Starting phenix.real_space_refine on Fri Feb 16 23:57:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uab_26419/02_2024/7uab_26419.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uab_26419/02_2024/7uab_26419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uab_26419/02_2024/7uab_26419.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uab_26419/02_2024/7uab_26419.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uab_26419/02_2024/7uab_26419.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uab_26419/02_2024/7uab_26419.pdb" } resolution = 3.7 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= 0.002 sd= 0.031 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: 6 Type Number sf(0) Gaussians Ca 7 9.91 5 Zn 4 6.06 5 S 74 5.16 5 C 10669 2.51 5 N 2808 2.21 5 O 3315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 100": "OE1" <-> "OE2" Residue "A GLU 116": "OE1" <-> "OE2" Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 331": "OE1" <-> "OE2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 463": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 498": "OE1" <-> "OE2" Residue "A GLU 502": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 100": "OE1" <-> "OE2" Residue "D GLU 114": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 156": "OE1" <-> "OE2" Residue "D GLU 166": "OE1" <-> "OE2" Residue "D GLU 251": "OE1" <-> "OE2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D GLU 299": "OE1" <-> "OE2" Residue "D GLU 325": "OE1" <-> "OE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D GLU 428": "OE1" <-> "OE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D GLU 463": "OE1" <-> "OE2" Residue "D GLU 492": "OE1" <-> "OE2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D GLU 502": "OE1" <-> "OE2" Residue "D GLU 514": "OE1" <-> "OE2" Residue "D GLU 594": "OE1" <-> "OE2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E GLU 45": "OE1" <-> "OE2" Residue "E GLU 100": "OE1" <-> "OE2" Residue "E GLU 116": "OE1" <-> "OE2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 272": "OE1" <-> "OE2" Residue "E GLU 299": "OE1" <-> "OE2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E GLU 331": "OE1" <-> "OE2" Residue "E GLU 397": "OE1" <-> "OE2" Residue "E GLU 398": "OE1" <-> "OE2" Residue "E TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 428": "OE1" <-> "OE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 477": "OE1" <-> "OE2" Residue "E PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 492": "OE1" <-> "OE2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E GLU 502": "OE1" <-> "OE2" Residue "E GLU 514": "OE1" <-> "OE2" Residue "E GLU 594": "OE1" <-> "OE2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 100": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 156": "OE1" <-> "OE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H GLU 234": "OE1" <-> "OE2" Residue "H PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 272": "OE1" <-> "OE2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "H TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 325": "OE1" <-> "OE2" Residue "H GLU 326": "OE1" <-> "OE2" Residue "H GLU 331": "OE1" <-> "OE2" Residue "H GLU 397": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H GLU 446": "OE1" <-> "OE2" Residue "H GLU 463": "OE1" <-> "OE2" Residue "H GLU 477": "OE1" <-> "OE2" Residue "H GLU 492": "OE1" <-> "OE2" Residue "H GLU 498": "OE1" <-> "OE2" Residue "H GLU 502": "OE1" <-> "OE2" Residue "H GLU 514": "OE1" <-> "OE2" Residue "H GLU 594": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16877 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 3859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3859 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 464} Chain breaks: 10 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "D" Number of atoms: 3833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3833 Classifications: {'peptide': 475} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 459} Chain breaks: 11 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 544, 4363 Classifications: {'peptide': 544} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 526} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 5} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 4365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 542, 4365 Classifications: {'peptide': 542} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 524} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' CA': 1, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 31 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 17 Unusual residues: {' CA': 2, ' ZN': 1, 'NAG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.06, per 1000 atoms: 0.54 Number of scatterers: 16877 At special positions: 0 Unit cell: (100.7, 111.3, 179.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 Ca 7 19.99 S 74 16.00 O 3315 8.00 N 2808 7.00 C 10669 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 147 " distance=2.05 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 431 " distance=2.03 Simple disulfide: pdb=" SG CYS A 557 " - pdb=" SG CYS A 559 " distance=2.05 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 431 " distance=2.03 Simple disulfide: pdb=" SG CYS D 557 " - pdb=" SG CYS D 559 " distance=2.02 Simple disulfide: pdb=" SG CYS E 107 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 269 " - pdb=" SG CYS E 277 " distance=2.04 Simple disulfide: pdb=" SG CYS E 343 " - pdb=" SG CYS E 431 " distance=2.03 Simple disulfide: pdb=" SG CYS E 557 " - pdb=" SG CYS E 559 " distance=2.03 Simple disulfide: pdb=" SG CYS H 107 " - pdb=" SG CYS H 259 " distance=2.03 Simple disulfide: pdb=" SG CYS H 128 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 269 " - pdb=" SG CYS H 277 " distance=2.04 Simple disulfide: pdb=" SG CYS H 343 " - pdb=" SG CYS H 431 " distance=2.03 Simple disulfide: pdb=" SG CYS H 557 " - pdb=" SG CYS H 559 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG G 1 " - " FUC G 3 " " NAG J 1 " - " FUC J 3 " " NAG N 1 " - " FUC N 3 " NAG-ASN " NAG A 701 " - " ASN A 440 " " NAG A 702 " - " ASN A 222 " " NAG B 1 " - " ASN A 140 " " NAG C 1 " - " ASN A 414 " " NAG D 701 " - " ASN D 222 " " NAG D 702 " - " ASN D 440 " " NAG E 701 " - " ASN E 258 " " NAG E 702 " - " ASN E 440 " " NAG F 1 " - " ASN D 140 " " NAG G 1 " - " ASN D 414 " " NAG H 701 " - " ASN H 258 " " NAG I 1 " - " ASN E 140 " " NAG J 1 " - " ASN E 414 " " NAG K 1 " - " ASN E 222 " " NAG L 1 " - " ASN H 222 " " NAG M 1 " - " ASN H 440 " " NAG N 1 " - " ASN H 414 " " NAG O 1 " - " ASN H 140 " Time building additional restraints: 6.69 Conformation dependent library (CDL) restraints added in 2.