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 24832 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7879 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 50, 'TRANS': 959} Chain breaks: 7 Chain: "B" Number of atoms: 7993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7993 Classifications: {'peptide': 1024} Link IDs: {'PTRANS': 51, 'TRANS': 972} Chain breaks: 6 Chain: "C" Number of atoms: 7913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7913 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 50, 'TRANS': 962} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 12.96, per 1000 atoms: 0.52 Number of scatterers: 24832 At special positions: 0 Unit cell: (140.8, 141.9, 200.2, 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 105 16.00 O 4906 8.00 N 4027 7.00 C 15794 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 331 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 282 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 282 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 616 " " NAG a 1 " - " ASN C 709 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 10.70 Conformation dependent library (CDL) restraints added in 4.4 seconds 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5704 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 46 sheets defined 25.2% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.596A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.242A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.808A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 753 Processing helix chain 'A' and resid 754 through 757 removed outlier: 3.905A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.665A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.859A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.504A pdb=" N ALA A 890 " --> pdb=" O THR A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 909 removed outlier: 4.029A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.576A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.557A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.594A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.540A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.756A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.617A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.354A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.790A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 630 through 632 No H-bonds generated for 'chain 'B' and resid 630 through 632' Processing helix chain 'B' and resid 633 through 638 removed outlier: 4.018A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 759 through 783 removed outlier: 3.821A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.788A 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 removed outlier: 3.527A pdb=" N ALA B 890 " --> pdb=" O THR B 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.529A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.706A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.529A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) 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 982 removed outlier: 3.781A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.524A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.749A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.647A 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 removed outlier: 3.511A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.626A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.167A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 removed outlier: 4.302A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.278A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.616A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 removed outlier: 3.682A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.672A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.914A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.617A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.625A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.837A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.530A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.421A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.823A 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 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 230 removed outlier: 6.642A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.233A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.280A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 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 573 through 576 removed outlier: 4.012A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.686A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.056A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 722 removed outlier: 6.711A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1078 removed outlier: 3.728A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.538A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.127A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 268 " --> pdb=" O TYR B 91 