Starting phenix.real_space_refine on Wed Feb 21 09:50:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/02_2024/7cak_30333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/02_2024/7cak_30333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/02_2024/7cak_30333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/02_2024/7cak_30333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/02_2024/7cak_30333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/02_2024/7cak_30333.pdb" } resolution = 3.58 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= 0.000 sd= 0.002 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 129 5.16 5 C 19264 2.51 5 N 4934 2.21 5 O 5936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 34": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1019": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 1019": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 23": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30263 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8029 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8033 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 8033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8033 Classifications: {'peptide': 1028} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 50, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 837 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 16.15, per 1000 atoms: 0.53 Number of scatterers: 30263 At special positions: 0 Unit cell: (174.72, 165.36, 192.4, 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 129 16.00 O 5936 8.00 N 4934 7.00 C 19264 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " 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 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.01 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.01 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " 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=2.01 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 87 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.02 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 Atom "HETATM30205 O5 NAG C1306 .*. O " rejected from bonding due to valence issues. Atom "HETATM30093 O5 NAG B1308 .*. O " rejected from bonding due to valence issues. Atom "HETATM30233 O5 NAG C1308 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " 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 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " 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 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " 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 J 1 " - " ASN A 234 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 234 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 5.7 seconds 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7068 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 75 sheets defined 18.7% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.25 Creating SS restraints... Processing helix chain 'A' and resid 153 through 157 removed outlier: 3.792A pdb=" N PHE A 157 " --> pdb=" O GLU A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.895A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 405 through 408' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.833A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.682A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 783 removed outlier: 4.307A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG A 765 " --> pdb=" O THR A 761 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.723A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 875 " --> pdb=" O ALA A 871 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 901 Processing helix chain 'A' and resid 903 through 908 removed outlier: 3.621A pdb=" N ASN A 907 " --> pdb=" O ALA A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 940 removed outlier: 3.638A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.529A pdb=" N THR A 961 " --> pdb=" O GLN A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.968A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 3.568A pdb=" N ALA A 989 " --> pdb=" O ASP A 985 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A1023 " --> pdb=" O ARG A1019 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1030 " --> pdb=" O ALA A1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 157 removed outlier: 3.791A pdb=" N PHE B 157 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.895A pdb=" N CYS B 301 " --> pdb=" O SER B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 368 Processing helix chain 'B' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.834A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.683A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.307A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 