Starting phenix.real_space_refine on Wed Feb 21 23:39:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws1_32740/02_2024/7ws1_32740_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws1_32740/02_2024/7ws1_32740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws1_32740/02_2024/7ws1_32740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws1_32740/02_2024/7ws1_32740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws1_32740/02_2024/7ws1_32740_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws1_32740/02_2024/7ws1_32740_neut.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 142 5.16 5 C 20439 2.51 5 N 5280 2.21 5 O 6351 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C GLU 748": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "E GLU 103": "OE1" <-> "OE2" Residue "I GLU 103": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32212 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 8060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 8060 Classifications: {'peptide': 1041} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 52, 'TRANS': 988} Chain breaks: 7 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "B" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8039 Classifications: {'peptide': 1038} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1039, 8053 Classifications: {'peptide': 1039} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 52, 'TRANS': 986} Chain breaks: 7 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.93, per 1000 atoms: 0.53 Number of scatterers: 32212 At special positions: 0 Unit cell: (143.5, 173.84, 238.62, 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 142 16.00 O 6351 8.00 N 5280 7.00 C 20439 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.02 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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-ASN " NAG A1301 " - " ASN A 165 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 61 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 331 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG B1301 " - " ASN B 165 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 61 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG C1301 " - " ASN C 165 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 61 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG L 1 " - " ASN A 343 " " NAG M 1 " - " ASN A 717 " " NAG N 1 " - " ASN A 801 " " NAG O 1 " - " ASN A 17 " " NAG P 1 " - " ASN A1098 " " NAG Q 1 " - " ASN A1134 " " NAG R 1 " - " ASN B 17 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 17 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 717 " " NAG a 1 " - " ASN C 801 " " NAG b 1 " - " ASN C1098 " " NAG c 1 " - " ASN C1134 " Time building additional restraints: 13.14 Conformation dependent library (CDL) restraints added in 6.1 seconds 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7548 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 78 sheets defined 19.5% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.923A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.701A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.585A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 748 through 754 removed outlier: 3.504A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.059A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.588A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.985A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.673A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.218A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.865A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 982 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.190A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.521A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.678A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.619A pdb=" N SER B 371 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.718A pdb=" N GLN B 409 " --> pdb=" O GLU B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.585A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 752 removed outlier: 3.817A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 4.214A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 826 removed outlier: 3.820A pdb=" N PHE B 823 " --> pdb=" O GLU B 819 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.961A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.775A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 940 " --> pdb=" O ASP B 936 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.340A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.903A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.133A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.048A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.548A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.683A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.988A pdb=" N ALA C 766 " --> pdb=" O GLN C 762 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.597A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.549A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.962A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.758A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.565A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.921A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.686A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.255A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.888A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.579A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.579A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.580A