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.698A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 169 through 172 removed outlier: 3.839A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.413A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.999A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.197A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.751A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 701 through 702 removed outlier: 6.998A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 719 Processing sheet with id=AD3, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.652A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.917A 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: 4.727A 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 1122 Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.972A 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: 3.521A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 191 through 197 removed outlier: 3.567A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.743A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 323 through 328 removed outlier: 4.399A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.779A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.645A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.593A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.505A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 892 hydrogen bonds defined for protein. 2415 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: 10.98 Time building geometry restraints manager: 11.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7832 1.35 - 1.47: 6516 1.47 - 1.59: 10899 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25376 Sorted by residual: bond pdb=" N SER C 640 " pdb=" CA SER C 640 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.26e+00 bond pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.32e-02 5.74e+03 8.93e+00 bond pdb=" N GLY B 639 " pdb=" CA GLY B 639 " ideal model delta sigma weight residual 1.449 1.484 -0.035 1.45e-02 4.76e+03 5.84e+00 bond pdb=" C1 NAG C2001 " pdb=" O5 NAG C2001 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.81e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 ... (remaining 25371 not shown) Histogram of bond angle deviations from ideal: 99.99 - 107.34: 842 107.34 - 114.69: 15157 114.69 - 122.04: 13373 122.04 - 129.39: 5076 129.39 - 136.74: 92 Bond angle restraints: 34540 Sorted by residual: angle pdb=" C LEU C 984 " pdb=" N ASP C 985 " pdb=" CA ASP C 985 " ideal model delta sigma weight residual 120.94 130.32 -9.38 1.90e+00 2.77e-01 2.44e+01 angle pdb=" N VAL C 130 " pdb=" CA VAL C 130 " pdb=" C VAL C 130 " ideal model delta sigma weight residual 112.29 108.29 4.00 9.40e-01 1.13e+00 1.81e+01 angle pdb=" C SER B 640 " pdb=" N ASN B 641 " pdb=" CA ASN B 641 " ideal model delta sigma weight residual 120.82 115.07 5.75 1.41e+00 5.03e-01 1.66e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.58 -4.88 1.22e+00 6.72e-01 1.60e+01 angle pdb=" CA SER B 640 " pdb=" C SER B 640 " pdb=" O SER B 640 " ideal model delta sigma weight residual 121.07 117.03 4.04 1.08e+00 8.57e-01 1.40e+01 ... (remaining 34535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.98: 14911 21.98 - 43.97: 958 43.97 - 65.95: 128 65.95 - 87.94: 35 87.94 - 109.92: 15 Dihedral angle restraints: 16047 sinusoidal: 7184 harmonic: 8863 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 175.60 -82.60 1 1.00e+01 1.00e-02 8.36e+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 93.00 169.56 -76.56 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -157.77 71.77 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 16044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 4135 0.150 - 0.300: 14 0.300 - 0.451: 1 0.451 - 0.601: 0 0.601 - 0.751: 1 Chirality restraints: 4151 Sorted by residual: chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4148 not shown) Planarity restraints: 4414 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 61 " 0.023 2.00e-02 2.50e+03 2.16e-02 5.84e+00 pdb=" CG ASN C 61 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 61 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 61 " -0.020 2.00e-02 2.50e+03 pdb=" C1 NAG C2001 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 640 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C SER C 640 " 0.033 2.00e-02 2.50e+03 pdb=" O SER C 640 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN C 641 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 329 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 330 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 330 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 330 " -0.026 5.00e-02 4.00e+02 ... (remaining 4411 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 759 2.70 - 3.25: 23847 3.25 - 3.80: 36647 3.80 - 4.35: 44021 4.35 - 4.90: 75911 Nonbonded interactions: 181185 Sorted by model distance: nonbonded pdb=" OH TYR C 756 " pdb=" OD2 ASP C 994 " model vdw 2.156 2.440 nonbonded pdb=" OG1 THR B 716 " pdb=" O GLN B1071 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.220 2.440 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.238 