764 " --> pdb=" O CYS B 760 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.640A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.723A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER B 875 " --> pdb=" O ALA B 871 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 901 Processing helix chain 'B' and resid 903 through 908 removed outlier: 3.622A pdb=" N ASN B 907 " --> pdb=" O ALA B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 940 removed outlier: 3.640A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.528A pdb=" N THR B 961 " --> pdb=" O GLN B 957 " (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: 3.968A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.567A pdb=" N ALA B 989 " --> pdb=" O ASP B 985 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B1023 " --> pdb=" O ARG B1019 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU B1024 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER B1030 " --> pdb=" O ALA B1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 157 removed outlier: 3.791A pdb=" N PHE C 157 " --> pdb=" O GLU C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.895A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 368 Processing helix chain 'C' and resid 405 through 408 removed outlier: 3.556A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 405 through 408' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.834A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.682A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 757 through 783 removed outlier: 4.308A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN C 764 " --> pdb=" O CYS C 760 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.722A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER C 875 " --> pdb=" O ALA C 871 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 903 through 908 removed outlier: 3.621A pdb=" N ASN C 907 " --> pdb=" O ALA C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 940 removed outlier: 3.639A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.529A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (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 984 removed outlier: 3.968A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.568A pdb=" N ALA C 989 " --> pdb=" O ASP C 985 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C1020 " --> pdb=" O ALA C1016 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN C1023 " --> pdb=" O ARG C1019 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C1024 " --> pdb=" O ALA C1020 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 30 No H-bonds generated for 'chain 'G' and resid 28 through 30' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.596A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 52 removed outlier: 3.631A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.519A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR A 170 " --> pdb=" O ILE A 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 90 Processing sheet with id=AA6, first strand: chain 'A' and resid 89 through 90 removed outlier: 7.110A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.323A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.421A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 327 through 328 Processing sheet with id=AB1, first strand: chain 'A' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.672A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 576 through 577 Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.883A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.557A pdb=" N LYS A1073 " --> pdb=" O ILE A 714 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 725 through 728 removed outlier: 7.034A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1089 through 1090 Processing sheet with id=AC2, first strand: chain 'A' and resid 1095 through 1097 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 3.597A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 52 removed outlier: 3.631A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.520A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TRP B 104 " --> pdb=" O ILE B 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE B 119 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AC8, first strand: chain 'B' and resid 89 through 90 removed outlier: 7.110A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.323A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 311 through 317 removed outlier: 6.422A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 327 through 328 Processing sheet with id=AD3, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.178A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 