pdb=" N LYS G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'K' and resid 28 through 32 removed outlier: 4.055A pdb=" N ASP K 31 " --> pdb=" O THR K 28 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 28 through 32' Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 removed outlier: 4.010A pdb=" N THR K 91 " --> pdb=" O ALA K 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.717A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU A 96 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.747A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.743A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.715A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 142 removed outlier: 6.742A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.992A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.085A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316 removed outlier: 6.843A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.657A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.941A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 538 through 540 Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566 removed outlier: 6.768A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.264A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 6.584A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 722 removed outlier: 6.476A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 725 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.218A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.546A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.839A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.892A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.108A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 132 through 134 removed outlier: 3.996A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 140 through 142 removed outlier: 3.909A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.072A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.139A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.879A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 573 through 575 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.093A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.701A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD6, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.675A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 712 through 722 removed outlier: 6.675A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.332A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B1081 " --> pdb=" O HIS B1088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.300A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.563A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 10.125A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.563A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE5, first strand: chain 'C' and resid 132 through 135 removed outlier: 3.740A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.223A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.838A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 361 through 362 removed outlier: 5.806A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.759A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.662A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.523A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.681A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AF7, first strand: chain 'C' and resid 1086 through 1090 removed outlier: 4.702A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF9, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AG1, first strand: chain 'D' and resid 10 through 13 removed outlier: 5.555A pdb=" N LEU D 11 " --> pdb=" O GLU D 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.796A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AG5, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 4 through 6 removed outlier: 4.200A pdb=" N ASP H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER H 67 " --> pdb=" O ASP H 70 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.555A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.797A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 98 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.878A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 6 removed outlier: 4.201A pdb=" N ASP F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 67 " --> pdb=" O ASP F 70 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 10 through 13 removed outlier: 5.554A pdb=" N LEU F 11 " --> pdb=" O GLU F 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.796A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.879A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AH8, first strand: chain 'G' and resid 58 through 60 removed outlier: 6.716A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 4 through 6 removed outlier: 3.764A pdb=" N VAL J 19 " --> pdb=" O ILE J 