2.440 nonbonded pdb=" NZ LYS B 811 " pdb=" OD2 ASP B 820 " model vdw 2.239 2.520 ... (remaining 181180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 622 or resid 636 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2005)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.250 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 70.560 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.400 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25376 Z= 0.238 Angle : 0.621 11.741 34540 Z= 0.311 Chirality : 0.047 0.751 4151 Planarity : 0.004 0.046 4369 Dihedral : 14.117 109.923 10241 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.87 % Favored : 95.07 % Rotamer: Outliers : 0.04 % Allowed : 0.45 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3001 helix: 1.66 (0.22), residues: 644 sheet: -0.12 (0.21), residues: 659 loop : -1.72 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.002 0.000 HIS C1083 PHE 0.015 0.001 PHE C 823 TYR 0.016 0.001 TYR C 369 ARG 0.008 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 131 time to evaluate : 2.968 Fit side-chains revert: symmetry clash REVERT: A 377 PHE cc_start: 0.6908 (t80) cc_final: 0.6509 (t80) REVERT: A 396 TYR cc_start: 0.8082 (m-80) cc_final: 0.7804 (m-10) REVERT: A 697 MET cc_start: 0.8587 (ttm) cc_final: 0.8115 (ttp) REVERT: B 775 ASP cc_start: 0.7584 (t0) cc_final: 0.7362 (t0) REVERT: C 87 ASN cc_start: 0.7471 (m110) cc_final: 0.7229 (m110) REVERT: C 191 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7063 (tm-30) REVERT: C 238 PHE cc_start: 0.7267 (p90) cc_final: 0.6503 (p90) REVERT: C 574 ASP cc_start: 0.8099 (t70) cc_final: 0.7717 (t0) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.3361 time to fit residues: 74.1637 Evaluate side-chains 92 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 3.9990 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 78 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 177 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 777 ASN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 ASN B 919 ASN B 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25376 Z= 0.406 Angle : 0.693 12.034 34540 Z= 0.349 Chirality : 0.048 0.606 4151 Planarity : 0.004 0.068 4369 Dihedral : 8.609 93.649 4830 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.63 % Favored : 92.34 % Rotamer: Outliers : 0.71 % Allowed : 8.83 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 3001 helix: 0.96 (0.20), residues: 696 sheet: -0.44 (0.20), residues: 685 loop : -1.97 (0.14), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 436 HIS 0.008 0.001 HIS A1048 PHE 0.028 0.002 PHE B1121 TYR 0.022 0.002 TYR C1067 ARG 0.005 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 2.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8499 (p90) cc_final: 0.8268 (p90) REVERT: A 994 ASP cc_start: 0.8063 (m-30) cc_final: 0.7861 (m-30) REVERT: A 1029 MET cc_start: 0.8577 (tmm) cc_final: 0.8263 (tmm) REVERT: B 775 ASP cc_start: 0.7699 (t0) cc_final: 0.7461 (t0) REVERT: C 238 PHE cc_start: 0.7582 (p90) cc_final: 0.6531 (p90) REVERT: C 239 GLN cc_start: 0.7556 (mm110) cc_final: 0.6798 (mm110) REVERT: C 441 LEU cc_start: 0.9135 (mm) cc_final: 0.8580 (tt) REVERT: C 985 ASP cc_start: 0.7331 (t0) cc_final: 0.7114 (t0) REVERT: C 1031 GLU cc_start: 0.8186 (tm-30) cc_final: 0.7880 (tm-30) outliers start: 19 outliers final: 16 residues processed: 114 average time/residue: 0.3059 time to fit residues: 60.3505 Evaluate side-chains 103 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 640 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 6.9990 chunk 187 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 276 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 221 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25376 Z= 0.181 Angle : 0.562 11.623 34540 Z= 0.280 Chirality : 0.045 0.514 4151 Planarity : 0.004 0.057 4369 Dihedral : 7.965 90.043 4830 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 0.75 % Allowed : 11.46 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.15), residues: 3001 helix: 1.34 (0.21), residues: 684 sheet: -0.33 (0.20), residues: 661 loop : -1.79 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.003 0.000 HIS C1083 PHE 0.036 0.001 PHE C 86 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 2.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8567 (p90) cc_final: 0.8215 (p90) REVERT: A 441 LEU cc_start: 0.8605 (mt) cc_final: 0.8351 (tp) REVERT: A 661 GLU cc_start: 0.8034 (tp30) cc_final: 0.7694 (mm-30) REVERT: A 990 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6670 (mt-10) REVERT: A 994 ASP cc_start: 0.8108 (m-30) cc_final: 0.7871 (m-30) REVERT: A 1029 MET cc_start: 0.8614 (tmm) cc_final: 0.8168 (tmm) REVERT: B 775 ASP cc_start: 0.7629 (t0) cc_final: 0.7425 (t0) REVERT: B 858 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8687 (pp) REVERT: C 238 PHE cc_start: 0.7620 (p90) cc_final: 0.6649 (p90) REVERT: C 239 GLN cc_start: 0.7485 (mm110) cc_final: 0.6691 (mm110) REVERT: C 441 LEU cc_start: 0.9238 (mm) cc_final: 0.8747 (tt) REVERT: C 985 ASP cc_start: 0.7427 (t0) cc_final: 0.7111 (t0) REVERT: C 1029 MET cc_start: 0.8594 (tmm) cc_final: 0.8278 (tmm) outliers start: 20 outliers final: 11 residues processed: 115 average time/residue: 0.3417 time to fit residues: 67.8028 Evaluate side-chains 105 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 2.