Starting phenix.real_space_refine on Fri Dec 15 04:40:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/12_2023/7cak_30333.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/12_2023/7cak_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_30333/12_2023/7cak_30333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/12_2023/7cak_30333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/12_2023/7cak_30333.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cak_30333/12_2023/7cak_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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 16.35, per 1000 atoms: 0.54 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: 13.06 Conformation dependent library (CDL) restraints added in 5.6 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: 3.87 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: 14.26 Time building geometry restraints manager: 14.18 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.280 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 85.350 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.410 ------------------------------------------------------------------------------- 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 : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 35 residues processed: 239 average time/residue: 0.4514 time to fit residues: 171.1649 Evaluate side-chains 121 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 86 time to evaluate : 3.036 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.3263 time to fit residues: 23.9542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 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: 4.9990 chunk 337 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 437 ASN B 580 GLN B 655 HIS B1088 HIS B1119 ASN C 66 HIS C 134 GLN C 164 ASN 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 6 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: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30950 Z= 0.270 Angle : 0.815 10.003 42100 Z= 0.430 Chirality : 0.053 0.587 4929 Planarity : 0.006 0.134 5342 Dihedral : 10.166 117.214 5295 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.85 % Favored : 94.91 % Rotamer: Outliers : 1.74 % Allowed : 4.91 % Favored : 93.35 % 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: -3.09 (0.12), residues: 3711 helix: -2.64 (0.15), residues: 618 sheet: -1.98 (0.14), residues: 954 loop : -1.88 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP H 93 HIS 0.011 0.002 HIS I 35 PHE 0.026 0.002 PHE E 54 TYR 0.042 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 224 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 167 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 25 residues processed: 216 average time/residue: 0.3794 time to fit residues: 138.7311 Evaluate side-chains 119 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 time to evaluate : 3.097 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.2577 time to fit residues: 16.3732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 0.0970 chunk 104 optimal weight: 7.9990 chunk 281 optimal weight: 1.9990 chunk 230 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 338 optimal weight: 40.0000 chunk 365 optimal weight: 30.0000 chunk 301 optimal weight: 0.9990 chunk 335 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- 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** B 134 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS 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 6 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 30950 Z= 0.310 Angle : 0.709 9.052 42100 Z= 0.367 Chirality : 0.049 0.567 4929 Planarity : 0.005 0.129 5342 Dihedral : 9.079 112.778 5295 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.98 % Favored : 93.86 % Rotamer: Outliers : 1.53 % Allowed : 7.41 % Favored : 91.06 % 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: -2.31 (0.13), residues: 3711 helix: -1.07 (0.20), residues: 630 sheet: -1.70 (0.15), residues: 948 loop : -1.58 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP H 93 HIS 0.007 0.001 HIS I 35 PHE 0.029 0.002 PHE E 54 TYR 0.034 0.002 TYR H 95 ARG 0.007 0.001 ARG G 98 *********************** 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 178 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 128 time to evaluate : 3.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 24 residues processed: 166 average time/residue: 0.3875 time to fit residues: 113.2632 Evaluate side-chains 116 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 3.531 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2814 time to fit residues: 17.6624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 20.0000 chunk 254 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 37 optimal weight: 30.0000 chunk 161 optimal weight: 0.0060 chunk 227 optimal weight: 0.5980 chunk 339 optimal weight: 20.0000 chunk 359 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 chunk 321 optimal weight: 30.0000 chunk 96 optimal weight: 0.