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 165 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 159 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 155 " pdb=" ZN D 703 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 159 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 165 " pdb="ZN ZN D 703 " - pdb=" NE2 HIS D 155 " pdb=" ZN E 704 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 159 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 165 " pdb="ZN ZN E 704 " - pdb=" NE2 HIS E 155 " pdb=" ZN H 703 " pdb="ZN ZN H 703 " - pdb=" NE2 HIS H 159 " pdb="ZN ZN H 703 " - pdb=" NE2 HIS H 165 " pdb="ZN ZN H 703 " - pdb=" NE2 HIS H 155 " 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3806 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 35 sheets defined 22.6% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 149 through 163 removed outlier: 3.919A pdb=" N PHE A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 186 through 192 removed outlier: 4.458A pdb=" N HIS A 189 " --> pdb=" O GLY A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 252 Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'A' and resid 546 through 551 Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.595A pdb=" N LYS A 577 " --> pdb=" O HIS A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 586 Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 54 through 58 Processing helix chain 'D' and resid 88 through 106 Processing helix chain 'D' and resid 149 through 162 Processing helix chain 'D' and resid 179 through 183 Processing helix chain 'D' and resid 187 through 192 Processing helix chain 'D' and resid 246 through 253 Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 516 through 520 removed outlier: 3.647A pdb=" N ARG D 520 " --> pdb=" O VAL D 517 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 551 removed outlier: 3.583A pdb=" N VAL D 550 " --> pdb=" O ARG D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 558 Processing helix chain 'D' and resid 573 through 579 removed outlier: 3.608A pdb=" N LYS D 577 " --> pdb=" O HIS D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 586 Processing helix chain 'D' and resid 597 through 600 Processing helix chain 'E' and resid 42 through 50 Processing helix chain 'E' and resid 54 through 58 removed outlier: 3.719A pdb=" N GLY E 57 " --> pdb=" O LEU E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 106 Processing helix chain 'E' and resid 149 through 162 Processing helix chain 'E' and resid 165 through 169 Processing helix chain 'E' and resid 171 through 174 Processing helix chain 'E' and resid 180 through 183 removed outlier: 3.707A pdb=" N ILE E 183 " --> pdb=" O TRP E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 180 through 183' Processing helix chain 'E' and resid 187 through 192 Processing helix chain 'E' and resid 232 through 238 removed outlier: 4.052A pdb=" N SER E 237 " --> pdb=" O GLU E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 258 Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 411 through 415 removed outlier: 3.722A pdb=" N SER E 415 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 448 Processing helix chain 'E' and resid 516 through 520 Processing helix chain 'E' and resid 546 through 551 Processing helix chain 'E' and resid 573 through 579 removed outlier: 3.578A pdb=" N ARG E 579 " --> pdb=" O MET E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 removed outlier: 6.909A pdb=" N ASN E 584 " --> pdb=" O PHE E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 600 Processing helix chain 'H' and resid 42 through 50 Processing helix chain 'H' and resid 88 through 106 Processing helix chain 'H' and resid 149 through 162 Processing helix chain 'H' and resid 165 through 170 removed outlier: 6.004A pdb=" N THR H 170 " --> pdb=" O GLN H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 175 removed outlier: 3.865A pdb=" N TYR H 175 " --> pdb=" O ASP H 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 171 through 175' Processing helix chain 'H' and resid 180 through 183 Processing helix chain 'H' and resid 186 through 192 removed outlier: 3.866A pdb=" N HIS H 189 " --> pdb=" O GLY H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 238 removed outlier: 4.244A pdb=" N SER H 237 " --> pdb=" O GLU H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 258 Processing helix chain 'H' and resid 275 through 279 Processing helix chain 'H' and resid 411 through 415 removed outlier: 3.883A pdb=" N SER H 415 " --> pdb=" O PRO H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 448 Processing helix chain 'H' and resid 546 through 551 removed outlier: 3.918A pdb=" N VAL H 550 " --> pdb=" O ARG H 546 " (cutoff:3.500A) Processing helix chain 'H' and resid 573 through 578 removed outlier: 3.782A pdb=" N ARG H 578 " --> pdb=" O GLN H 574 " (cutoff:3.500A) Processing helix chain 'H' and resid 582 through 586 Processing helix chain 'H' and resid 597 through 600 Processing sheet with id=AA1, first strand: chain 'A' and resid 110 through 112 removed outlier: 5.960A pdb=" N ILE A 79 " --> pdb=" O LYS A 111 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE A 122 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ILE A 82 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 269 removed outlier: 5.616A pdb=" N LEU A 421 " --> pdb=" O LYS A 349 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS A 349 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP A 423 " --> pdb=" O PHE A 347 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE A 347 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.188A pdb=" N VAL A 362 " --> pdb=" O LYS A 376 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS A 376 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG A 364 " --> pdb=" O LEU A 374 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU A 374 " --> pdb=" O ARG A 364 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 434 through 438 Processing sheet with id=AA6, first strand: chain 'A' and resid 454 through 455 Processing sheet with id=AA7, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.788A pdb=" N ILE A 571 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU A 484 " --> pdb=" O GLY A 569 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLY A 569 " --> pdb=" O LEU A 484 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N PHE A 486 " --> pdb=" O TRP A 567 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N TRP A 567 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N VAL A 488 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N LEU A 565 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 552 through 554 Processing sheet with id=AA9, first strand: chain 'D' and resid 110 through 112 removed outlier: 5.815A pdb=" N ILE D 79 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N PHE D 122 " --> pdb=" O PRO D 80 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE D 82 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE D 121 " --> pdb=" O GLN D 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 265 through 269 Processing sheet with id=AB2, first strand: chain 'D' and resid 265 through 269 removed outlier: 5.515A pdb=" N LEU D 421 " --> pdb=" O LYS D 349 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS D 349 " --> pdb=" O LEU D 421 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ASP D 423 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 347 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 327 through 330 removed outlier: 