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 chunk 143 optimal weight: 40.0000 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 277 optimal weight: 0.8980 chunk 293 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 263 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25376 Z= 0.236 Angle : 0.570 11.372 34540 Z= 0.284 Chirality : 0.045 0.526 4151 Planarity : 0.004 0.052 4369 Dihedral : 7.553 85.125 4830 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.60 % Favored : 93.37 % Rotamer: Outliers : 1.35 % Allowed : 13.83 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3001 helix: 1.39 (0.21), residues: 681 sheet: -0.30 (0.20), residues: 657 loop : -1.80 (0.14), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.005 0.001 HIS A1048 PHE 0.029 0.001 PHE C 86 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 94 time to evaluate : 2.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8571 (p90) cc_final: 0.8256 (p90) REVERT: A 441 LEU cc_start: 0.8624 (mt) cc_final: 0.8390 (tp) REVERT: A 990 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6610 (mt-10) REVERT: A 994 ASP cc_start: 0.8181 (m-30) cc_final: 0.7901 (m-30) REVERT: B 775 ASP cc_start: 0.7591 (t0) cc_final: 0.7378 (t0) REVERT: B 858 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8678 (pp) REVERT: C 238 PHE cc_start: 0.7715 (p90) cc_final: 0.6856 (p90) REVERT: C 239 GLN cc_start: 0.7519 (mm110) cc_final: 0.6898 (mm110) REVERT: C 441 LEU cc_start: 0.9257 (mm) cc_final: 0.8708 (tt) REVERT: C 985 ASP cc_start: 0.7460 (t0) cc_final: 0.7104 (t0) REVERT: C 1029 MET cc_start: 0.8595 (tmm) cc_final: 0.8233 (tmm) outliers start: 36 outliers final: 21 residues processed: 125 average time/residue: 0.3083 time to fit residues: 67.3321 Evaluate side-chains 112 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 89 time to evaluate : 2.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 8.9990 chunk 166 optimal weight: 6.9990 chunk 4 optimal weight: 0.0470 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.0050 chunk 250 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 263 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 overall best weight: 1.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25376 Z= 0.250 Angle : 0.572 10.927 34540 Z= 0.286 Chirality : 0.045 0.512 4151 Planarity : 0.004 0.052 4369 Dihedral : 7.323 80.027 4830 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 1.80 % Allowed : 14.77 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3001 helix: 1.38 (0.21), residues: 687 sheet: -0.37 (0.20), residues: 675 loop : -1.77 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 633 HIS 0.005 0.001 HIS A1048 PHE 0.021 0.001 PHE C 86 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 97 time to evaluate : 3.018 Fit side-chains revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8586 (p90) cc_final: 0.8363 (p90) REVERT: A 441 LEU cc_start: 0.8609 (mt) cc_final: 0.8368 (tp) REVERT: A 948 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7732 (mt) REVERT: A 990 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6602 (mt-10) REVERT: A 994 ASP cc_start: 0.8224 (m-30) cc_final: 0.7905 (m-30) REVERT: A 1029 MET cc_start: 0.8547 (tmm) cc_final: 0.8132 (tmm) REVERT: B 775 ASP cc_start: 0.7602 (t0) cc_final: 0.7388 (t0) REVERT: B 858 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8663 (pp) REVERT: C 238 PHE cc_start: 0.7763 (p90) cc_final: 0.6920 (p90) REVERT: C 239 GLN cc_start: 0.7510 (mm110) cc_final: 0.6882 (mm110) REVERT: C 441 LEU cc_start: 0.9157 (mm) cc_final: 0.8603 (tt) REVERT: C 985 ASP cc_start: 0.7427 (t0) cc_final: 0.7046 (t0) REVERT: C 1029 MET cc_start: 0.8614 (tmm) cc_final: 0.8230 (tmm) REVERT: C 1031 GLU cc_start: 0.8265 (tm-30) cc_final: 0.8025 (tm-30) outliers start: 48 outliers final: 33 residues processed: 139 average time/residue: 0.3330 time to fit residues: 79.6390 Evaluate side-chains 128 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 172 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 chunk 136 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25376 Z= 0.203 Angle : 0.561 11.040 34540 Z= 0.278 Chirality : 0.045 0.502 4151 Planarity : 0.004 0.050 4369 Dihedral : 7.099 75.556 4830 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.03 % Favored : 93.94 % Rotamer: Outliers : 1.95 % Allowed : 16.16 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.15), residues: 3001 helix: 1.41 (0.21), residues: 688 sheet: -0.29 (0.20), residues: 669 loop : -1.74 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 PHE 0.025 0.001 PHE A 377 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 96 time to evaluate : 2.737 Fit side-chains revert: symmetry clash REVERT: A 400 PHE cc_start: 0.8494 (p90) cc_final: 0.8259 (p90) REVERT: A 441 LEU cc_start: 0.8614 (mt) cc_final: 0.8370 (tp) REVERT: A 661 GLU cc_start: 0.7972 (tp30) cc_final: 0.7043 (pp20) REVERT: A 948 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7645 (mt) REVERT: A 990 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6481 (mt-10) REVERT: B 775 ASP cc_start: 0.7568 (t0) cc_final: 0.7355 (t0) REVERT: B 858 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8685 (pp) REVERT: C 238 PHE cc_start: 0.7663 (p90) cc_final: 0.6874 (p90) REVERT: C 239 GLN cc_start: 0.7443 (mm110) cc_final: 0.6827 (mm110) REVERT: C 441 LEU cc_start: 0.9254 (mm) cc_final: 0.8710 (tt) REVERT: C 985 ASP cc_start: 0.7706 (t0) cc_final: 0.7306 (t0) REVERT: C 1029 MET cc_start: 0.8638 (tmm) cc_final: 0.8259 (tmm) REVERT: C 1050 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7944 (ptt) outliers start: 52 outliers final: 31 residues processed: 141 average time/residue: 0.3087 time to fit residues: 76.2408 Evaluate side-chains 127 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 92 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 167 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 247 optimal weight: 0.0570 chunk 164 optimal weight: 4.9990 chunk 293 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 178 optimal weight: 0.8980 chunk 135 optimal weight: 30.0000 overall best weight: 1.3300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25376 Z= 0.221 Angle : 0.563 10.549 34540 Z= 0.280 Chirality : 0.045 0.502 4151 Planarity : 0.004 0.050 4369 Dihedral : 6.944 70.016 4830 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.33 % Favored : 93.64 % Rotamer: Outliers : 1.88 % Allowed : 17.10 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.15), residues: 3001 helix: 1.40 (0.21), residues: 687 sheet: -0.24 (0.20), residues: 661 loop : -1.72 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 PHE 0.027 0.001 PHE A 377 TYR 0.018 0.001 TYR C1067 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 94 time to evaluate : 2.882 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8622 (mt) cc_final: 0.8378 (tp) REVERT: A 661 GLU cc_start: 0.7945 (tp30) cc_final: 0.7007 (pp20) REVERT: A 948 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7656 (mt) REVERT: A 1029 MET cc_start: 0.8516 (tmm) cc_final: 0.8115 (tmm) REVERT: B 775 ASP cc_start: 0.7595 (t0) cc_final: 0.7380 (t0) REVERT: B 858 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8666 (pp) REVERT: C 238 PHE cc_start: 0.7641 (p90) cc_final: 0.6827 (p90) REVERT: C 239 GLN cc_start: 0.7447 (mm110) cc_final: 0.6810 (mm110) REVERT: C 441 LEU cc_start: 0.9171 (mm) cc_final: 0.8624 (tt) REVERT: C 985 ASP cc_start: 0.7849 (t0) cc_final: 0.7425 (t0) REVERT: C 1029 MET cc_start: 0.8667 (tmm) cc_final: 0.8422 (tmm) outliers start: 50 outliers final: 39 residues processed: 135 average time/residue: 0.3396 time to fit residues: 80.5256 Evaluate side-chains 132 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 91 time to evaluate : 2.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 724 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 3.9990 chunk 117 optimal weight: 0.9990 chunk 174 optimal weight: 0.0770 chunk 88 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 199 optimal weight: 0.3980 chunk 144 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 230 optimal weight: 3.9990 overall best weight: 0.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25376 Z= 0.162 Angle : 0.545 10.620 34540 Z= 0.268 Chirality : 0.044 0.473 4151 Planarity : 0.004 0.051 4369 Dihedral : 6.670 63.080 4830 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.50 % Rotamer: Outliers : 1.50 % Allowed : 17.89 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 3001 helix: 1.68 (0.21), residues: 668 sheet: -0.12 (0.20), residues: 661 loop : -1.65 (0.14), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 633 HIS 0.004 0.000 HIS C1083 PHE 0.031 0.001 PHE A 377 TYR 0.016 0.001 TYR C1067 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 106 time to evaluate : 2.984 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8615 (mt) cc_final: 0.8375 (tp) REVERT: A 661 GLU cc_start: 0.7883 (tp30) cc_final: 0.6906 (pp20) REVERT: A 948 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7556 (mt) REVERT: B 775 ASP cc_start: 0.7559 (t0) cc_final: 0.7330 (t0) REVERT: B 858 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8691 (pp) REVERT: C 238 PHE cc_start: 0.7533 (p90) cc_final: 0.6745 (p90) REVERT: C 239 GLN cc_start: 0.7397 (mm110) cc_final: 0.6714 (mm110) REVERT: C 441 LEU cc_start: 0.9171 (mm) cc_final: 0.8614 (tt) REVERT: C 563 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7206 (mm-40) REVERT: C 985 ASP cc_start: 0.7647 (t0) cc_final: 0.7221 (t0) REVERT: C 1029 MET cc_start: 0.8615 (tmm) cc_final: 0.8228 (tmm) outliers start: 40 outliers final: 26 residues processed: 139 average time/residue: 0.3109 time to fit residues: 76.0274 Evaluate side-chains 123 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 2.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.5980 chunk 280 optimal weight: 0.0970 chunk 256 optimal weight: 4.9990 chunk 273 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 chunk 272 optimal weight: 0.6980 overall best weight: 1.