576 through 577 Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.882A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 695 " --> pdb=" O CYS B 671 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY B 667 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.557A pdb=" N LYS B1073 " --> pdb=" O ILE B 714 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 725 through 728 removed outlier: 7.034A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 735 through 736 Processing sheet with id=AE4, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AE5, first strand: chain 'B' and resid 1095 through 1097 Processing sheet with id=AE6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.596A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.631A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE9, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.520A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 89 through 90 Processing sheet with id=AF2, first strand: chain 'C' and resid 89 through 90 removed outlier: 7.111A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.322A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 311 through 317 removed outlier: 6.422A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 327 through 328 Processing sheet with id=AF6, first strand: chain 'C' and resid 357 through 358 removed outlier: 4.179A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AF9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AG1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AG2, first strand: chain 'C' and resid 576 through 577 Processing sheet with id=AG3, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.884A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 695 " --> pdb=" O CYS C 671 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY C 667 " --> pdb=" O ILE C 670 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.557A pdb=" N LYS C1073 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 725 through 728 removed outlier: 7.035A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AG7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AG8, first strand: chain 'C' and resid 1095 through 1097 Processing sheet with id=AG9, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AH1, first strand: chain 'D' and resid 9 through 12 removed outlier: 3.512A pdb=" N GLN D 10 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.587A pdb=" N ILE E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AH5, first strand: chain 'F' and resid 9 through 12 removed outlier: 6.338A pdb=" N GLN F 10 " --> pdb=" O GLU F 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'F' and resid 44 through 47 removed outlier: 6.086A pdb=" N TRP F 34 " --> pdb=" O LEU F 46 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AH8, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.524A pdb=" N ILE G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N TYR G 50 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR G 50 " --> pdb=" O SER G 59 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AI1, first strand: chain 'H' and resid 9 through 12 removed outlier: 3.511A pdb=" N GLN H 10 " --> pdb=" O LYS H 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP H 34 " --> pdb=" O LEU H 46 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 3 through 6 removed outlier: 3.553A pdb=" N THR I 69 " --> pdb=" O GLU I 82 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.588A pdb=" N ILE I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR I 50 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) 895 hydrogen bonds defined for protein. 2319 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: 13.08 Time building geometry restraints manager: 13.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6661 1.32 - 1.45: 9162 1.45 - 1.57: 14965 1.57 - 1.70: 3 1.70 - 1.83: 159 Bond restraints: 30950 Sorted by residual: bond pdb=" C LEU A 335 " pdb=" N CYS A 336 " ideal model delta sigma weight residual 1.331 1.456 -0.125 1.24e-02 6.50e+03 1.02e+02 bond pdb=" C LEU C 335 " pdb=" N CYS C 336 " ideal model delta sigma weight residual 1.331 1.455 -0.125 1.24e-02 6.50e+03 1.01e+02 bond pdb=" C LEU B 335 " pdb=" N CYS B 336 " ideal model delta sigma weight residual 1.331 1.455 -0.124 1.24e-02 6.50e+03 1.00e+02 bond pdb=" C CYS C 336 " pdb=" N PRO C 337 " ideal model delta sigma weight residual 1.334 1.503 -0.169 2.34e-02 1.83e+03 5.21e+01 bond pdb=" C CYS B 336 " pdb=" N PRO B 337 " ideal model delta sigma weight residual 1.334 1.502 -0.168 2.34e-02 1.83e+03 5.18e+01 ... (remaining 30945 not shown) Histogram of bond angle deviations from ideal: 92.94 - 101.21: 91 101.21 - 109.48: 6835 109.48 - 117.76: 16785 117.76 - 