6.213A pdb=" N VAL D 362 " --> pdb=" O LYS D 376 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LYS D 376 " --> pdb=" O VAL D 362 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU D 374 " --> pdb=" O ARG D 364 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 434 through 438 Processing sheet with id=AB5, first strand: chain 'D' and resid 454 through 455 Processing sheet with id=AB6, first strand: chain 'D' and resid 454 through 455 removed outlier: 3.913A pdb=" N GLY D 466 " --> pdb=" O CYS D 489 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU D 482 " --> pdb=" O GLY D 569 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY D 569 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 484 " --> pdb=" O TRP D 567 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 552 through 554 Processing sheet with id=AB8, first strand: chain 'E' and resid 110 through 112 removed outlier: 5.942A pdb=" N ILE E 79 " --> pdb=" O LYS E 111 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE E 122 " --> pdb=" O PRO E 80 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE E 82 " --> pdb=" O PHE E 122 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 176 through 178 Processing sheet with id=AC1, first strand: chain 'E' and resid 265 through 269 Processing sheet with id=AC2, first strand: chain 'E' and resid 265 through 269 removed outlier: 5.629A pdb=" N LEU E 421 " --> pdb=" O LYS E 349 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N LYS E 349 " --> pdb=" O LEU E 421 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP E 423 " --> pdb=" O PHE E 347 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE E 347 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 280 through 281 removed outlier: 3.536A pdb=" N ARG E 357 " --> pdb=" O THR E 408 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 362 " --> pdb=" O LYS E 376 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS E 376 " --> pdb=" O VAL E 362 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG E 364 " --> pdb=" O LEU E 374 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU E 374 " --> pdb=" O ARG E 364 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 434 through 438 Processing sheet with id=AC5, first strand: chain 'E' and resid 454 through 455 Processing sheet with id=AC6, first strand: chain 'E' and resid 454 through 455 removed outlier: 7.522A pdb=" N LEU E 484 " --> pdb=" O GLY E 569 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY E 569 " --> pdb=" O LEU E 484 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N PHE E 486 " --> pdb=" O TRP E 567 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N TRP E 567 " --> pdb=" O PHE E 486 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N VAL E 488 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU E 565 " --> pdb=" O VAL E 488 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 552 through 554 Processing sheet with id=AC8, first strand: chain 'H' and resid 59 through 60 Processing sheet with id=AC9, first strand: chain 'H' and resid 110 through 112 removed outlier: 7.843A pdb=" N PHE H 122 " --> pdb=" O PRO H 80 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE H 82 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 176 through 178 Processing sheet with id=AD2, first strand: chain 'H' and resid 265 through 269 removed outlier: 3.605A pdb=" N ASP H 267 " --> pdb=" O LEU H 426 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 265 through 269 removed outlier: 3.605A pdb=" N ASP H 267 " --> pdb=" O LEU H 426 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 421 " --> pdb=" O LYS H 349 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N LYS H 349 " --> pdb=" O LEU H 421 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ASP H 423 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE H 347 " --> pdb=" O ASP H 423 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 280 through 281 removed outlier: 6.838A pdb=" N LEU H 358 " --> pdb=" O THR H 379 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N THR H 379 " --> pdb=" O LEU H 358 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL H 360 " --> pdb=" O VAL H 377 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 434 through 438 Processing sheet with id=AD6, first strand: chain 'H' and resid 454 through 455 Processing sheet with id=AD7, first strand: chain 'H' and resid 454 through 455 removed outlier: 4.076A pdb=" N GLY H 466 " --> pdb=" O CYS H 489 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE H 571 " --> pdb=" O LEU H 482 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 552 through 554 583 hydrogen bonds defined for protein. 1413 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: 5.59 Time building geometry restraints manager: 7.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3250 1.32 - 1.45: 4617 1.45 - 1.57: 9286 1.57 - 1.70: 0 1.70 - 1.83: 106 Bond restraints: 17259 Sorted by residual: bond pdb=" C GLY A 162 " pdb=" N PHE A 163 " ideal model delta sigma weight residual 1.331 1.244 0.087 1.23e-02 6.61e+03 4.95e+01 bond pdb=" C PHE A 163 " pdb=" N TYR A 164 " ideal model delta sigma weight residual 1.331 1.257 0.074 1.41e-02 5.03e+03 2.72e+01 bond pdb=" N ASP E 58 " pdb=" CA ASP E 58 " ideal model delta sigma weight residual 1.458 1.500 -0.041 9.00e-03 1.23e+04 2.13e+01 bond pdb=" N ASP A 58 " pdb=" CA ASP A 58 " ideal model delta sigma weight residual 1.458 1.499 -0.041 9.00e-03 1.23e+04 2.03e+01 bond pdb=" N ASP D 58 " pdb=" CA ASP D 58 " ideal model delta sigma weight residual 1.458 1.503 -0.045 1.00e-02 1.00e+04 2.00e+01 ... (remaining 17254 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.75: 344 105.75 - 113.09: 8422 113.09 - 120.43: 8375 120.43 - 127.77: 6074 127.77 - 135.12: 151 Bond angle restraints: 23366 Sorted by residual: angle pdb=" CA PHE D 590 " pdb=" CB PHE D 590 " pdb=" CG PHE D 590 " ideal model delta sigma weight residual 113.80 120.70 -6.90 1.00e+00 1.00e+00 4.77e+01 angle pdb=" N LEU A 211 " pdb=" CA LEU A 211 " pdb=" C LEU A 211 " ideal model delta sigma weight residual 111.28 103.77 7.51 1.09e+00 8.42e-01 4.74e+01 angle pdb=" CA PHE E 590 " pdb=" CB PHE E 590 " pdb=" CG PHE E 590 " ideal model delta sigma weight residual 113.80 120.43 -6.63 1.00e+00 1.00e+00 4.40e+01 angle pdb=" N GLU A 166 " pdb=" CA GLU A 166 " pdb=" C GLU A 166 " ideal model delta sigma weight residual 113.15 106.42 6.73 1.19e+00 7.06e-01 3.20e+01 angle pdb=" CA ASP D 564 " pdb=" CB ASP D 564 " pdb=" CG ASP D 564 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 ... (remaining 23361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.34: 10014 22.34 - 44.68: 393 44.68 - 67.03: 85 67.03 - 89.37: 24 89.37 - 111.71: 17 Dihedral angle restraints: 10533 sinusoidal: 4637 harmonic: 5896 Sorted by residual: dihedral pdb=" C THR D 73 " pdb=" N THR D 73 " pdb=" CA THR D 73 " pdb=" CB THR D 73 " ideal model delta harmonic sigma weight residual -122.00 -137.08 15.08 0 2.50e+00 1.60e-01 3.64e+01 dihedral pdb=" N THR D 73 " pdb=" C THR D 73 " pdb=" CA THR D 73 " pdb=" CB THR D 73 " ideal model delta harmonic sigma weight residual 