Starting phenix.real_space_refine (version: dev) on Sun May 15 12:34:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/05_2022/7v7n_31775.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/05_2022/7v7n_31775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/05_2022/7v7n_31775.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/05_2022/7v7n_31775.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/05_2022/7v7n_31775.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v7n_31775/05_2022/7v7n_31775.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 425": "OD1" <-> "OD2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1073": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 25430 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} 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: 1 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 chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.25, per 1000 atoms: 0.56 Number of scatterers: 25430 At special positions: 0 Unit cell: (145.2, 148.5, 178.2, 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 108 16.00 O 5031 8.00 N 4139 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.02 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.02 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 329 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 329 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 341 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 232 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 11.96 Conformation dependent library (CDL) restraints added in 3.7 seconds 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 25.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.24 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.577A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 388 removed outlier: 4.522A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.921A pdb=" N VAL A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.672A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.976A pdb=" N THR A 636 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.645A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.502A pdb=" N LYS A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.779A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.186A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 4.009A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.119A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.685A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.039A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.793A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.712A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.638A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.975A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.567A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.647A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.364A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 removed outlier: 3.577A pdb=" N GLU C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.721A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.607A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.765A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.591A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.500A pdb=" N SER C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.962A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.712A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.578A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.633A pdb=" N GLY C 887 " --> pdb=" O TRP C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.931A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1032 removed outlier: 4.531A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.731A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.635A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.014A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.116A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.478A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 326 removed outlier: 5.097A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.590A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.041A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 701 removed outlier: 7.083A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.561A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.604A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.337A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.971A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.555A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.455A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.374A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.058A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.127A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.493A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 786 through 788 removed outlier: 5.745A pdb=" N ILE B 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.049A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 30 removed outlier: 8.391A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.919A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.069A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.582A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.892A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.212A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.810A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.598A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE9, first strand: chain 'C' and resid 1092 through 1095 993 hydrogen bonds defined for protein. 