75 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.043A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'J' and resid 53 through 54 removed outlier: 6.936A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN J 90 " --> pdb=" O THR J 98 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR J 98 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 4 through 7 removed outlier: 3.826A pdb=" N SER K 21 " --> pdb=" O SER K 7 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR K 80 " --> pdb=" O SER K 71 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 11 through 12 Processing sheet with id=AI5, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.660A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR K 112 " --> pdb=" O LYS K 98 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.660A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR K 94 " --> pdb=" O THR K 117 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3069 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: 15.37 Time building geometry restraints manager: 14.12 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: 10249 1.34 - 1.46: 7827 1.46 - 1.58: 14671 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 32931 Sorted by residual: bond pdb=" N ASP B 442 " pdb=" CA ASP B 442 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.05e+01 bond pdb=" N ASP I 31 " pdb=" CA ASP I 31 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.03e+01 bond pdb=" N ASP G 31 " pdb=" CA ASP G 31 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01 bond pdb=" N ASP C 442 " pdb=" CA ASP C 442 " ideal model delta sigma weight residual 1.456 1.493 -0.037 1.18e-02 7.18e+03 9.88e+00 bond pdb=" N ASP E 31 " pdb=" CA ASP E 31 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.19e-02 7.06e+03 9.83e+00 ... (remaining 32926 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.81: 965 106.81 - 113.61: 18041 113.61 - 120.41: 11849 120.41 - 127.20: 13656 127.20 - 134.00: 303 Bond angle restraints: 44814 Sorted by residual: angle pdb=" C THR D 69 " pdb=" N ASP D 70 " pdb=" CA ASP D 70 " ideal model delta sigma weight residual 122.87 116.84 6.03 1.61e+00 3.86e-01 1.40e+01 angle pdb=" C GLN A 506 " pdb=" N PRO A 507 " pdb=" CA PRO A 507 " ideal model delta sigma weight residual 119.78 123.13 -3.35 1.03e+00 9.43e-01 1.06e+01 angle pdb=" C ASP D 70 " pdb=" CA ASP D 70 " pdb=" CB ASP D 70 " ideal model delta sigma weight residual 109.37 115.17 -5.80 1.83e+00 2.99e-01 1.01e+01 angle pdb=" N TYR I 102 " pdb=" CA TYR I 102 " pdb=" C TYR I 102 " ideal model delta sigma weight residual 114.31 110.28 4.03 1.29e+00 6.01e-01 9.77e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 114.31 110.30 4.01 1.29e+00 6.01e-01 9.69e+00 ... (remaining 44809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.97: 19080 21.97 - 43.93: 1083 43.93 - 65.90: 165 65.90 - 87.87: 57 87.87 - 109.84: 7 Dihedral angle restraints: 20392 sinusoidal: 8643 harmonic: 11749 Sorted by residual: dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -173.64 87.64 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 177.03 -84.03 1 1.00e+01 1.00e-02 8.60e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -2.74 -83.26 1 1.00e+01 1.00e-02 8.47e+01 ... (remaining 20389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.138: 5209 0.138 - 0.275: 28 0.275 - 0.413: 3 0.413 - 0.550: 2 0.550 - 0.688: 2 Chirality restraints: 5244 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 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 Y 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.14e+00 chirality pdb=" C1 NAG C1305 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG C1305 " pdb=" O5 NAG C1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.49e+00 ... (remaining 5241 not shown) Planarity restraints: 5763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.155 2.00e-02 2.50e+03 1.99e-01 4.94e+02 pdb=" CG ASN B1074 " -0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.338 2.00e-02 2.50e+03 pdb=" C1 NAG B1310 " 0.235 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 874 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C THR C 874 " 0.052 2.00e-02 2.50e+03 pdb=" O THR C 874 " -0.019 2.00e-02 2.50e+03 pdb=" N SER C 875 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 961 " -0.015 2.00e-02 2.50e+03 3.00e-02 8.98e+00 pdb=" C THR B 961 " 0.052 2.00e-02 2.50e+03 pdb=" O THR B 961 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 962 " -0.018 2.00e-02 2.50e+03 ... (remaining 5760 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 5853 2.77 - 3.31: 28984 3.31 - 3.84: 50360 3.84 - 4.37: 56715 4.37 - 4.90: 102858 Nonbonded interactions: 244770 Sorted by model distance: nonbonded pdb=" NE2 GLN C 804 " pdb=" OE1 GLN C 935 " model vdw 2.244 2.520 nonbonded pdb=" OG SER A 721 " pdb=" OG1 THR A1066 " model vdw 2.244 2.440 nonbonded pdb=" OG1 THR B 323 " pdb=" NZ LYS B 537 " model vdw 2.257 2.520 nonbonded pdb=" ND2 ASN C1125 " pdb=" OD2 ASP C1127 " model vdw 2.258 2.520 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.259 2.440 ... (remaining 244765 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 15 through 527 or (resid 528 through 532 and (name N or na \ me CA or name C or name O or name CB )) or resid 533 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 or (resid 