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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** A1119 ASN 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 6 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6376 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30950 Z= 0.191 Angle : 0.623 8.307 42100 Z= 0.323 Chirality : 0.047 0.537 4929 Planarity : 0.005 0.114 5342 Dihedral : 8.292 111.984 5295 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.66 % Rotamer: Outliers : 0.70 % Allowed : 8.05 % Favored : 91.24 % 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: -1.83 (0.13), residues: 3711 helix: -0.23 (0.21), residues: 639 sheet: -1.38 (0.16), residues: 936 loop : -1.43 (0.13), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 PHE 0.020 0.001 PHE B 133 TYR 0.019 0.001 TYR G 50 ARG 0.004 0.000 ARG A 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 154 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 131 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 8 residues processed: 151 average time/residue: 0.3825 time to fit residues: 100.6548 Evaluate side-chains 102 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3041 time to fit residues: 9.0794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 267 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 306 optimal weight: 0.3980 chunk 248 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 322 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 30950 Z= 0.288 Angle : 0.633 9.952 42100 Z= 0.324 Chirality : 0.047 0.542 4929 Planarity : 0.004 0.107 5342 Dihedral : 7.888 109.089 5295 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.58 % Favored : 94.23 % Rotamer: Outliers : 0.95 % Allowed : 8.97 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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 (0.13), residues: 3711 helix: 0.03 (0.21), residues: 639 sheet: -1.22 (0.16), residues: 948 loop : -1.46 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP G 110 HIS 0.009 0.001 HIS I 35 PHE 0.022 0.002 PHE C 133 TYR 0.022 0.002 TYR G 50 ARG 0.004 0.000 ARG G 98 *********************** 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 125 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 4.061 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 120 average time/residue: 0.3681 time to fit residues: 79.6467 Evaluate side-chains 100 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 3.487 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2891 time to fit residues: 15.0606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 2.9990 chunk 323 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 0.0370 chunk 88 optimal weight: 0.5980 chunk 359 optimal weight: 0.6980 chunk 298 optimal weight: 0.7980 chunk 166 optimal weight: 0.9990 chunk 29 optimal weight: 0.0670 chunk 119 optimal weight: 0.4980 chunk 188 optimal weight: 7.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 901 GLN ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 6 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6360 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 30950 Z= 0.160 Angle : 0.580 7.887 42100 Z= 0.298 Chirality : 0.045 0.523 4929 Planarity : 0.004 0.109 5342 Dihedral : 7.548 108.861 5295 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.83 % Rotamer: Outliers : 0.73 % Allowed : 9.82 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.11 % 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: -1.42 (0.14), residues: 3711 helix: 0.47 (0.21), residues: 642 sheet: -1.05 (0.16), residues: 972 loop : -1.34 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP G 110 HIS 0.008 0.001 HIS I 35 PHE 0.032 0.001 PHE E 54 TYR 0.016 0.001 TYR G 50 ARG 0.004 0.000 ARG G 98 *********************** 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 133 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 15 residues processed: 130 average time/residue: 0.3590 time to fit residues: 83.7990 Evaluate side-chains 106 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2767 time to fit residues: 12.8047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 205 optimal weight: 5.9990 chunk 262 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 358 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** 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** ** G 39 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: 0.6462 moved from start: 0.4196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 30950 Z= 0.334 Angle : 0.628 8.380 42100 Z= 0.321 Chirality : 0.047 0.517 4929 Planarity : 0.004 0.106 5342 Dihedral : 7.483 106.307 5295 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.96 % Favored : 93.88 % Rotamer: Outliers : 0.46 % Allowed : 10.80 % Favored : 88.74 % 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: -1.53 (0.14), residues: 3711 helix: 0.31 (0.21), residues: 645 sheet: -0.97 (0.16), residues: 951 loop : -1.47 (0.13), residues: 2115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP G 110 HIS 0.008 0.001 HIS I 35 PHE 0.024 0.002 PHE E 54 TYR 0.022 0.002 TYR G 50 ARG 0.004 0.000 ARG B 905 *********************** 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 108 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 93 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 103 average time/residue: 0.3859 time to fit residues: 71.2002 Evaluate side-chains 93 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 3.148 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3078 time to fit residues: 10.5613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 0.0570 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 70 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 227 optimal weight: 0.5980 chunk 244 optimal weight: 8.9990 chunk 177 optimal weight: 0.3980 chunk 33 optimal weight: 30.0000 chunk 281 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.4527 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= 0.165 Angle : 0.582 9.771 42100 Z= 0.297 Chirality : 0.045 0.510 4929 Planarity : 0.004 0.094 5342 Dihedral : 7.260 106.635 5295 