126.03: 18002 126.03 - 134.31: 387 Bond angle restraints: 42100 Sorted by residual: angle pdb=" C LYS A 733 " pdb=" N THR A 734 " pdb=" CA THR A 734 " ideal model delta sigma weight residual 122.73 108.74 13.99 1.92e+00 2.71e-01 5.31e+01 angle pdb=" C LYS C 733 " pdb=" N THR C 734 " pdb=" CA THR C 734 " ideal model delta sigma weight residual 122.73 108.79 13.94 1.92e+00 2.71e-01 5.27e+01 angle pdb=" C LYS B 733 " pdb=" N THR B 734 " pdb=" CA THR B 734 " ideal model delta sigma weight residual 122.73 108.80 13.93 1.92e+00 2.71e-01 5.26e+01 angle pdb=" C HIS A1088 " pdb=" N PHE A1089 " pdb=" CA PHE A1089 " ideal model delta sigma weight residual 123.56 110.05 13.51 1.98e+00 2.55e-01 4.66e+01 angle pdb=" C HIS B1088 " pdb=" N PHE B1089 " pdb=" CA PHE B1089 " ideal model delta sigma weight residual 123.56 110.06 13.50 1.98e+00 2.55e-01 4.65e+01 ... (remaining 42095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 17769 17.13 - 34.25: 1095 34.25 - 51.38: 196 51.38 - 68.51: 86 68.51 - 85.63: 18 Dihedral angle restraints: 19164 sinusoidal: 8175 harmonic: 10989 Sorted by residual: dihedral pdb=" CA TRP F 93 " pdb=" C TRP F 93 " pdb=" N PRO F 94 " pdb=" CA PRO F 94 " ideal model delta harmonic sigma weight residual -180.00 -129.50 -50.50 0 5.00e+00 4.00e-02 1.02e+02 dihedral pdb=" CA TRP D 93 " pdb=" C TRP D 93 " pdb=" N PRO D 94 " pdb=" CA PRO D 94 " ideal model delta harmonic sigma weight residual 180.00 -132.83 -47.17 0 5.00e+00 4.00e-02 8.90e+01 dihedral pdb=" CA TRP H 93 " pdb=" C TRP H 93 " pdb=" N PRO H 94 " pdb=" CA PRO H 94 " ideal model delta harmonic sigma weight residual -180.00 -132.84 -47.16 0 5.00e+00 4.00e-02 8.90e+01 ... (remaining 19161 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.332: 4908 0.332 - 0.664: 16 0.664 - 0.996: 4 0.996 - 1.328: 0 1.328 - 1.660: 1 Chirality restraints: 4929 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 603 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -0.74 -1.66 2.00e-01 2.50e+01 6.89e+01 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.36e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.50 0.10 2.00e-02 2.50e+03 2.34e+01 ... (remaining 4926 not shown) Planarity restraints: 5387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.062 2.00e-02 2.50e+03 6.09e-02 4.63e+01 pdb=" CG ASN A 603 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.087 2.00e-02 2.50e+03 pdb=" C1 NAG A1306 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP D 93 " 0.099 5.00e-02 4.00e+02 1.50e-01 3.60e+01 pdb=" N PRO D 94 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO D 94 " 0.085 5.00e-02 4.00e+02 pdb=" CD PRO D 94 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP H 93 " -0.099 5.00e-02 4.00e+02 1.50e-01 3.59e+01 pdb=" N PRO H 94 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO H 94 " -0.085 5.00e-02 4.00e+02 pdb=" CD PRO H 94 " -0.075 5.00e-02 4.00e+02 ... (remaining 5384 not shown) Histogram of nonbonded interaction distances: 1.08 - 1.85: 8 1.85 - 2.61: 1567 2.61 - 3.37: 43921 3.37 - 4.14: 77509 4.14 - 4.90: 135927 Nonbonded interactions: 258932 Sorted by model distance: nonbonded pdb=" OE2 GLU B 324 " pdb=" O SER B 325 " model vdw 1.082 3.040 nonbonded pdb=" O ASN A 856 " pdb=" CD1 LEU A 858 " model vdw 1.222 3.460 nonbonded pdb=" O PHE C 855 " pdb=" ND2 ASN C 856 " model vdw 1.310 2.520 nonbonded pdb=" CZ PHE A 559 " pdb=" O PHE A 565 " model vdw 1.367 3.340 nonbonded pdb=" CB ARG A 408 " pdb=" OD1 ASP E 102 " model vdw 1.433 3.440 ... (remaining 258927 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147 or resid 1301 through 1310 \ )) selection = (chain 'C' and (resid 25 through 320 or (resid 321 and (name N or name CA or nam \ e C or name O or name CB )) or resid 322 through 1147 or resid 1301 through 1310 \ )) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.440 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 83.050 Find NCS groups from input model: 1.810 Set up NCS constraints: 0.370 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 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 : 0.027 0.196 30950 Z= 1.797 Angle : 1.665 17.502 42100 Z= 0.885 Chirality : 0.093 1.660 4929 Planarity : 0.009 0.150 5342 Dihedral : 12.230 83.546 11979 Min Nonbonded Distance : 1.082 Molprobity Statistics. All-atom Clashscore : 48.79 Ramachandran Plot: Outliers : 0.81 % Allowed : 9.40 % Favored : 89.79 % Rotamer: Outliers : 1.80 % Allowed : 2.23 % Favored : 95.97 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.59 % 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: -4.79 (0.10), residues: 3711 helix: -5.11 (0.06), residues: 621 sheet: -2.67 (0.13), residues: 918 loop : -2.87 (0.11), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.007 TRP B 64 HIS 0.022 0.005 HIS A1058 PHE 