5 \ 56 and (name N or name CA or name C or name O or name CB )) or resid 557 through \ 827 or resid 854 through 984 or (resid 985 and (name N or name CA or name C or \ name O or name CB )) or resid 986 through 1044 or (resid 1045 and (name N or nam \ e CA or name C or name O or name CB )) or resid 1046 through 1147 or resid 1301 \ through 1310)) selection = (chain 'B' and (resid 15 through 555 or (resid 556 and (name N or name CA or nam \ e C or name O or name CB )) or resid 557 or (resid 558 through 559 and (name N o \ r name CA or name C or name O or name CB )) or resid 560 through 613 or (resid 6 \ 14 and (name N or name CA or name C or name O or name CB )) or resid 615 through \ 785 or (resid 786 and (name N or name CA or name C or name O or name CB )) or r \ esid 787 through 827 or (resid 854 and (name N or name CA or name C or name O or \ name CB )) or resid 855 through 903 or (resid 904 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or resid 905 through 1044 or (resid 1045 and (name N or name C \ A or name C or name O or name CB )) or resid 1046 through 1147 or resid 1301 thr \ ough 1310)) selection = (chain 'C' and (resid 15 through 527 or (resid 528 through 532 and (name N or na \ me CA or name C or name O or name CB )) or resid 533 through 553 or (resid 554 a \ nd (name N or name CA or name C or name O or name CB )) or resid 555 through 557 \ or (resid 558 through 559 and (name N or name CA or name C or name O or name CB \ )) or resid 560 through 613 or (resid 614 and (name N or name CA or name C or n \ ame O or name CB )) or resid 615 through 827 or resid 854 through 903 or (resid \ 904 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or resid 905 through 984 or ( \ resid 985 and (name N or name CA or name C or name O or name CB )) or resid 986 \ through 1147 or resid 1301 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.940 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: 29.450 Check model and map are aligned: 0.480 Set scattering table: 0.350 Process input model: 86.930 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 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 0.048 32931 Z= 0.241 Angle : 0.625 6.735 44814 Z= 0.338 Chirality : 0.048 0.688 5244 Planarity : 0.004 0.053 5715 Dihedral : 13.841 109.837 12712 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.03 % Allowed : 0.26 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.86 (0.13), residues: 3986 helix: 1.43 (0.22), residues: 647 sheet: -0.47 (0.15), residues: 1188 loop : -1.25 (0.13), residues: 2151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 64 HIS 0.002 0.000 HIS C 49 PHE 0.021 0.001 PHE C 759 TYR 0.023 0.001 TYR J 92 ARG 0.010 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 473 time to evaluate : 3.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 572 THR cc_start: 0.7861 (m) cc_final: 0.7605 (m) REVERT: C 153 MET cc_start: 0.3937 (ppp) cc_final: 0.2697 (tmm) REVERT: C 584 ILE cc_start: 0.8962 (mm) cc_final: 0.8570 (mm) REVERT: C 796 ASP cc_start: 0.6867 (p0) cc_final: 0.6547 (p0) REVERT: C 814 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7816 (mmmt) REVERT: F 5 THR cc_start: 0.5367 (p) cc_final: 0.4752 (p) outliers start: 1 outliers final: 0 residues processed: 474 average time/residue: 0.4418 time to fit residues: 334.3041 Evaluate side-chains 295 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 336 optimal weight: 0.9980 chunk 301 optimal weight: 0.0980 chunk 167 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 203 optimal weight: 2.9990 chunk 161 optimal weight: 6.9990 chunk 311 optimal weight: 0.0070 chunk 120 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 361 optimal weight: 40.0000 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN A 907 ASN B 81 ASN B 439 ASN D 34 ASN H 34 ASN H 38 HIS ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32931 Z= 0.166 Angle : 0.561 13.496 44814 Z= 0.287 Chirality : 0.045 0.449 5244 Planarity : 0.004 0.048 5715 Dihedral : 7.332 87.487 5732 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.02 % Allowed : 7.74 % Favored : 91.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.54 (0.13), residues: 3986 helix: 2.09 (0.22), residues: 626 sheet: -0.10 (0.15), residues: 1131 loop : -1.25 (0.12), residues: 2229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 353 HIS 0.006 0.001 HIS J 38 PHE 0.020 0.001 PHE B 855 TYR 0.021 0.001 TYR D 49 ARG 0.006 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 315 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.3942 (ppp) cc_final: 0.2879 (tmm) REVERT: C 584 ILE cc_start: 0.8925 (mm) cc_final: 0.8499 (mm) REVERT: C 796 ASP cc_start: 0.6929 (p0) cc_final: 0.6601 (p0) REVERT: C 814 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7875 (mmmt) REVERT: J 37 GLN cc_start: 0.6935 (tp-100) cc_final: 0.6600 (tp-100) outliers start: 35 outliers final: 26 residues processed: 330 average time/residue: 0.4606 time to fit residues: 242.0919 Evaluate side-chains 298 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 152 TRP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 59 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain K residue 95 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 200 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 300 optimal weight: 4.9990 