123.40 138.41 -15.01 0 2.50e+00 1.60e-01 3.60e+01 dihedral pdb=" CB CYS D 128 " pdb=" SG CYS D 128 " pdb=" SG CYS D 147 " pdb=" CB CYS D 147 " ideal model delta sinusoidal sigma weight residual -86.00 -135.90 49.90 1 1.00e+01 1.00e-02 3.42e+01 ... (remaining 10530 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 2249 0.144 - 0.288: 322 0.288 - 0.432: 25 0.432 - 0.577: 4 0.577 - 0.721: 3 Chirality restraints: 2603 Sorted by residual: chirality pdb=" C1 FUC G 3 " pdb=" O6 NAG G 1 " pdb=" C2 FUC G 3 " pdb=" O5 FUC G 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 8.98e+02 chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.47e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.17e+01 ... (remaining 2600 not shown) Planarity restraints: 2994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 701 " 0.365 2.00e-02 2.50e+03 3.08e-01 1.19e+03 pdb=" C7 NAG E 701 " -0.097 2.00e-02 2.50e+03 pdb=" C8 NAG E 701 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG E 701 " -0.540 2.00e-02 2.50e+03 pdb=" O7 NAG E 701 " 0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG C 1 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.041 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.500 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " 0.204 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 702 " -0.319 2.00e-02 2.50e+03 2.72e-01 9.22e+02 pdb=" C7 NAG E 702 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 702 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG E 702 " 0.475 2.00e-02 2.50e+03 pdb=" O7 NAG E 702 " -0.059 2.00e-02 2.50e+03 ... (remaining 2991 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 3 2.01 - 2.74: 485 2.74 - 3.46: 22867 3.46 - 4.18: 42005 4.18 - 4.90: 70284 Nonbonded interactions: 135644 Sorted by model distance: nonbonded pdb=" OD2 ASP H 58 " pdb="ZN ZN H 703 " model vdw 1.293 2.230 nonbonded pdb=" OD1 ASP E 58 " pdb="ZN ZN E 704 " model vdw 1.869 2.230 nonbonded pdb=" OD1 ASP D 58 " pdb="ZN ZN D 703 " model vdw 1.886 2.230 nonbonded pdb=" OD1 ASP A 58 " pdb="ZN ZN A 704 " model vdw 2.042 2.230 nonbonded pdb=" OD2 ASP A 58 " pdb="ZN ZN A 704 " model vdw 2.059 2.230 ... (remaining 135639 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 40 through 62 or resid 72 through 168 or resid 178 through \ 193 or resid 210 through 213 or (resid 214 and (name N or name CA or name C or \ name O or name CB )) or resid 215 through 241 or (resid 242 and (name N or name \ CA or name C or name O or name CB )) or resid 243 through 272 or resid 284 throu \ gh 294 or resid 299 through 330 or resid 337 through 457 or (resid 458 and (name \ N or name CA or name C or name O or name CB )) or resid 459 through 560 or (res \ id 561 and (name N or name CA or name C or name O or name CB )) or resid 562 thr \ ough 577 or (resid 578 and (name N or name CA or name C or name O or name CB )) \ or resid 579 through 600 or resid 701)) selection = (chain 'D' and (resid 40 through 168 or resid 178 through 193 or resid 210 throu \ gh 228 or resid 236 through 241 or (resid 242 and (name N or name CA or name C o \ r name O or name CB )) or resid 243 through 252 or resid 263 through 401 or (res \ id 402 and (name N or name CA or name C or name O or name CB )) or resid 403 thr \ ough 452 or (resid 453 through 455 and (name N or name CA or name C or name O or \ name CB )) or resid 456 through 457 or (resid 458 and (name N or name CA or nam \ e C or name O or name CB )) or resid 459 through 545 or (resid 546 and (name N o \ r name CA or name C or name O or name CB )) or resid 547 through 548 or (resid 5 \ 49 and (name N or name CA or name C or name O or name CB )) or resid 550 through \ 555 or (resid 556 and (name N or name CA or name C or name O or name CB )) or r \ esid 557 or (resid 558 and (name N or name CA or name C or name O or name CB )) \ or resid 559 through 600 or resid 701)) selection = (chain 'E' and (resid 40 through 168 or resid 178 through 193 or resid 210 throu \ gh 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 through 228 or resid 236 through 252 or resid 263 through 272 or resi \ d 284 through 294 or resid 299 through 303 or resid 313 through 330 or resid 337 \ through 401 or (resid 402 and (name N or name CA or name C or name O or name CB \ )) or resid 403 through 452 or (resid 453 through 455 and (name N or name CA or \ name C or name O or name CB )) or resid 456 through 475 or resid 479 through 54 \ 5 or (resid 546 and (name N or name CA or name C or name O or name CB )) or resi \ d 547 through 555 or (resid 556 and (name N or name CA or name C or name O or na \ me CB )) or resid 557 or (resid 558 and (name N or name CA or name C or name O o \ r name CB )) or resid 559 through 577 or (resid 578 and (name N or name CA or na \ me C or name O or name CB )) or resid 579 through 600 or resid 701)) selection = (chain 'H' and (resid 40 through 168 or resid 178 through 193 or resid 210 throu \ gh 213 or (resid 214 and (name N or name CA or name C or name O or name CB )) or \ resid 215 through 228 or resid 236 through 241 or (resid 242 and (name N or nam \ e CA or name C or name O or name CB )) or resid 243 through 252 or resid 263 thr \ ough 272 or resid 284 through 294 or resid 299 through 303 or resid 313 through \ 330 or resid 337 through 401 or (resid 402 and (name N or name CA or name C or n \ ame O or name CB )) or resid 403 through 452 or (resid 453 through 455 and (name \ N or name CA or name C or name O or name CB )) or resid 456 through 457 or (res \ id 458 and (name N or name CA or name C or name O or name CB )) or resid 459 thr \ ough 475 or resid 479 through 545 or (resid 546 and (name N or name CA or name C \ or name O or name CB )) or resid 547 through 555 or (resid 556 and (name N or n \ ame CA or name C or name O or name CB )) or resid 557 or (resid 558 and (name N \ or name CA or name C or name O or name CB )) or resid 559 through 577 or (resid \ 578 and (name N or name CA or name C or name O or name CB )) or resid 579 throug \ h 600 or resid 701)) } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'J' selection = chain 'N' } 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.260 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 48.070 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6805 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 : 0.013 0.087 17259 Z= 0.815 Angle : 1.724 9.932 23366 Z= 1.175 Chirality : 0.104 0.721 2603 Planarity : 0.019 0.308 2976 Dihedral : 13.984 111.711 6679 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.99 % Favored : 95.96 % Rotamer: Outliers : 0.44 % Allowed : 4.44 % Favored : 95.12 % Cbeta Deviations : 0.42 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.17), residues: 1978 helix: -0.60 (0.27), residues: 272 sheet: 0.12 (0.22), residues: 530 loop : -0.50 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.011 TRP E 361 HIS 0.022 0.003 HIS E 165 PHE 0.090 0.012 PHE E 163 TYR 0.087 0.011 TYR D 460 ARG 0.011 0.001 ARG H 255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 758 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8065 (mt) cc_final: 0.7847 (mm) REVERT: A 113 TYR cc_start: 0.7328 (t80) cc_final: 0.7065 (t80) REVERT: A 121 ILE cc_start: 0.7769 (tt) cc_final: 0.7156 (pt) REVERT: A 141 ILE cc_start: 0.8237 (mt) cc_final: 0.8019 (mm) REVERT: A 154 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6199 (mt-10) REVERT: A 156 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6040 (mm-30) REVERT: A 212 MET cc_start: 0.7130 (mmm) cc_final: 0.6772 (mmm) REVERT: A 302 HIS cc_start: 0.8078 (t-90) cc_final: 0.7710 (t70) REVERT: A 314 PHE cc_start: 0.8142 (p90) cc_final: 0.7692 (p90) REVERT: A 315 MET cc_start: 0.6593 (mmm) cc_final: 0.5506 (mmm) REVERT: A 341 GLN cc_start: 0.7743 (tt0) cc_final: 0.7522 (tt0) REVERT: A 345 GLN cc_start: 0.7966 (tt0) cc_final: 0.7451 (tt0) REVERT: A 347 PHE cc_start: 0.8269 (m-80) cc_final: 0.8054 (m-80) REVERT: A 348 TYR cc_start: 0.7721 (p90) cc_final: 0.7330 (p90) REVERT: A 351 THR cc_start: 0.7209 (p) cc_final: 0.6985 (t) REVERT: A 375 VAL cc_start: 0.7962 (t) cc_final: 0.7545 (m) REVERT: A 376 LYS cc_start: 0.7935 (tttt) cc_final: 0.7720 (tttt) REVERT: A 385 ASP cc_start: 0.6362 (t0) cc_final: 0.6153 (t0) REVERT: A 392 HIS cc_start: 0.7942 (m90) cc_final: 0.7272 (m90) REVERT: A 423 ASP cc_start: 0.6907 (m-30) cc_final: 0.6533 (m-30) REVERT: A 438 VAL cc_start: 0.8204 (t) cc_final: 0.7803 (p) REVERT: A 447 ASN cc_start: 0.7322 (m-40) cc_final: 0.7014 (m-40) REVERT: A 465 TYR cc_start: 0.7788 (m-80) cc_final: 0.7317 (m-80) REVERT: A 474 ASN cc_start: 0.7510 (m-40) cc_final: 0.7083 (m-40) REVERT: A 521 MET cc_start: 0.6803 (mtp) cc_final: 0.6420 (mtp) REVERT: A 529 THR cc_start: 0.7744 (p) cc_final: 0.7500 (p) REVERT: A 575 MET cc_start: 0.6999 (tpp) cc_final: 0.6606 (tpp) REVERT: A 583 LYS cc_start: 0.7851 (tptt) cc_final: 0.7543 (tptt) REVERT: A 597 THR cc_start: 0.7781 (m) cc_final: 0.7441 (p) REVERT: A 598 HIS cc_start: 0.8192 (p-80) cc_final: 0.7963 (p90) REVERT: D 45 GLU cc_start: 0.7811 (tt0) cc_final: 0.7326 (tt0) REVERT: D 143 ILE cc_start: 0.7405 (mm) cc_final: 0.7117 (mm) REVERT: D 156 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6430 (mm-30) REVERT: D 212 MET cc_start: 0.6127 (mmm) cc_final: 0.5805 (mmm) REVERT: D 244 ASP cc_start: 0.7074 (t70) cc_final: 0.6497 (t70) REVERT: D 270 THR cc_start: 0.7189 (p) cc_final: 0.6895 (t) REVERT: D 285 ASP cc_start: 0.4934 (p0) cc_final: 0.4588 (p0) REVERT: D 287 THR cc_start: 0.7048 (t) cc_final: 0.6743 (m) REVERT: D 315 MET cc_start: 0.6417 (mmm) cc_final: 0.6156 (mmm) REVERT: D 349 LYS cc_start: 0.8211 (ttpt) cc_final: 0.7949 (ttpp) REVERT: D 355 SER cc_start: 0.7711 (m) cc_final: 0.7472 (p) REVERT: D 356 ASP cc_start: 0.6557 (m-30) cc_final: 0.6350 (m-30) REVERT: D 363 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7275 (ttp-170) REVERT: D 373 LYS cc_start: 0.8274 (tttt) cc_final: 0.7782 (ttmm) REVERT: D 387 ASN cc_start: 0.7488 (m-40) cc_final: 0.7014 (m-40) REVERT: D 393 VAL cc_start: 0.8012 (t) cc_final: 0.7766 (p) REVERT: D 399 GLN cc_start: 0.6842 (mt0) cc_final: 0.6633 (mt0) REVERT: D 400 LYS cc_start: 0.7275 (pttt) cc_final: 0.7016 (pttt) REVERT: D 421 LEU cc_start: 0.7899 (mt) cc_final: 0.7597 (mt) REVERT: D 442 SER cc_start: 0.7914 (m) cc_final: 0.7096 (p) REVERT: D 465 TYR cc_start: 0.7851 (m-80) cc_final: 0.7288 (m-80) REVERT: D 481 TYR cc_start: 0.6615 (m-80) cc_final: 0.6408 (m-80) REVERT: D 497 LEU cc_start: 0.8118 (mt) cc_final: 0.7853 (mt) REVERT: D 512 ASP cc_start: 0.7319 (t0) cc_final: 0.7020 (t0) REVERT: D 531 LYS cc_start: 0.7706 (mttp) cc_final: 0.7234 (mttp) REVERT: D 573 HIS cc_start: 0.7122 (m170) cc_final: 0.6834 (m170) REVERT: E 42 ASP cc_start: 0.7020 (t70) cc_final: 0.6494 (t0) REVERT: E 43 ILE cc_start: 0.7758 (mt) cc_final: 0.7397 (mm) REVERT: E 73 THR cc_start: 0.7471 (p) cc_final: 0.6625 (m) REVERT: E 131 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6513 (mt-10) REVERT: E 153 ILE cc_start: 0.7965 (mt) cc_final: 0.7684 (mm) REVERT: E 156 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6330 (mm-30) REVERT: E 168 SER cc_start: 0.7942 (m) cc_final: 0.7425 (t) REVERT: E 212 MET cc_start: 0.6400 (mmm) cc_final: 0.6182 (mmm) REVERT: E 224 SER cc_start: 0.6923 (m) cc_final: 0.6502 (p) REVERT: E 234 GLU cc_start: 0.7302 (mp0) cc_final: 0.7074 (mp0) REVERT: E 241 GLN cc_start: 0.7715 (pp30) cc_final: 0.7321 (pp30) REVERT: E 251 GLU cc_start: 0.7061 (tp30) cc_final: 0.6446 (tp30) REVERT: E 256 MET cc_start: 0.7254 (ttp) cc_final: 0.5648 (ttp) REVERT: E 279 MET cc_start: 0.7387 (mtp) cc_final: 0.7173 (mtp) REVERT: E 301 ASP cc_start: 0.7622 (p0) cc_final: 0.7391 (p0) REVERT: E 303 THR cc_start: 0.8238 (m) cc_final: 0.8002 (t) REVERT: E 304 LEU cc_start: 0.7996 (mt) cc_final: 0.7722 (mt) REVERT: E 315 MET cc_start: 0.7452 (mmm) cc_final: 0.7132 (mmm) REVERT: E 320 SER cc_start: 0.8316 (p) cc_final: 0.7799 (t) REVERT: E 334 ILE cc_start: 0.8015 (mt) cc_final: 0.7752 (mt) REVERT: E 356 ASP cc_start: 0.6779 (m-30) cc_final: 0.6522 (m-30) REVERT: E 412 PRO cc_start: 0.8679 (Cg_endo) cc_final: 0.8456 (Cg_exo) REVERT: E 443 GLN cc_start: 0.8195 (tt0) cc_final: 0.7842 (tt0) REVERT: E 446 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6600 (mt-10) REVERT: E 474 ASN cc_start: 0.7501 (m-40) cc_final: 0.6916 (p0) REVERT: E 486 PHE cc_start: 0.7695 (t80) cc_final: 0.7192 (t80) REVERT: E 504 ARG cc_start: 0.7656 (mpt180) cc_final: 0.7412 (mmt180) REVERT: E 505 GLN cc_start: 0.7754 (tt0) cc_final: 0.7536 (tt0) REVERT: E 521 MET cc_start: 0.7041 (mtp) cc_final: 0.5463 (mtp) REVERT: E 525 MET cc_start: 0.7331 (mmt) cc_final: 0.7036 (mmm) REVERT: E 579 ARG cc_start: 0.6799 (ttt90) cc_final: 0.6004 (mmm-85) REVERT: E 588 ILE cc_start: 0.8260 (mt) cc_final: 0.7732 (tt) REVERT: E 590 PHE cc_start: 0.8271 (m-10) cc_final: 0.8038 (m-10) REVERT: H 45 GLU cc_start: 0.7778 (tt0) cc_final: 0.7409 (tt0) REVERT: H 74 ARG cc_start: 0.6937 (mtt90) cc_final: 0.6395 (mtt-85) REVERT: H 76 THR cc_start: 0.7758 (m) cc_final: 0.7446 (p) REVERT: H 100 GLU cc_start: 0.6866 (mm-30) cc_final: 0.6503 (mm-30) REVERT: H 101 MET cc_start: 0.7331 (mmm) cc_final: 0.7002 (mmm) REVERT: H 102 PHE cc_start: 0.7796 (m-80) cc_final: 0.7545 (m-10) REVERT: H 111 LYS cc_start: 0.7775 (pttt) cc_final: 0.7198 (pttt) REVERT: H 113 TYR cc_start: 0.7055 (t80) cc_final: 0.6776 (t80) REVERT: H 130 SER cc_start: 0.8405 (t) cc_final: 0.6826 (p) REVERT: H 131 GLU cc_start: 0.6626 (mt-10) cc_final: 0.6282 (mt-10) REVERT: H 134 ASP cc_start: 0.6941 (t0) cc_final: 0.6273 (t0) REVERT: H 156 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6120 (mm-30) REVERT: H 173 ASP cc_start: 0.7520 (m-30) cc_final: 0.7191 (m-30) REVERT: H 207 ASP cc_start: 0.6266 (t0) cc_final: 0.6011 (t0) REVERT: H 209 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6892 (mt-10) REVERT: H 212 MET cc_start: 0.7026 (mmm) cc_final: 0.6805 (mmm) REVERT: H 218 SER cc_start: 0.7816 (m) cc_final: 0.7591 (p) REVERT: H 241 GLN cc_start: 0.7445 (pp30) cc_final: 0.7049 (pp30) REVERT: H 256 MET cc_start: 0.7291 (ttp) cc_final: 0.6629 (ttp) REVERT: H 267 ASP cc_start: 0.7113 (t0) cc_final: 0.6896 (t0) REVERT: H 275 ASN cc_start: 0.7687 (p0) cc_final: 0.7387 (p0) REVERT: H 283 THR