2709 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.08 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8014 1.34 - 1.46: 6436 1.46 - 1.58: 11402 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25984 Sorted by residual: bond pdb=" C PRO C 984 " pdb=" N PRO C 985 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.66e+00 bond pdb=" CB ASN C 775 " pdb=" CG ASN C 775 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.90e+00 bond pdb=" CB CYS C 736 " pdb=" SG CYS C 736 " ideal model delta sigma weight residual 1.808 1.764 0.044 3.30e-02 9.18e+02 1.76e+00 bond pdb=" CB CYS B 736 " pdb=" SG CYS B 736 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.59e+00 bond pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " ideal model delta sigma weight residual 1.808 1.767 0.041 3.30e-02 9.18e+02 1.54e+00 ... (remaining 25979 not shown) Histogram of bond angle deviations from ideal: 99.74 - 106.58: 685 106.58 - 113.43: 14623 113.43 - 120.28: 8802 120.28 - 127.13: 11033 127.13 - 133.98: 214 Bond angle restraints: 35357 Sorted by residual: angle pdb=" C2 NAG J 1 " pdb=" N2 NAG J 1 " pdb=" C7 NAG J 1 " ideal model delta sigma weight residual 123.12 129.03 -5.91 1.28e+00 6.08e-01 2.12e+01 angle pdb=" C CYS A 660 " pdb=" N ASP A 661 " pdb=" CA ASP A 661 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.45 -3.75 1.22e+00 6.72e-01 9.45e+00 angle pdb=" N VAL C 339 " pdb=" CA VAL C 339 " pdb=" C VAL C 339 " ideal model delta sigma weight residual 113.39 109.20 4.19 1.47e+00 4.63e-01 8.14e+00 angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 122.29 117.99 4.30 1.65e+00 3.67e-01 6.80e+00 ... (remaining 35352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13889 17.83 - 35.66: 1190 35.66 - 53.49: 190 53.49 - 71.32: 31 71.32 - 89.15: 29 Dihedral angle restraints: 15329 sinusoidal: 6302 harmonic: 9027 Sorted by residual: dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -2.39 -83.61 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 536 " pdb=" SG CYS B 536 " pdb=" SG CYS B 588 " pdb=" CB CYS B 588 " ideal model delta sinusoidal sigma weight residual -86.00 -10.56 -75.44 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 536 " pdb=" SG CYS C 536 " pdb=" SG CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sinusoidal sigma weight residual -86.00 -11.49 -74.51 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 15326 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4232 0.137 - 0.275: 25 0.275 - 0.412: 1 0.412 - 0.550: 1 0.550 - 0.687: 2 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 4258 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.027 2.00e-02 2.50e+03 2.51e-02 7.90e+00 pdb=" CG ASN B1072 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " -0.001 2.00e-02 2.50e+03 2.26e-02 6.36e+00 pdb=" CG ASN B 232 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 904 " -0.019 2.00e-02 2.50e+03 1.75e-02 5.36e+00 pdb=" CG PHE C 904 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 904 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 904 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 904 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 904 " -0.001 2.00e-02 2.50e+03 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1156 2.72 - 3.26: 25010 3.26 - 3.81: 39404 3.81 - 4.35: 45870 4.35 - 4.90: 81156 Nonbonded interactions: 192596 Sorted by model distance: nonbonded pdb=" OD1 ASP C 566 " pdb=" OG1 THR C 570 " model vdw 2.171 2.440 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.190 2.440 nonbonded pdb=" O GLU A 154 " pdb=" OH TYR A 158 " model vdw 2.195 2.440 nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.211 2.440 nonbonded pdb=" O ARG A 212 " pdb=" OH TYR A 264 " model vdw 2.212 2.440 ... (remaining 192591 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' and (resid 14 through 619 or resid 631 through 1144 or resid 2001 thr \ ough 2004)) selection = (chain 'B' and (resid 14 through 825 or resid 852 through 1144 or resid 2001 thr \ ough 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 631 through 1144 or resid 2001 thr \ ough 2004)) } 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' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16152 2.51 5 N 4139 2.21 5 O 5031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 0.020 Extract box with map and model: 15.580 Check model and map are aligned: 0.420 Convert atoms to be neutral: 0.240 Process input model: 70.150 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 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 0.044 25984 Z= 0.268 Angle : 0.547 8.008 35357 Z= 0.297 Chirality : 0.047 0.687 4261 Planarity : 0.004 0.043 4463 Dihedral : 13.437 89.152 9397 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.11 (0.15), residues: 3053 helix: 2.05 (0.22), residues: 646 sheet: 0.76 (0.19), residues: 721 loop : -1.08 (0.15), residues: 1686 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.903 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 1.1416 time to fit residues: 152.4715 Evaluate side-chains 70 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 2.971 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 260 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 180 optimal weight: 4.9990 chunk 280 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 448 ASN B 504 GLN C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.059 25984 Z= 0.482 Angle : 0.629 8.295 35357 Z= 0.339 Chirality : 0.049 0.706 4261 Planarity : 0.004 0.057 4463 Dihedral : 5.030 23.782 3840 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.80 % Favored : 94.07 % Rotamer Outliers : 0.70 % 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: -0.13 (0.15), residues: 3053 helix: 1.73 (0.21), residues: 671 sheet: 0.53 (0.19), residues: 732 loop : -1.20 (0.15), residues: 1650 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 3.191 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 83 average time/residue: 1.3471 time to fit residues: 133.6761 Evaluate side-chains 73 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 68 time to evaluate : 3.108 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.8429 time to fit residues: 6.0906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 155 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 233 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 281 optimal weight: 0.8980 chunk 303 optimal weight: 0.4980 chunk 250 optimal weight: 10.0000 chunk 278 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 25984 Z= 0.187 Angle : 0.514 7.896 35357 Z= 0.277 Chirality : 0.046 0.674 4261 Planarity : 0.004 0.056 4463 Dihedral : 4.740 22.210 3840 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.77 % Rotamer Outliers : 1.18 % 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: 0.10 (0.15), residues: 3053 helix: 2.07 (0.22), residues: 658 sheet: 0.67 (0.19), residues: 720 loop : -1.08 (0.15), residues: 1675 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 3.055 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 11 residues processed: 106 average time/residue: 1.1846 time to fit residues: 152.3048 Evaluate side-chains 82 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 2.929 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 8 residues processed: 3 average time/residue: 1.1845 time to fit residues: 8.2048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 277 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 134 optimal weight: 8.9990 chunk 188 optimal weight: 3.9990 chunk 282 optimal weight: 0.7980 chunk 298 optimal weight: 3.9990 chunk 147 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 899 GLN C 14 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.044 25984 Z= 0.367 Angle : 0.569 8.142 35357 Z= 0.306 Chirality : 0.047 0.686 4261 Planarity : 0.004 0.061 4463 Dihedral : 4.873 22.659 3840 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.93 % Favored : 93.94 % Rotamer Outliers : 1.62 % 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: -0.03 (0.15), residues: 3053 helix: 1.90 (0.21), residues: 670 sheet: 0.65 (0.19), residues: 714 loop : -1.19 (0.15), residues: 1669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 72 time to evaluate : 3.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 16 residues processed: 107 average time/residue: 1.0841 time to fit residues: 142.0932 Evaluate side-chains 85 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 69 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 4.1790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 248 optimal weight: 30.0000 chunk 169 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 chunk 123 optimal weight: 0.9980 chunk 254 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 152 optimal weight: 6.9990 chunk 268 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN B 899 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 25984 Z= 0.179 Angle : 0.511 7.867 35357 Z= 0.275 Chirality : 0.045 0.665 4261 Planarity : 0.004 0.060 4463 Dihedral : 4.680 21.811 3840 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer Outliers : 1.66 % 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: 0.15 (0.15), residues: 3053 helix: 2.19 (0.22), residues: 658 sheet: 0.67 (0.19), residues: 718 loop : -1.06 (0.15), residues: 1677 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 83 time to evaluate : 3.059 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 19 residues processed: 124 average time/residue: 1.0991 time to fit residues: 167.4957 Evaluate side-chains 90 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 4.1332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 100 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 175 optimal weight: 0.1980 chunk 73 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 chunk 248 optimal weight: 20.0000 chunk 138 optimal weight: 7.9990 chunk 24 optimal weight: 0.0980 chunk 98 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 25984 Z= 0.186 Angle : 0.514 7.882 35357 Z= 0.276 Chirality : 0.045 0.664 4261 Planarity : 0.004 0.060 4463 Dihedral : 4.625 21.736 3840 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.73 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.21 (0.15), residues: 3053 helix: 2.17 (0.21), residues: 674 sheet: 0.67 (0.19), residues: 721 loop : -1.02 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 79 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 22 residues processed: 121 average time/residue: 0.9665 time to fit residues: 146.2193 Evaluate side-chains 97 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 2.0040 time to fit residues: 6.4446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 288 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 chunk 251 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 297 optimal weight: 0.6980 chunk 186 optimal weight: 0.6980 chunk 181 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 25984 Z= 0.162 Angle : 0.508 7.866 35357 Z= 0.272 Chirality : 0.045 0.658 4261 Planarity : 0.004 0.062 4463 Dihedral : 4.557 20.722 3840 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.13 % Favored : 95.74 % Rotamer Outliers : 1.47 % 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: 0.25 (0.16), residues: 3053 helix: 2.23 (0.21), residues: 674 sheet: 0.68 (0.19), residues: 723 loop : -0.99 (0.15), residues: 1656 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 84 time to evaluate : 3.