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 25376 Z= 0.213 Angle : 0.564 11.077 34540 Z= 0.279 Chirality : 0.045 0.489 4151 Planarity : 0.004 0.051 4369 Dihedral : 6.612 57.535 4830 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.70 % Rotamer: Outliers : 1.69 % Allowed : 18.15 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3001 helix: 1.52 (0.21), residues: 680 sheet: -0.11 (0.21), residues: 654 loop : -1.68 (0.14), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 633 HIS 0.004 0.001 HIS A1048 PHE 0.074 0.001 PHE C 456 TYR 0.018 0.001 TYR C1067 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 95 time to evaluate : 2.784 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8623 (mt) cc_final: 0.8387 (tp) REVERT: A 948 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7642 (mt) REVERT: B 775 ASP cc_start: 0.7586 (t0) cc_final: 0.7362 (t0) REVERT: B 858 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8672 (pp) REVERT: C 238 PHE cc_start: 0.7485 (p90) cc_final: 0.6685 (p90) REVERT: C 239 GLN cc_start: 0.7379 (mm110) cc_final: 0.6727 (mm110) REVERT: C 441 LEU cc_start: 0.9174 (mm) cc_final: 0.8617 (tt) REVERT: C 563 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.7329 (mm-40) REVERT: C 985 ASP cc_start: 0.7611 (t0) cc_final: 0.7168 (t0) REVERT: C 1029 MET cc_start: 0.8671 (tmm) cc_final: 0.8424 (tmm) REVERT: C 1050 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7781 (ptt) outliers start: 45 outliers final: 33 residues processed: 134 average time/residue: 0.3014 time to fit residues: 70.9838 Evaluate side-chains 128 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 91 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 176 optimal weight: 0.6980 chunk 136 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 278 optimal weight: 0.9990 chunk 241 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 chunk 147 optimal weight: 0.0870 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25376 Z= 0.201 Angle : 0.575 12.032 34540 Z= 0.284 Chirality : 0.045 0.485 4151 Planarity : 0.004 0.051 4369 Dihedral : 6.548 58.701 4830 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 1.62 % Allowed : 18.30 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.15), residues: 3001 helix: 1.59 (0.21), residues: 668 sheet: -0.06 (0.21), residues: 649 loop : -1.68 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 633 HIS 0.004 0.001 HIS B 625 PHE 0.064 0.001 PHE C 456 TYR 0.018 0.001 TYR C1067 ARG 0.009 0.000 ARG B 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6002 Ramachandran restraints generated. 3001 Oldfield, 0 Emsley, 3001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 92 time to evaluate : 2.493 Fit side-chains revert: symmetry clash REVERT: A 441 LEU cc_start: 0.8613 (mt) cc_final: 0.8399 (tp) REVERT: A 948 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7626 (mt) REVERT: B 775 ASP cc_start: 0.7586 (t0) cc_final: 0.7362 (t0) REVERT: B 858 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8684 (pp) REVERT: C 238 PHE cc_start: 0.7461 (p90) cc_final: 0.6695 (p90) REVERT: C 239 GLN cc_start: 0.7387 (mm110) cc_final: 0.6773 (mm110) REVERT: C 441 LEU cc_start: 0.9187 (mm) cc_final: 0.8627 (tt) REVERT: C 563 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7335 (mm-40) REVERT: C 985 ASP cc_start: 0.7590 (t0) cc_final: 0.7138 (t0) REVERT: C 1029 MET cc_start: 0.8670 (tmm) cc_final: 0.8428 (tmm) REVERT: C 1050 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7817 (ptt) outliers start: 43 outliers final: 36 residues processed: 129 average time/residue: 0.3205 time to fit residues: 73.2369 Evaluate side-chains 131 residues out of total 2661 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 91 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 948 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 140 PHE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 490 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1012 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1082 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 222 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 248 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN A1106 GLN C 544 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.129088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.081457 restraints weight = 57012.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.087356 restraints weight = 31895.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087508 restraints weight = 18690.146| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 25376 Z= 0.463 Angle : 0.710 13.056 34540 Z= 0.358 Chirality : 0.049 0.567 4151 Planarity : 0.004 0.051 4369 Dihedral : 6.908 59.807 4830 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.56 % Favored : 91.40 % Rotamer: Outliers : 1.73 % Allowed : 18.45 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.15), residues: 3001 helix: 1.00 (0.20), residues: 686 sheet: -0.46 (0.20), residues: 674 loop : -1.90 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 633 HIS 0.009 0.001 HIS A1048 PHE 0.060 0.002 PHE C 456 TYR 0.025 0.002 TYR C1067 ARG 0.004 0.001 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.23 seconds wall clock time: 69 minutes 10.32 seconds (4150.32 seconds total)