cc_start: 0.7401 (p) cc_final: 0.7183 (t) REVERT: H 313 TYR cc_start: 0.7494 (m-80) cc_final: 0.7257 (m-80) REVERT: H 315 MET cc_start: 0.7259 (mmm) cc_final: 0.6873 (mmm) REVERT: H 333 ARG cc_start: 0.7704 (ptt90) cc_final: 0.7494 (ptt90) REVERT: H 336 TYR cc_start: 0.8176 (m-80) cc_final: 0.7897 (m-80) REVERT: H 338 LYS cc_start: 0.7878 (mttt) cc_final: 0.7567 (mttt) REVERT: H 341 GLN cc_start: 0.7706 (tt0) cc_final: 0.7492 (tt0) REVERT: H 342 GLN cc_start: 0.8082 (mp10) cc_final: 0.7846 (mp10) REVERT: H 349 LYS cc_start: 0.8254 (ttpt) cc_final: 0.8034 (ttpt) REVERT: H 364 ARG cc_start: 0.7483 (ptp-170) cc_final: 0.6750 (ptm160) REVERT: H 381 GLN cc_start: 0.6751 (tp40) cc_final: 0.6385 (mm-40) REVERT: H 394 VAL cc_start: 0.8477 (t) cc_final: 0.8165 (m) REVERT: H 404 LEU cc_start: 0.8454 (mp) cc_final: 0.7977 (mp) REVERT: H 419 ILE cc_start: 0.8366 (mt) cc_final: 0.8158 (mm) REVERT: H 425 THR cc_start: 0.8078 (m) cc_final: 0.7858 (p) REVERT: H 438 VAL cc_start: 0.8372 (t) cc_final: 0.8024 (p) REVERT: H 463 GLU cc_start: 0.7232 (mt-10) cc_final: 0.6735 (mt-10) REVERT: H 471 LEU cc_start: 0.8046 (tp) cc_final: 0.7563 (tp) REVERT: H 489 CYS cc_start: 0.7896 (m) cc_final: 0.7686 (m) REVERT: H 498 GLU cc_start: 0.6815 (tt0) cc_final: 0.6487 (tt0) REVERT: H 502 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6713 (mt-10) REVERT: H 504 ARG cc_start: 0.7870 (mpt180) cc_final: 0.7318 (mmt180) REVERT: H 510 ILE cc_start: 0.8384 (mt) cc_final: 0.8060 (mm) REVERT: H 521 MET cc_start: 0.7157 (mtp) cc_final: 0.6564 (mtp) REVERT: H 522 SER cc_start: 0.8281 (m) cc_final: 0.7954 (p) REVERT: H 575 MET cc_start: 0.6491 (tpp) cc_final: 0.6165 (tpp) REVERT: H 581 PHE cc_start: 0.8168 (m-80) cc_final: 0.7853 (m-80) REVERT: H 583 LYS cc_start: 0.7647 (tttp) cc_final: 0.7393 (tttp) REVERT: H 592 ASP cc_start: 0.6747 (m-30) cc_final: 0.6513 (m-30) REVERT: H 593 PHE cc_start: 0.8370 (t80) cc_final: 0.7252 (t80) outliers start: 8 outliers final: 4 residues processed: 763 average time/residue: 0.3123 time to fit residues: 344.2788 Evaluate side-chains 625 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 621 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 TYR Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 414 ASN Chi-restraints excluded: chain H residue 140 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 184 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 123 GLN A 139 GLN A 189 HIS A 342 GLN A 505 GLN A 554 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 GLN D 386 HIS D 474 ASN D 493 ASN E 86 ASN E 136 HIS E 182 GLN ** E 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 598 HIS H 47 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17259 Z= 0.194 Angle : 0.634 14.599 23366 Z= 0.334 Chirality : 0.046 0.253 2603 Planarity : 0.004 0.049 2976 Dihedral : 8.720 116.450 2862 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.55 % Allowed : 11.10 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.18), residues: 1978 helix: 1.08 (0.31), residues: 288 sheet: 0.68 (0.21), residues: 567 loop : -0.09 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 361 HIS 0.010 0.001 HIS A 554 PHE 0.023 0.002 PHE A 527 TYR 0.018 0.002 TYR H 472 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 677 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 631 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ILE cc_start: 0.7694 (mt) cc_final: 0.7361 (mm) REVERT: A 113 TYR cc_start: 0.7309 (t80) cc_final: 0.7036 (t80) REVERT: A 121 ILE cc_start: 0.7762 (tt) cc_final: 0.7163 (pt) REVERT: A 132 VAL cc_start: 0.7785 (p) cc_final: 0.7584 (t) REVERT: A 141 ILE cc_start: 0.8178 (mt) cc_final: 0.7917 (mm) REVERT: A 152 ILE cc_start: 0.8248 (mt) cc_final: 0.8045 (mm) REVERT: A 156 GLU cc_start: 0.6786 (mm-30) cc_final: 0.6355 (mm-30) REVERT: A 190 ASN cc_start: 0.8017 (m-40) cc_final: 0.7803 (m110) REVERT: A 271 PHE cc_start: 0.8065 (m-10) cc_final: 0.7603 (m-10) REVERT: A 292 GLN cc_start: 0.7467 (tp40) cc_final: 0.7040 (tt0) REVERT: A 293 ASP cc_start: 0.6324 (p0) cc_final: 0.5831 (p0) REVERT: A 314 PHE cc_start: 0.7995 (p90) cc_final: 0.7470 (p90) REVERT: A 315 MET cc_start: 0.6473 (mmm) cc_final: 0.5878 (mmm) REVERT: A 317 PHE cc_start: 0.7863 (t80) cc_final: 0.7364 (t80) REVERT: A 363 ARG cc_start: 0.7903 (ttm170) cc_final: 0.7579 (ttp-110) REVERT: A 375 VAL cc_start: 0.8159 (t) cc_final: 0.7765 (p) REVERT: A 385 ASP cc_start: 0.6374 (t0) cc_final: 0.6138 (t0) REVERT: A 396 LYS cc_start: 0.7925 (mttt) cc_final: 0.7541 (mtpt) REVERT: A 443 GLN cc_start: 0.7780 (mp10) cc_final: 0.7420 (mp10) REVERT: A 447 ASN cc_start: 0.7484 (m-40) cc_final: 0.7184 (m-40) REVERT: A 465 TYR cc_start: 0.7679 (m-80) cc_final: 0.7479 (m-80) REVERT: A 474 ASN cc_start: 0.7806 (m-40) cc_final: 0.7540 (m-40) REVERT: A 498 GLU cc_start: 0.6545 (tt0) cc_final: 0.6342 (tt0) REVERT: A 502 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6452 (mt-10) REVERT: A 527 PHE cc_start: 0.8064 (p90) cc_final: 0.7639 (p90) REVERT: A 529 THR cc_start: 0.7981 (p) cc_final: 0.7749 (p) REVERT: A 575 MET cc_start: 0.6534 (tpp) cc_final: 0.6210 (tpp) REVERT: A 583 LYS cc_start: 0.7812 (tptt) cc_final: 0.7467 (tptt) REVERT: A 585 ASP cc_start: 0.6475 (t0) cc_final: 0.6223 (t0) REVERT: D 45 GLU cc_start: 0.7820 (tt0) cc_final: 0.7360 (tt0) REVERT: D 135 GLN cc_start: 0.7190 (mm-40) cc_final: 0.6971 (mm-40) REVERT: D 141 ILE cc_start: 0.7898 (mt) cc_final: 0.7508 (mm) REVERT: D 163 PHE cc_start: 0.6973 (m-80) cc_final: 0.6433 (m-80) REVERT: D 212 MET cc_start: 0.6076 (mmm) cc_final: 0.5648 (mmm) REVERT: D 244 ASP cc_start: 0.6784 (t70) cc_final: 0.6341 (t70) REVERT: D 252 ARG cc_start: 0.7484 (mtp180) cc_final: 0.6744 (mtp180) REVERT: D 270 THR cc_start: 0.7322 (p) cc_final: 0.7107 (t) REVERT: D 285 ASP cc_start: 0.5181 (p0) cc_final: 0.4792 (p0) REVERT: D 287 THR cc_start: 0.7362 (t) cc_final: 0.6848 (m) REVERT: D 330 LEU cc_start: 0.7670 (mt) cc_final: 0.7241 (mt) REVERT: D 355 SER cc_start: 0.7653 (m) cc_final: 0.7356 (p) REVERT: D 393 VAL cc_start: 0.7932 (t) cc_final: 0.7643 (p) REVERT: D 396 LYS cc_start: 0.7634 (mttt) cc_final: 0.7386 (mttt) REVERT: D 397 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6321 (mm-30) REVERT: D 428 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6216 (mm-30) REVERT: D 441 PHE cc_start: 0.8493 (t80) cc_final: 0.7709 (t80) REVERT: D 445 LEU cc_start: 0.8230 (tp) cc_final: 0.8017 (mt) REVERT: D 453 LYS cc_start: 0.6828 (pttt) cc_final: 0.5854 (pttt) REVERT: D 460 TYR cc_start: 0.8386 (m-80) cc_final: 0.8010 (m-10) REVERT: D 481 TYR cc_start: 0.6740 (m-80) cc_final: 0.6533 (m-80) REVERT: D 486 PHE cc_start: 0.7907 (t80) cc_final: 0.7385 (t80) REVERT: D 502 GLU cc_start: 0.7050 (mt-10) cc_final: 0.5825 (mt-10) REVERT: D 512 ASP cc_start: 0.7175 (t0) cc_final: 0.6936 (t0) REVERT: D 531 LYS cc_start: 0.7574 (mttp) cc_final: 0.7088 (mttt) REVERT: D 546 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7214 (ptm160) REVERT: D 573 HIS cc_start: 0.7266 (m170) cc_final: 0.6268 (m170) REVERT: D 577 LYS cc_start: 0.7399 (mmtt) cc_final: 0.7185 (mmtt) REVERT: E 73 THR cc_start: 0.7715 (p) cc_final: 0.6895 (m) REVERT: E 101 MET cc_start: 0.7651 (mmm) cc_final: 0.7309 (mmm) REVERT: E 136 HIS cc_start: 0.6904 (m-70) cc_final: 0.6512 (m-70) REVERT: E 153 ILE cc_start: 0.7840 (mt) cc_final: 0.7608 (mm) REVERT: E 156 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6452 (mm-30) REVERT: E 166 GLU cc_start: 0.7111 (tp30) cc_final: 0.6844 (tp30) REVERT: E 182 GLN cc_start: 0.7433 (mm110) cc_final: 0.7230 (mm-40) REVERT: E 211 LEU cc_start: 0.8325 (tp) cc_final: 0.8112 (tt) REVERT: E 215 GLN cc_start: 0.7106 (mt0) cc_final: 0.6716 (mt0) REVERT: E 234 GLU cc_start: 0.7309 (mp0) cc_final: 0.7050 (mp0) REVERT: E 241 GLN cc_start: 0.7810 (pp30) cc_final: 0.7399 (pp30) REVERT: E 265 LEU cc_start: 0.8224 (tp) cc_final: 0.7956 (tp) REVERT: E 266 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8093 (mm) REVERT: E 267 ASP cc_start: 0.7050 (t0) cc_final: 0.6346 (t0) REVERT: E 279 MET cc_start: 0.7496 (mtp) cc_final: 0.7282 (mtp) REVERT: E 299 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6243 (mt-10) REVERT: E 303 THR cc_start: 0.8471 (m) cc_final: 0.7884 (t) REVERT: E 304 LEU cc_start: 0.8007 (mt) cc_final: 0.7690 (mt) REVERT: E 315 MET cc_start: 0.7339 (mmm) cc_final: 0.6967 (mmm) REVERT: E 400 LYS cc_start: 0.7961 (pttt) cc_final: 0.7664 (ptpp) REVERT: E 409 LYS cc_start: 0.8289 (mtpt) cc_final: 0.7545 (ttpp) REVERT: E 412 PRO cc_start: 0.8772 (Cg_endo) cc_final: 0.8326 (Cg_exo) REVERT: E 428 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6990 (mt-10) REVERT: E 474 ASN cc_start: 0.7665 (m-40) cc_final: 0.7269 (m-40) REVERT: E 486 PHE cc_start: 0.7764 (t80) cc_final: 0.7347 (t80) REVERT: E 518 ARG cc_start: 0.8200 (ttp-110) cc_final: 0.7684 (mtp-110) REVERT: E 521 MET cc_start: 0.7037 (mtp) cc_final: 0.6353 (mtp) REVERT: E 525 MET cc_start: 0.7247 (mmt) cc_final: 0.6874 (mmt) REVERT: E 577 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7509 (mtpp) REVERT: E 588 ILE cc_start: 0.8454 (mt) cc_final: 0.7947 (tt) REVERT: H 74 ARG cc_start: 0.6997 (mtt90) cc_final: 0.6423 (mtt-85) REVERT: H 76 THR cc_start: 0.7681 (m) cc_final: 0.7366 (p) REVERT: H 81 TYR cc_start: 0.7940 (p90) cc_final: 0.7473 (p90) REVERT: H 100 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6812 (mm-30) REVERT: H 101 MET cc_start: 0.7423 (mmm) cc_final: 0.7159 (mmm) REVERT: H 111 LYS cc_start: 0.7878 (pttt) cc_final: 0.7258 (pttt) REVERT: H 124 GLN cc_start: 0.6958 (tt0) cc_final: 0.6718 (tm-30) REVERT: H 130 SER cc_start: 0.8255 (t) cc_final: 0.7956 (p) REVERT: H 134 ASP cc_start: 0.6503 (t0) cc_final: 0.6250 (t0) REVERT: H 140 ASN cc_start: 0.7547 (OUTLIER) cc_final: 0.6206 (m-40) REVERT: H 154 GLU cc_start: 0.6865 (mt-10) cc_final: 0.6344 (mt-10) REVERT: H 190 ASN cc_start: 0.8139 (m-40) cc_final: 0.7828 (m-40) REVERT: H 207 ASP cc_start: 0.6345 (t0) cc_final: 0.6112 (t0) REVERT: H 209 GLU cc_start: 0.7339 (mt-10) cc_final: 0.6948 (mt-10) REVERT: H 212 MET cc_start: 0.7019 (mmm) cc_final: 0.6783 (mmm) REVERT: H 218 SER cc_start: 0.8163 (m) cc_final: 0.7745 (p) REVERT: H 241 GLN cc_start: 0.7712 (pp30) cc_final: 0.7091 (pp30) REVERT: H 252 ARG cc_start: 0.7508 (ttm170) cc_final: 0.7241 (mtm-85) REVERT: H 256 MET cc_start: 0.7271 (ttp) cc_final: 0.6771 (ttp) REVERT: H 275 ASN cc_start: 0.7531 (p0) cc_final: 0.7281 (p0) REVERT: H 315 MET cc_start: 0.7270 (mmm) cc_final: 0.7064 (mmm) REVERT: H 330 LEU cc_start: 0.8096 (tp) cc_final: 0.7698 (tt) REVERT: H 331 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6480 (mt-10) REVERT: H 338 LYS cc_start: 0.7920 (mttt) cc_final: 0.7640 (mttt) REVERT: H 349 LYS cc_start: 0.8321 (ttpt) cc_final: 0.8056 (ttpt) REVERT: H 364 ARG cc_start: 0.7597 (ptp-170) cc_final: 0.7206 (ptm160) REVERT: H 381 GLN cc_start: 0.6980 (tp40) cc_final: 0.6598 (mm-40) REVERT: H 394 VAL cc_start: 0.8524 (t) cc_final: 0.8285 (m) REVERT: H 397 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6529 (mm-30) REVERT: H 404 LEU cc_start: 0.8489 (mp) cc_final: 0.7839 (mt) REVERT: H 471 LEU cc_start: 0.7968 (tp) cc_final: 0.7606 (tp) REVERT: H 498 GLU cc_start: 0.6869 (tt0) cc_final: 0.6565 (tt0) REVERT: H 521 MET cc_start: 0.7414 (mtp) cc_final: 0.6847 (mtp) REVERT: H 593 PHE cc_start: 0.8059 (t80) cc_final: 0.7460 (t80) outliers start: 46 outliers final: 30 residues processed: 655 average time/residue: 0.3189 time to fit residues: 301.7673 Evaluate side-chains 625 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 593 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 323 SER Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 204 THR Chi-restraints excluded: chain H residue 239 ILE Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 323 SER Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 532 SER Chi-restraints excluded: chain H residue 563 ILE Chi-restraints excluded: chain H residue 564 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 102 optimal weight: 0.4980 chunk 57 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS A 139 GLN A 381 GLN A 487 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 ASN E 139 GLN E 268 HIS E 505 GLN E 598 HIS H 47 ASN H 215 GLN H 302 HIS H 474 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17259 Z= 0.279 Angle : 0.620 9.279 23366 Z= 0.333 Chirality : 0.046 0.233 2603 Planarity : 0.004 0.045 2976 Dihedral : 6.952 121.854 2856 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.66 % Allowed : 14.65 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 1978 helix: 1.32 (0.31), residues: 288 sheet: 0.60 (0.21), residues: 581 loop : -0.29 (0.18), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 361 HIS 0.009 0.002 HIS A 189 PHE 0.023 0.002 PHE D 314 TYR 0.024 0.002 TYR H 553 ARG 0.008 0.001 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 641 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7388 (mmm) cc_final: 0.7056 (mmm) REVERT: A 113 TYR cc_start: 0.7561 (t80) cc_final: 0.7334 (t80) REVERT: A 121 ILE cc_start: 0.7809 (tt) cc_final: 0.7214 (pt) REVERT: A 130 SER cc_start: 0.7523 (t) cc_final: 0.6550 (t) REVERT: A 141 ILE cc_start: 0.8160 (mt) cc_final: 0.7955 (mm) REVERT: A 153 ILE cc_start: 0.8274 (mt) cc_final: 0.7756 (tp) REVERT: A 156 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6588 (mm-30) REVERT: A 271 PHE cc_start: 0.8063 (m-10) cc_final: 0.7773 (m-10) REVERT: A 293 ASP cc_start: 0.6499 (p0) cc_final: 0.5902 (p0) REVERT: A 315 MET cc_start: 0.6419 (mmm) cc_final: 0.5787 (mmm) REVERT: A 341 GLN cc_start: 0.7664 (tt0) cc_final: 0.7085 (tt0) REVERT: A 363 ARG cc_start: 0.8002 (ttm170) cc_final: 0.7653 (ttp-110) REVERT: A 375 VAL cc_start: 0.8077 (t) cc_final: 0.7701 (p) REVERT: A 376 LYS cc_start: 0.8073 (tttt) cc_final: 0.7698 (tttt) REVERT: A 396 LYS cc_start: 0.7795 (mttt) cc_final: 0.7179 (mtpt) REVERT: A 428 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6494 (mt-10) REVERT: A 471 LEU cc_start: 0.8370 (tp) cc_final: 0.8150 (tp) REVERT: A 502 GLU cc_start: 0.6836 (mt-10) cc_final: 0.6533 (mt-10) REVERT: A 527 PHE cc_start: 0.7882 (p90) cc_final: 0.7547 (p90) REVERT: A 560 PHE cc_start: 0.7668 (m-80) cc_final: 0.7391 (m-10) REVERT: A 583 LYS cc_start: 0.7827 (tptt) cc_final: 