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 23 residues processed: 119 average time/residue: 1.0671 time to fit residues: 158.2550 Evaluate side-chains 100 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 3.124 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 22 residues processed: 1 average time/residue: 1.2798 time to fit residues: 5.5063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 184 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 177 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 189 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 234 optimal weight: 10.0000 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B 917 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 25984 Z= 0.245 Angle : 0.542 12.781 35357 Z= 0.287 Chirality : 0.046 0.667 4261 Planarity : 0.004 0.062 4463 Dihedral : 4.621 21.082 3840 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.79 % Rotamer Outliers : 1.47 % 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: 0.22 (0.15), residues: 3053 helix: 2.21 (0.21), residues: 674 sheet: 0.65 (0.19), residues: 721 loop : -1.01 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 76 time to evaluate : 3.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 109 average time/residue: 1.0750 time to fit residues: 145.0961 Evaluate side-chains 101 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 2.871 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 2 average time/residue: 0.8184 time to fit residues: 5.7263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 270 optimal weight: 0.0020 chunk 285 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 277 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 217 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 262 optimal weight: 8.9990 chunk 276 optimal weight: 3.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 25984 Z= 0.216 Angle : 0.538 16.157 35357 Z= 0.285 Chirality : 0.045 0.655 4261 Planarity : 0.004 0.066 4463 Dihedral : 4.611 21.156 3840 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.42 % Favored : 95.45 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.22 (0.15), residues: 3053 helix: 2.23 (0.21), residues: 674 sheet: 0.61 (0.19), residues: 725 loop : -1.00 (0.15), residues: 1654 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 73 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 27 residues processed: 106 average time/residue: 1.1208 time to fit residues: 147.1878 Evaluate side-chains 101 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 26 residues processed: 1 average time/residue: 1.5636 time to fit residues: 5.8435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 182 optimal weight: 2.9990 chunk 293 optimal weight: 0.6980 chunk 179 optimal weight: 1.9990 chunk 139 optimal weight: 0.8980 chunk 204 optimal weight: 0.8980 chunk 307 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 245 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 150 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 25984 Z= 0.171 Angle : 0.537 14.779 35357 Z= 0.284 Chirality : 0.045 0.647 4261 Planarity : 0.004 0.098 4463 Dihedral : 4.572 21.207 3840 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer Outliers : 1.14 % 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: 0.27 (0.15), residues: 3053 helix: 2.30 (0.21), residues: 673 sheet: 0.63 (0.19), residues: 726 loop : -0.97 (0.15), residues: 1654 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 79 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 25 residues processed: 108 average time/residue: 1.0415 time to fit residues: 140.2709 Evaluate side-chains 97 residues out of total 2714 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 3.180 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 25 residues processed: 0 time to fit residues: 4.2180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 226 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.078582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.048291 restraints weight = 86977.930| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.97 r_work: 0.2857 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work: 0.2837 rms_B_bonded: 3.69 restraints_weight: 0.1250 r_work: 0.2828 rms_B_bonded: 3.70 restraints_weight: 0.0625 r_work: 0.2818 rms_B_bonded: 3.74 restraints_weight: 0.0312 r_work: 0.2808 rms_B_bonded: 3.79 restraints_weight: 0.0156 r_work: 0.2798 rms_B_bonded: 3.85 restraints_weight: 0.0078 r_work: 0.2788 rms_B_bonded: 3.93 restraints_weight: 0.0039 r_work: 0.2777 rms_B_bonded: 4.02 restraints_weight: 0.0020 r_work: 0.2767 rms_B_bonded: 4.12 restraints_weight: 0.0010 r_work: 0.2756 rms_B_bonded: 4.24 restraints_weight: 0.0005 r_work: 0.2744 rms_B_bonded: 4.37 restraints_weight: 0.0002 r_work: 0.2733 rms_B_bonded: 4.52 restraints_weight: 0.0001 r_work: 0.2721 rms_B_bonded: 4.69 restraints_weight: 0.0001 r_work: 0.2709 rms_B_bonded: 4.87 restraints_weight: 0.0000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 25984 Z= 0.410 Angle : 0.612 9.898 35357 Z= 0.327 Chirality : 0.048 0.673 4261 Planarity : 0.004 0.077 4463 Dihedral : 4.869 21.889 3840 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.10 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.07 (0.15), residues: 3053 helix: 2.15 (0.21), residues: 663 sheet: 0.55 (0.19), residues: 720 loop : -1.11 (0.15), residues: 1670 =============================================================================== Job complete usr+sys time: 4552.82 seconds wall clock time: 84 minutes 46.69 seconds (5086.69 seconds total)