0.070 0.006 PHE C1042 TYR 0.055 0.005 TYR F 95 ARG 0.012 0.002 ARG B 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 182 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 800 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.8547 (m-80) REVERT: A 850 ILE cc_start: 0.3066 (OUTLIER) cc_final: 0.2517 (mp) REVERT: A 853 GLN cc_start: 0.3906 (OUTLIER) cc_final: 0.3581 (mt0) REVERT: A 1089 PHE cc_start: 0.9307 (OUTLIER) cc_final: 0.8719 (m-10) REVERT: A 1113 GLN cc_start: 0.7784 (mt0) cc_final: 0.7114 (mt0) REVERT: B 864 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8029 (tp) REVERT: C 858 LEU cc_start: 0.8441 (mp) cc_final: 0.8224 (mt) REVERT: C 902 MET cc_start: 0.8927 (mmm) cc_final: 0.8647 (mmm) REVERT: C 1113 GLN cc_start: 0.7859 (mt0) cc_final: 0.7536 (mt0) REVERT: G 6 GLN cc_start: 0.3204 (mt0) cc_final: 0.2110 (tt0) outliers start: 59 outliers final: 35 residues processed: 239 average time/residue: 0.4364 time to fit residues: 164.7612 Evaluate side-chains 128 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 88 time to evaluate : 3.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 559 PHE Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 800 PHE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 GLN Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1089 PHE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 800 PHE Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 864 LEU Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1089 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 319 ARG Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 800 PHE Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 853 GLN Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1089 PHE Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 7.9990 chunk 281 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 177 optimal weight: 0.6980 chunk 217 optimal weight: 5.9990 chunk 337 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 164 ASN A 218 GLN A 414 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 GLN A1088 HIS A1119 ASN B 66 HIS B 164 ASN B 218 GLN B 437 ASN B 580 GLN B 655 HIS B1088 HIS B1119 ASN C 66 HIS C 164 ASN C 218 GLN C 437 ASN C 580 GLN C 655 HIS C1088 HIS C1119 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN ** F 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN G 55 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30950 Z= 0.265 Angle : 0.812 10.013 42100 Z= 0.428 Chirality : 0.052 0.582 4929 Planarity : 0.006 0.133 5342 Dihedral : 10.849 115.413 5373 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.07 % Favored : 94.69 % Rotamer: Outliers : 2.10 % Allowed : 4.64 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -3.14 (0.12), residues: 3711 helix: -2.71 (0.15), residues: 618 sheet: -1.97 (0.14), residues: 933 loop : -1.95 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP H 93 HIS 0.011 0.002 HIS I 35 PHE 0.027 0.002 PHE E 54 TYR 0.044 0.002 TYR H 95 ARG 0.006 0.001 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 168 time to evaluate : 3.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 549 THR cc_start: 0.8382 (m) cc_final: 0.8180 (p) REVERT: B 564 GLN cc_start: 0.7460 (OUTLIER) cc_final: 0.7192 (tp40) REVERT: F 37 GLN cc_start: 0.3676 (pp30) cc_final: 0.3049 (pt0) REVERT: G 6 GLN cc_start: 0.3092 (mt0) cc_final: 0.2159 (tt0) outliers start: 69 outliers final: 35 residues processed: 229 average time/residue: 0.3931 time to fit residues: 150.1844 Evaluate side-chains 133 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 97 time to evaluate : 3.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 563 GLN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 48 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.3980 chunk 104 optimal weight: 5.9990 chunk 281 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 338 optimal weight: 40.0000 chunk 365 optimal weight: 40.0000 chunk 301 optimal weight: 0.0770 chunk 335 optimal weight: 40.0000 chunk 115 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN B 134 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN C 437 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN F 37 GLN F 89 GLN ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 ASN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 30950 Z= 0.272 Angle : 0.694 8.665 42100 Z= 0.360 Chirality : 0.049 0.565 4929 Planarity : 0.005 0.126 5342 Dihedral : 9.377 113.417 5323 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.90 % Favored : 93.94 % Rotamer: Outliers : 2.20 % Allowed : 6.65 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: -2.27 (0.13), residues: 3711 helix: -0.97 (0.20), residues: 636 sheet: -1.66 (0.15), residues: 933 loop : -1.59 (0.13), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP H 93 HIS 0.009 0.001 HIS D 33 PHE 0.030 0.002 PHE E 54 TYR 0.035 0.002 TYR H 95 ARG 0.004 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 134 time to evaluate : 3.359 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: B 740 MET cc_start: 0.5584 (tpt) cc_final: 0.4972 (tpt) REVERT: B 1050 MET cc_start: 0.8340 (ptm) cc_final: 0.7869 (ptm) REVERT: C 796 ASP cc_start: 0.6853 (OUTLIER) cc_final: 0.6409 (p0) REVERT: C 957 GLN cc_start: 0.7994 (tm-30) cc_final: 0.7784 (tm-30) REVERT: G 6 GLN cc_start: 0.3141 (mt0) cc_final: 0.2298 (tt0) outliers start: 72 outliers final: 43 residues processed: 195 average time/residue: 0.3840 time to fit residues: 127.5117 Evaluate side-chains 137 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 93 time to evaluate : 3.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain I residue 48 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 7.9990 chunk 254 optimal weight: 8.9990 chunk 175 optimal weight: 0.0470 chunk 37 optimal weight: 30.0000 chunk 161 optimal weight: 0.9990 chunk 227 optimal weight: 0.0470 chunk 339 optimal weight: 30.0000 chunk 359 optimal weight: 10.0000 chunk 177 optimal weight: 0.5980 chunk 321 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 30950 Z= 0.179 Angle : 0.619 8.056 42100 Z= 0.320 Chirality : 0.047 0.538 4929 Planarity : 0.004 0.114 5342 Dihedral : 8.417 111.916 5315 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer: Outliers : 1.77 % Allowed : 7.47 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3711 helix: -0.13 (0.21), residues: 636 sheet: -1.33 (0.16), residues: 936 loop : -1.42 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 PHE 0.021 0.001 PHE B 133 TYR 0.022 0.001 TYR B 380 ARG 0.004 0.000 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 129 time to evaluate : 3.229 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: A 906 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.8178 (m-80) REVERT: B 1050 MET cc_start: 0.8318 (ptm) cc_final: 0.7941 (ptm) REVERT: G 6 GLN cc_start: 0.2570 (mt0) cc_final: 0.1980 (tt0) outliers start: 58 outliers final: 38 residues processed: 178 average time/residue: 0.3657 time to fit residues: 112.1618 Evaluate side-chains 134 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 95 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 148 optimal weight: 10.0000 chunk 306 optimal weight: 0.0070 chunk 248 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 322 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 30950 Z= 0.392 Angle : 0.664 7.773 42100 Z= 0.340 Chirality : 0.048 0.540 4929 Planarity : 0.005 0.106 5342 Dihedral : 8.184 109.274 5312 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.04 % Favored : 93.78 % Rotamer: Outliers : 2.20 % Allowed : 8.24 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.13), residues: 3711 helix: -0.08 (0.21), residues: 639 sheet: -1.29 (0.16), residues: 948 loop : -1.54 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 110 HIS 0.007 0.001 HIS I 35 PHE 0.018 0.002 PHE B 133 TYR 0.022 0.002 TYR G 50 ARG 0.003 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 95 time to evaluate : 3.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASP cc_start: 0.6829 (OUTLIER) cc_final: 0.6340 (p0) REVERT: A 906 PHE cc_start: 0.8911 (OUTLIER) cc_final: 0.8525 (m-80) REVERT: B 796 ASP cc_start: 0.6855 (OUTLIER) cc_final: 0.6443 (p0) REVERT: E 23 LYS cc_start: 0.4710 (OUTLIER) cc_final: 0.4237 (mmmm) REVERT: E 80 TYR cc_start: 0.4093 (OUTLIER) cc_final: 0.3542 (t80) REVERT: G 6 GLN cc_start: 0.2791 (mt0) cc_final: 0.1986 (tt0) outliers start: 72 outliers final: 56 residues processed: 160 average time/residue: 0.3516 time to fit residues: 98.4499 Evaluate side-chains 141 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 80 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 319 ARG Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 711 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 796 ASP Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 32 TYR Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 5.9990 chunk 323 optimal weight: 8.9990 chunk 71 optimal weight: 0.0270 chunk 211 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 359 optimal weight: 7.9990 chunk 298 optimal weight: 0.6980 chunk 166 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 chunk 188 optimal weight: 7.