chunk 246 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 362 optimal weight: 6.9990 chunk 391 optimal weight: 7.9990 chunk 322 optimal weight: 1.9990 chunk 359 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 290 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 394 ASN ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 23 GLN B 185 ASN C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C 901 GLN C1005 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.073 32931 Z= 0.494 Angle : 0.695 12.194 44814 Z= 0.356 Chirality : 0.049 0.491 5244 Planarity : 0.005 0.108 5715 Dihedral : 6.790 63.982 5732 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.15 % Allowed : 10.85 % Favored : 86.99 % 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: -0.88 (0.13), residues: 3986 helix: 1.58 (0.21), residues: 655 sheet: -0.22 (0.15), residues: 1152 loop : -1.51 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 47 HIS 0.011 0.002 HIS J 38 PHE 0.031 0.002 PHE C 906 TYR 0.019 0.002 TYR H 92 ARG 0.009 0.001 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 267 time to evaluate : 3.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 153 MET cc_start: 0.4001 (ppp) cc_final: 0.2757 (ptm) REVERT: E 87 ARG cc_start: 0.7776 (ptp-110) cc_final: 0.7204 (ptp90) REVERT: G 83 MET cc_start: 0.4379 (mtt) cc_final: 0.4178 (mtt) REVERT: G 95 TYR cc_start: 0.3642 (OUTLIER) cc_final: 0.2464 (m-80) outliers start: 74 outliers final: 50 residues processed: 317 average time/residue: 0.4398 time to fit residues: 224.9898 Evaluate side-chains 288 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 237 time to evaluate : 3.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 94 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 357 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 chunk 187 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 243 optimal weight: 0.3980 chunk 363 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 189 optimal weight: 0.7980 chunk 344 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN G 84 ASN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 GLN ** K 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 32931 Z= 0.168 Angle : 0.542 11.776 44814 Z= 0.277 Chirality : 0.045 0.447 5244 Planarity : 0.003 0.051 5715 Dihedral : 6.056 55.791 5732 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.30 % Allowed : 12.13 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.60 (0.13), residues: 3986 helix: 2.00 (0.22), residues: 651 sheet: 0.01 (0.15), residues: 1096 loop : -1.40 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 47 HIS 0.009 0.001 HIS J 38 PHE 0.024 0.001 PHE K 68 TYR 0.028 0.001 TYR J 87 ARG 0.007 0.000 ARG G 16 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 273 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7327 (p90) REVERT: C 153 MET cc_start: 0.4036 (ppp) cc_final: 0.3026 (tmm) REVERT: E 87 ARG cc_start: 0.7587 (ptp-110) cc_final: 0.7081 (ptp90) REVERT: H 49 TYR cc_start: 0.7819 (p90) cc_final: 0.7496 (p90) REVERT: G 95 TYR cc_start: 0.3553 (OUTLIER) cc_final: 0.2405 (m-80) REVERT: J 38 HIS cc_start: 0.6247 (m90) cc_final: 0.5799 (m90) outliers start: 79 outliers final: 50 residues processed: 328 average time/residue: 0.4483 time to fit residues: 239.1890 Evaluate side-chains 294 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 242 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 374 PHE Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 19 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 4 MET Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 320 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 286 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 328 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 196 optimal weight: 3.9990 chunk 345 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 481 ASN A 901 GLN A 955 ASN A1005 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 919 ASN C1002 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 32931 Z= 0.481 Angle : 0.679 11.538 44814 Z= 0.349 Chirality : 0.049 0.484 5244 Planarity : 0.004 0.054 5715 Dihedral : 5.983 55.152 5732 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.97 % Allowed : 13.85 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.88 (0.13), residues: 3986 helix: 1.64 (0.21), residues: 665 sheet: -0.14 (0.15), residues: 1109 loop : -1.58 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 113 HIS 0.013 0.002 HIS J 38 PHE 0.024 0.002 PHE B 86 TYR 0.020 0.002 TYR J 86 ARG 0.006 0.001 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 241 time to evaluate : 3.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7479 (p90) REVERT: C 153 MET cc_start: 0.4248 (ppp) cc_final: 0.2789 (tmm) REVERT: H 49 TYR cc_start: 0.8171 (p90) cc_final: 0.7847 (p90) REVERT: G 95 TYR cc_start: 0.3616 (OUTLIER) cc_final: 0.2405 (m-80) outliers start: 102 outliers final: 69 residues processed: 317 average time/residue: 0.4345 time to fit residues: 224.7447 Evaluate side-chains 297 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 226 time to evaluate : 4.