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.15 % Favored : 94.69 % Rotamer: Outliers : 0.31 % Allowed : 10.95 % Favored : 88.74 % 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: -1.29 (0.14), residues: 3711 helix: 0.70 (0.21), residues: 645 sheet: -0.96 (0.16), residues: 1002 loop : -1.30 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP G 110 HIS 0.010 0.001 HIS I 35 PHE 0.037 0.001 PHE B 855 TYR 0.016 0.001 TYR G 50 ARG 0.005 0.000 ARG B 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 111 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 3.347 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 109 average time/residue: 0.4092 time to fit residues: 80.7041 Evaluate side-chains 96 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 3.486 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2728 time to fit residues: 7.5767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 313 optimal weight: 30.0000 chunk 334 optimal weight: 30.0000 chunk 201 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 262 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 301 optimal weight: 0.6980 chunk 316 optimal weight: 30.0000 chunk 332 optimal weight: 5.9990 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1119 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1119 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 ASN D 10 GLN ** 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 88 GLN ** H 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 30950 Z= 0.575 Angle : 0.752 9.494 42100 Z= 0.379 Chirality : 0.051 0.500 4929 Planarity : 0.004 0.091 5342 Dihedral : 7.567 104.459 5295 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 0.52 % Allowed : 11.10 % Favored : 88.38 % 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: -1.78 (0.13), residues: 3711 helix: 0.03 (0.20), residues: 639 sheet: -1.18 (0.16), residues: 990 loop : -1.58 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP G 110 HIS 0.007 0.002 HIS C1058 PHE 0.027 0.002 PHE E 54 TYR 0.033 0.002 TYR H 35 ARG 0.008 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 104 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 3.543 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 102 average time/residue: 0.3955 time to fit residues: 72.9570 Evaluate side-chains 94 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 3.597 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3109 time to fit residues: 12.7375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 3.9990 chunk 353 optimal weight: 20.0000 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 5.9990 chunk 370 optimal weight: 0.2980 chunk 341 optimal weight: 30.0000 chunk 295 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 227 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 856 ASN ** 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 37 GLN H 88 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: 0.6429 moved from start: 0.4554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 30950 Z= 0.218 Angle : 0.602 8.865 42100 Z= 0.306 Chirality : 0.046 0.499 4929 Planarity : 0.004 0.088 5342 Dihedral : 7.175 106.421 5295 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 0.09 % Allowed : 11.35 % Favored : 88.56 % 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: -1.42 (0.14), residues: 3711 helix: 0.51 (0.21), residues: 642 sheet: -0.97 (0.17), residues: 975 loop : -1.39 (0.13), residues: 2094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 110 HIS 0.008 0.001 HIS I 35 PHE 0.027 0.001 PHE E 54 TYR 0.022 0.001 TYR H 35 ARG 0.004 0.000 ARG I 98 ********************** 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 92 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 3.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 91 average time/residue: 0.4100 time to fit residues: 65.7535 Evaluate side-chains 83 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 3.149 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3346 time to fit residues: 4.9052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 234 optimal weight: 6.9990 chunk 314 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 chunk 272 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 295 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 303 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 0.4980 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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** C1119 ASN ** D 89 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.147755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.104089 restraints weight = 80234.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102082 restraints weight = 50796.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101948 restraints weight = 46990.881| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30950 Z= 0.252 Angle : 0.605 9.517 42100 Z= 0.306 Chirality : 0.046 0.501 4929 Planarity : 0.004 0.086 5342 Dihedral : 6.904 105.737 5295 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.09 % Favored : 93.78 % Rotamer: Outliers : 0.09 % Allowed : 11.50 % Favored : 88.41 % 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: 0.64 (0.21), residues: 630 sheet: -0.87 (0.17), residues: 951 loop : -1.36 (0.13), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP G 110 HIS 0.006 0.001 HIS G 35 PHE 0.025 0.001 PHE E 54 TYR 0.018 0.001 TYR E 80 ARG 0.005 0.000 ARG E 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4321.87 seconds wall clock time: 96 minutes 1.93 seconds (5761.93 seconds total)