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 30950 Z= 0.181 Angle : 0.586 7.994 42100 Z= 0.301 Chirality : 0.046 0.521 4929 Planarity : 0.004 0.105 5342 Dihedral : 7.765 109.717 5312 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.99 % Favored : 94.85 % Rotamer: Outliers : 1.89 % Allowed : 9.52 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.56 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.14), residues: 3711 helix: 0.35 (0.21), residues: 642 sheet: -1.08 (0.16), residues: 954 loop : -1.45 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 PHE 0.021 0.001 PHE A 133 TYR 0.017 0.001 TYR G 50 ARG 0.003 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 109 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.8708 (OUTLIER) cc_final: 0.8326 (m-80) REVERT: B 775 ASP cc_start: 0.7143 (m-30) cc_final: 0.6811 (m-30) REVERT: B 902 MET cc_start: 0.8912 (mmm) cc_final: 0.8492 (mmm) REVERT: B 906 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8564 (m-80) REVERT: E 80 TYR cc_start: 0.3893 (OUTLIER) cc_final: 0.3168 (t80) REVERT: I 110 TRP cc_start: -0.0233 (m-10) cc_final: -0.0465 (m-10) outliers start: 62 outliers final: 48 residues processed: 165 average time/residue: 0.3588 time to fit residues: 103.6449 Evaluate side-chains 147 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 96 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 906 PHE Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 676 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 102 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 chunk 205 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 302 optimal weight: 0.8980 chunk 200 optimal weight: 1.9990 chunk 358 optimal weight: 10.0000 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 30950 Z= 0.435 Angle : 0.682 9.309 42100 Z= 0.347 Chirality : 0.048 0.517 4929 Planarity : 0.005 0.107 5342 Dihedral : 7.806 107.377 5306 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.25 % Favored : 93.59 % Rotamer: Outliers : 2.20 % Allowed : 9.67 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.13), residues: 3711 helix: 0.02 (0.21), residues: 645 sheet: -1.12 (0.16), residues: 939 loop : -1.59 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 PHE 0.032 0.002 PHE E 54 TYR 0.020 0.002 TYR G 50 ARG 0.005 0.001 ARG G 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 96 time to evaluate : 3.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6558 (p0) REVERT: A 906 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8548 (m-80) REVERT: E 80 TYR cc_start: 0.3934 (OUTLIER) cc_final: 0.3186 (t80) REVERT: G 18 VAL cc_start: 0.1173 (OUTLIER) cc_final: 0.0826 (t) REVERT: I 110 TRP cc_start: -0.0160 (m-10) cc_final: -0.0594 (m-10) outliers start: 72 outliers final: 59 residues processed: 161 average time/residue: 0.3855 time to fit residues: 110.0950 Evaluate side-chains 149 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 86 time to evaluate : 3.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 796 ASP Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 716 THR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 796 ASP Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 18 VAL Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.8980 chunk 143 optimal weight: 7.9990 chunk 214 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 0.0570 chunk 69 optimal weight: 0.3980 chunk 227 optimal weight: 1.9990 chunk 244 optimal weight: 0.9980 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 281 optimal weight: 0.9980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6394 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 30950 Z= 0.172 Angle : 0.591 10.239 42100 Z= 0.303 Chirality : 0.045 0.510 4929 Planarity : 0.004 0.095 5342 Dihedral : 7.426 108.312 5306 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.80 % Favored : 95.04 % Rotamer: Outliers : 1.65 % Allowed : 10.43 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.14), residues: 3711 helix: 0.52 (0.21), residues: 645 sheet: -0.91 (0.17), residues: 948 loop : -1.42 (0.13), residues: 2118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP G 110 HIS 0.010 0.001 HIS I 35 PHE 0.026 0.001 PHE E 54 TYR 0.020 0.001 TYR I 32 ARG 0.004 0.000 ARG A 765 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 105 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8355 (m-80) REVERT: E 80 TYR cc_start: 0.3563 (OUTLIER) cc_final: 0.2997 (t80) REVERT: G 18 VAL cc_start: 0.0910 (OUTLIER) cc_final: 0.0623 (t) REVERT: I 110 TRP cc_start: -0.0215 (m-10) cc_final: -0.0623 (m-10) outliers start: 54 outliers final: 47 residues processed: 151 average time/residue: 0.3516 time to fit residues: 93.8489 Evaluate side-chains 142 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 92 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 102 ASP Chi-restraints excluded: chain I residue 104 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 313 optimal weight: 7.9990 chunk 334 optimal weight: 40.0000 chunk 201 optimal weight: 0.9990 chunk 145 optimal weight: 30.0000 chunk 262 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 0.6980 chunk 316 optimal weight: 30.0000 chunk 332 optimal weight: 30.0000 overall best weight: 4.