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 177 MET Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 95 TYR Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain K residue 79 LEU Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 129 optimal weight: 0.9980 chunk 346 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 225 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 385 optimal weight: 9.9990 chunk 319 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 202 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32931 Z= 0.180 Angle : 0.552 11.055 44814 Z= 0.282 Chirality : 0.045 0.437 5244 Planarity : 0.004 0.056 5715 Dihedral : 5.454 51.903 5732 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.53 % Allowed : 15.10 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.63 (0.13), residues: 3986 helix: 2.00 (0.22), residues: 658 sheet: -0.00 (0.16), residues: 1087 loop : -1.44 (0.12), residues: 2241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP K 113 HIS 0.010 0.001 HIS J 38 PHE 0.027 0.001 PHE G 29 TYR 0.019 0.001 TYR B1067 ARG 0.010 0.000 ARG K 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 253 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7304 (p90) REVERT: C 153 MET cc_start: 0.4182 (ppp) cc_final: 0.3132 (tmm) REVERT: D 81 GLU cc_start: 0.8443 (pp20) cc_final: 0.8073 (pp20) REVERT: H 49 TYR cc_start: 0.8048 (p90) cc_final: 0.7717 (p90) REVERT: K 80 TYR cc_start: 0.3349 (OUTLIER) cc_final: 0.2401 (m-80) outliers start: 87 outliers final: 64 residues processed: 316 average time/residue: 0.4268 time to fit residues: 222.1528 Evaluate side-chains 302 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 236 time to evaluate : 4.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 29 ILE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 34 ASN Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 371 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 219 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 217 optimal weight: 0.8980 chunk 324 optimal weight: 0.9980 chunk 215 optimal weight: 9.9990 chunk 383 optimal weight: 30.0000 chunk 240 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C1002 GLN H 37 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 32931 Z= 0.307 Angle : 0.597 10.433 44814 Z= 0.304 Chirality : 0.046 0.448 5244 Planarity : 0.004 0.056 5715 Dihedral : 5.324 50.340 5732 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.91 % Allowed : 15.01 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.13), residues: 3986 helix: 1.94 (0.21), residues: 665 sheet: 0.00 (0.15), residues: 1128 loop : -1.51 (0.12), residues: 2193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP K 113 HIS 0.005 0.001 HIS K 35 PHE 0.018 0.001 PHE A 86 TYR 0.017 0.001 TYR C1067 ARG 0.004 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 243 time to evaluate : 4.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7406 (p90) REVERT: A 733 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8570 (mtpt) REVERT: B 390 LEU cc_start: 0.9090 (tp) cc_final: 0.8874 (pp) REVERT: C 153 MET cc_start: 0.4259 (ppp) cc_final: 0.2853 (tmm) REVERT: H 24 ARG cc_start: 0.6700 (ptm-80) cc_final: 0.6114 (ptm-80) REVERT: H 49 TYR cc_start: 0.8167 (p90) cc_final: 0.7826 (p90) REVERT: K 80 TYR cc_start: 0.3422 (OUTLIER) cc_final: 0.2392 (m-80) outliers start: 100 outliers final: 75 residues processed: 316 average time/residue: 0.4206 time to fit residues: 219.2235 Evaluate side-chains 309 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 231 time to evaluate : 3.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain K residue 80 TYR Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 237 optimal weight: 7.9990 chunk 153 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 243 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 301 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32931 Z= 0.200 Angle : 0.557 10.227 44814 Z= 0.285 Chirality : 0.045 0.435 5244 Planarity : 0.004 0.056 5715 Dihedral : 5.055 45.005 5732 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.62 % Allowed : 15.48 % Favored : 81.90 % 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: -0.54 (0.13), residues: 3986 helix: 2.15 (0.22), residues: 658 sheet: 0.10 (0.16), residues: 1076 loop : -1.42 (0.12), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 113 HIS 0.010 0.001 HIS G 35 PHE 0.020 0.001 PHE B 855 TYR 0.023 0.001 TYR G 112 ARG 0.008 0.000 ARG H 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 242 time to evaluate : 3.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7320 (p90) REVERT: A 733 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8611 (mtpt) REVERT: B 614 ASP cc_start: 0.7342 (t70) cc_final: 0.7077 (t0) REVERT: C 153 MET cc_start: 0.4258 (ppp) cc_final: 0.2857 (tmm) REVERT: D 81 GLU cc_start: 0.8428 (pp20) cc_final: 0.8014 (pp20) REVERT: H 49 TYR cc_start: 0.8115 (p90) cc_final: 0.7773 (p90) outliers start: 90 outliers final: 70 residues processed: 309 average time/residue: 0.4685 time to fit residues: 240.3160 Evaluate side-chains 305 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 233 time to evaluate : 3.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 733 LYS Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 74 ASN Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 348 optimal weight: 8.9990 chunk 367 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 357 optimal weight: 8.9990 chunk 215 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 280 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 323 optimal weight: 6.9990 chunk 338 optimal weight: 8.9990 chunk 356 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN C 115 GLN C 544 ASN C1002 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.115 32931 Z= 0.824 Angle : 0.875 13.148 44814 Z= 0.449 Chirality : 0.055 0.477 5244 Planarity : 0.005 0.064 5715 Dihedral : 6.464 57.015 5732 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 3.08 % Allowed : 15.51 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.13), residues: 3986 helix: 0.96 (0.20), residues: 670 sheet: -0.47 (0.15), residues: 1143 loop : -1.87 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP K 113 HIS 0.010 0.002 HIS D 38 PHE 0.035 0.003 PHE A 86 TYR 0.022 0.003 TYR E 95 ARG 0.006 0.001 ARG A1091 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 239 time to evaluate : 3.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7318 (p90) REVERT: C 153 MET cc_start: 0.4549 (ppp) cc_final: 0.3825 (ptm) REVERT: H 49 TYR cc_start: 0.8511 (p90) cc_final: 0.8243 (p90) outliers start: 106 outliers final: 85 residues processed: 314 average time/residue: 0.4141 time to fit residues: 216.7284 Evaluate side-chains 306 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 220 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 663 ASP Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 912 THR Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 104 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 21 ILE Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain J residue 4 MET Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 234 optimal weight: 0.6980 chunk 378 optimal weight: 9.9990 chunk 230 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 396 optimal weight: 0.0050 chunk 364 optimal weight: 0.9990 chunk 315 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 243 optimal weight: 0.7980 chunk 193 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 925 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** C1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32931 Z= 0.176 Angle : 0.595 13.650 44814 Z= 0.304 Chirality : 0.045 0.430 5244 Planarity : 0.004 0.065 5715 Dihedral : 5.554 52.653 5732 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.04 % Allowed : 16.82 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.83 (0.13), residues: 3986 helix: 1.81 (0.21), residues: 663 sheet: -0.14 (0.16), residues: 1108 loop : -1.58 (0.12), residues: 2215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP K 113 HIS 0.008 0.001 HIS G 35 PHE 0.013 0.001 PHE C 906 TYR 0.021 0.001 TYR B1067 ARG 0.005 0.000 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7972 Ramachandran restraints generated. 3986 Oldfield, 0 Emsley, 3986 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 254 time to evaluate : 3.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7731 (OUTLIER) cc_final: 0.7270 (p90) REVERT: B 505 TYR cc_start: 0.5861 (t80) cc_final: 0.5516 (t80) REVERT: B 614 ASP cc_start: 0.7362 (t70) cc_final: 0.7114 (t0) REVERT: C 153 MET cc_start: 0.4375 (ppp) cc_final: 0.3555 (ptm) REVERT: C 197 ILE cc_start: 0.8392 (mp) cc_final: 0.7771 (mp) REVERT: C 935 GLN cc_start: 0.8317 (tm-30) cc_final: 0.8063 (tm-30) REVERT: H 49 TYR cc_start: 0.8217 (p90) cc_final: 0.7889 (p90) outliers start: 70 outliers final: 62 residues processed: 306 average time/residue: 0.4378 time to fit residues: 219.7651 Evaluate side-chains 301 residues out of total 3514 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 238 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 369 TYR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 819 GLU Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 773 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 107 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 30 ASP Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 84 ASN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain F residue 88 CYS Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 110 PHE Chi-restraints excluded: chain K residue 110 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 250 optimal weight: 4.9990 chunk 336 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 316 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 324 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN B1002 GLN C1002 GLN C1005 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.099542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.061385 restraints weight = 84228.341| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.67 r_work: 0.2803 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 32931 Z= 0.306 Angle : 0.612 14.294 44814 Z= 0.311 Chirality : 0.046 0.445 5244 Planarity : 0.004 0.059 5715 Dihedral : 5.423 49.339 5732 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.01 % Allowed : 17.34 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.86 (0.13), residues: 3986 helix: 1.53 (0.21), residues: 696 sheet: -0.14 (0.15), residues: 1172 loop : -1.59 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP K 113 HIS 0.007 0.001 HIS G 35 PHE 0.033 0.001 PHE D 83 TYR 0.017 0.001 TYR B1067 ARG 0.013 0.000 ARG G 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7095.26 seconds wall clock time: 130 minutes 39.43 seconds (7839.43 seconds total)