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.082 30950 Z= 0.573 Angle : 0.767 10.421 42100 Z= 0.387 Chirality : 0.051 0.505 4929 Planarity : 0.005 0.092 5342 Dihedral : 7.727 105.894 5304 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.28 % Favored : 92.56 % Rotamer: Outliers : 2.07 % Allowed : 10.46 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.13), residues: 3711 helix: -0.06 (0.20), residues: 630 sheet: -1.28 (0.16), residues: 990 loop : -1.66 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP G 110 HIS 0.012 0.002 HIS I 35 PHE 0.034 0.002 PHE E 54 TYR 0.025 0.002 TYR G 95 ARG 0.007 0.001 ARG B 905 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 89 time to evaluate : 3.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: E 80 TYR cc_start: 0.3861 (OUTLIER) cc_final: 0.3175 (t80) REVERT: G 18 VAL cc_start: 0.1329 (OUTLIER) cc_final: 0.1001 (t) REVERT: G 46 GLU cc_start: 0.3351 (OUTLIER) cc_final: 0.3132 (pt0) REVERT: I 110 TRP cc_start: -0.0047 (m-10) cc_final: -0.0563 (m-10) outliers start: 68 outliers final: 57 residues processed: 149 average time/residue: 0.3770 time to fit residues: 97.8083 Evaluate side-chains 142 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 81 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 80 TYR Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 46 GLU Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 4.9990 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 9.9990 chunk 341 optimal weight: 9.9990 chunk 295 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 227 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30950 Z= 0.316 Angle : 0.639 9.763 42100 Z= 0.324 Chirality : 0.047 0.499 4929 Planarity : 0.004 0.089 5342 Dihedral : 7.418 107.727 5304 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.01 % Favored : 93.83 % Rotamer: Outliers : 2.01 % Allowed : 10.65 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.14), residues: 3711 helix: 0.22 (0.21), residues: 636 sheet: -1.19 (0.17), residues: 969 loop : -1.55 (0.13), residues: 2106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 110 HIS 0.014 0.001 HIS I 35 PHE 0.031 0.001 PHE E 54 TYR 0.019 0.001 TYR G 50 ARG 0.003 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7422 Ramachandran restraints generated. 3711 Oldfield, 0 Emsley, 3711 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 86 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 906 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8539 (m-80) outliers start: 66 outliers final: 58 residues processed: 144 average time/residue: 0.3615 time to fit residues: 92.0187 Evaluate side-chains 146 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 87 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 906 PHE Chi-restraints excluded: chain A residue 936 ASP Chi-restraints excluded: chain A residue 1032 CYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain B residue 1032 CYS Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 1032 CYS Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 31 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain G residue 18 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 110 TRP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 102 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 5.9990 chunk 314 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 272 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 295 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 303 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 99 GLN E 55 ASN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.147339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.104513 restraints weight = 79194.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.101837 restraints weight = 54359.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.101862 restraints weight = 52691.844| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 30950 Z= 0.184 Angle : 0.586 9.527 42100 Z= 0.297 Chirality : 0.045 0.504 4929 Planarity : 0.004 0.087 5342 Dihedral : 6.889 107.952 5304 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.63 % Favored : 94.23 % Rotamer: Outliers : 1.65 % Allowed : 10.92 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3711 helix: 0.69 (0.21), residues: 636 sheet: -0.94 (0.17), residues: 921 loop : -1.34 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP G 110 HIS 0.014 0.001 HIS I 35 PHE 0.030 0.001 PHE E 54 TYR 0.016 0.001 TYR B 904 ARG 0.004 0.000 ARG E 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4485.42 seconds wall clock time: 85 minutes 26.38 seconds (5126.38 seconds total)