0.7521 (tptt) REVERT: A 598 HIS cc_start: 0.8144 (p-80) cc_final: 0.7924 (p90) REVERT: D 45 GLU cc_start: 0.7858 (tt0) cc_final: 0.7360 (tt0) REVERT: D 74 ARG cc_start: 0.7245 (mtt-85) cc_final: 0.6987 (mmt-90) REVERT: D 79 ILE cc_start: 0.7448 (mm) cc_final: 0.7002 (mt) REVERT: D 85 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6923 (t0) REVERT: D 101 MET cc_start: 0.6924 (mmm) cc_final: 0.6705 (mmm) REVERT: D 105 LYS cc_start: 0.8113 (mttt) cc_final: 0.7530 (mtmt) REVERT: D 123 GLN cc_start: 0.7230 (OUTLIER) cc_final: 0.6658 (mm-40) REVERT: D 135 GLN cc_start: 0.7266 (mm-40) cc_final: 0.6986 (mm-40) REVERT: D 141 ILE cc_start: 0.7972 (mt) cc_final: 0.7607 (mm) REVERT: D 142 SER cc_start: 0.8075 (t) cc_final: 0.7200 (p) REVERT: D 163 PHE cc_start: 0.7057 (m-80) cc_final: 0.6307 (m-80) REVERT: D 212 MET cc_start: 0.6185 (mmm) cc_final: 0.5851 (mmm) REVERT: D 244 ASP cc_start: 0.6912 (t70) cc_final: 0.6386 (t70) REVERT: D 252 ARG cc_start: 0.7563 (mtp180) cc_final: 0.6579 (mtp180) REVERT: D 270 THR cc_start: 0.7387 (p) cc_final: 0.7187 (t) REVERT: D 285 ASP cc_start: 0.5774 (p0) cc_final: 0.5434 (p0) REVERT: D 287 THR cc_start: 0.7443 (t) cc_final: 0.6861 (m) REVERT: D 330 LEU cc_start: 0.7605 (mt) cc_final: 0.7191 (mt) REVERT: D 355 SER cc_start: 0.7659 (m) cc_final: 0.7368 (p) REVERT: D 396 LYS cc_start: 0.7720 (mttt) cc_final: 0.7465 (mttt) REVERT: D 397 GLU cc_start: 0.6651 (mm-30) cc_final: 0.6425 (mm-30) REVERT: D 400 LYS cc_start: 0.7803 (pttt) cc_final: 0.7597 (pttt) REVERT: D 404 LEU cc_start: 0.7831 (mp) cc_final: 0.7554 (mt) REVERT: D 405 PHE cc_start: 0.7702 (m-10) cc_final: 0.7382 (m-80) REVERT: D 428 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6348 (mm-30) REVERT: D 445 LEU cc_start: 0.8208 (tp) cc_final: 0.7969 (mt) REVERT: D 446 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6703 (mp0) REVERT: D 486 PHE cc_start: 0.7918 (t80) cc_final: 0.7500 (t80) REVERT: D 487 HIS cc_start: 0.7813 (p-80) cc_final: 0.7596 (p-80) REVERT: D 512 ASP cc_start: 0.7147 (t0) cc_final: 0.6933 (t0) REVERT: D 546 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7475 (ttm-80) REVERT: D 573 HIS cc_start: 0.7412 (m170) cc_final: 0.6493 (m170) REVERT: D 577 LYS cc_start: 0.7540 (mmtt) cc_final: 0.7296 (mmtt) REVERT: E 100 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6907 (tm-30) REVERT: E 111 LYS cc_start: 0.7755 (pttt) cc_final: 0.7495 (ptmt) REVERT: E 136 HIS cc_start: 0.7366 (m-70) cc_final: 0.6884 (m-70) REVERT: E 143 ILE cc_start: 0.8588 (mm) cc_final: 0.8337 (tp) REVERT: E 166 GLU cc_start: 0.6961 (tp30) cc_final: 0.6678 (tp30) REVERT: E 173 ASP cc_start: 0.7864 (m-30) cc_final: 0.7598 (t0) REVERT: E 182 GLN cc_start: 0.7407 (mm110) cc_final: 0.7164 (mm-40) REVERT: E 224 SER cc_start: 0.7017 (m) cc_final: 0.6542 (p) REVERT: E 234 GLU cc_start: 0.7356 (mp0) cc_final: 0.7110 (mp0) REVERT: E 241 GLN cc_start: 0.7902 (pp30) cc_final: 0.7522 (pp30) REVERT: E 256 MET cc_start: 0.7198 (ttp) cc_final: 0.6987 (tpp) REVERT: E 267 ASP cc_start: 0.7069 (t0) cc_final: 0.6451 (t0) REVERT: E 299 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6171 (mt-10) REVERT: E 320 SER cc_start: 0.8313 (p) cc_final: 0.7922 (t) REVERT: E 326 GLU cc_start: 0.6391 (mt-10) cc_final: 0.6146 (mt-10) REVERT: E 400 LYS cc_start: 0.7926 (pttt) cc_final: 0.7683 (ptpp) REVERT: E 409 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7726 (ttpp) REVERT: E 412 PRO cc_start: 0.8746 (Cg_endo) cc_final: 0.8387 (Cg_exo) REVERT: E 484 LEU cc_start: 0.7801 (mt) cc_final: 0.7567 (mm) REVERT: E 486 PHE cc_start: 0.8019 (t80) cc_final: 0.7605 (t80) REVERT: E 518 ARG cc_start: 0.8127 (ttp-110) cc_final: 0.7791 (mtp-110) REVERT: E 521 MET cc_start: 0.7196 (mtp) cc_final: 0.6589 (mtp) REVERT: E 525 MET cc_start: 0.7333 (mmt) cc_final: 0.6930 (mmt) REVERT: E 530 SER cc_start: 0.8317 (t) cc_final: 0.7733 (p) REVERT: E 577 LYS cc_start: 0.8018 (mtpp) cc_final: 0.7703 (mtpp) REVERT: E 588 ILE cc_start: 0.8468 (mt) cc_final: 0.8020 (tp) REVERT: H 74 ARG cc_start: 0.7037 (mtt90) cc_final: 0.6653 (mtt-85) REVERT: H 76 THR cc_start: 0.7714 (m) cc_final: 0.7356 (p) REVERT: H 79 ILE cc_start: 0.7773 (mt) cc_final: 0.7485 (mp) REVERT: H 111 LYS cc_start: 0.7880 (pttt) cc_final: 0.7405 (pttt) REVERT: H 122 PHE cc_start: 0.8403 (m-80) cc_final: 0.7751 (m-80) REVERT: H 140 ASN cc_start: 0.7463 (OUTLIER) cc_final: 0.6385 (m-40) REVERT: H 154 GLU cc_start: 0.6980 (mt-10) cc_final: 0.6714 (mt-10) REVERT: H 180 TRP cc_start: 0.7635 (m100) cc_final: 0.7366 (m100) REVERT: H 209 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6990 (mt-10) REVERT: H 212 MET cc_start: 0.6992 (mmm) cc_final: 0.6619 (mmm) REVERT: H 241 GLN cc_start: 0.7887 (pp30) cc_final: 0.7387 (pp30) REVERT: H 252 ARG cc_start: 0.7536 (ttm170) cc_final: 0.7260 (mtm-85) REVERT: H 256 MET cc_start: 0.7427 (ttp) cc_final: 0.6898 (ttp) REVERT: H 275 ASN cc_start: 0.7490 (p0) cc_final: 0.7253 (p0) REVERT: H 303 THR cc_start: 0.8263 (m) cc_final: 0.7635 (t) REVERT: H 314 PHE cc_start: 0.8604 (p90) cc_final: 0.8234 (p90) REVERT: H 315 MET cc_start: 0.7249 (mmm) cc_final: 0.6861 (mmm) REVERT: H 364 ARG cc_start: 0.7749 (ptp-170) cc_final: 0.7196 (ptm160) REVERT: H 381 GLN cc_start: 0.7211 (tp40) cc_final: 0.6670 (mm-40) REVERT: H 397 GLU cc_start: 0.6780 (mm-30) cc_final: 0.6439 (mm-30) REVERT: H 404 LEU cc_start: 0.8463 (mp) cc_final: 0.8058 (mt) REVERT: H 438 VAL cc_start: 0.8143 (t) cc_final: 0.7852 (p) REVERT: H 482 LEU cc_start: 0.7681 (tp) cc_final: 0.7472 (mt) REVERT: H 498 GLU cc_start: 0.6988 (tt0) cc_final: 0.6636 (tt0) REVERT: H 521 MET cc_start: 0.7451 (mtp) cc_final: 0.6932 (mtp) REVERT: H 522 SER cc_start: 0.8613 (p) cc_final: 0.8331 (p) REVERT: H 593 PHE cc_start: 0.8006 (t80) cc_final: 0.7595 (t80) outliers start: 66 outliers final: 39 residues processed: 672 average time/residue: 0.3283 time to fit residues: 317.9861 Evaluate side-chains 648 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 605 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 421 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 131 GLU Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 445 LEU Chi-restraints excluded: chain H residue 475 SER Chi-restraints excluded: chain H residue 496 ILE Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 532 SER Chi-restraints excluded: chain H residue 564 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 182 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 0.0050 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 175 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS A 302 HIS A 341 GLN A 406 GLN A 474 ASN A 487 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 190 ASN D 302 HIS ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 399 GLN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 ASN E 56 GLN E 268 HIS E 291 HIS E 505 GLN E 598 HIS H 302 HIS H 519 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17259 Z= 0.176 Angle : 0.551 8.979 23366 Z= 0.294 Chirality : 0.043 0.235 2603 Planarity : 0.004 0.042 2976 Dihedral : 6.440 114.868 2856 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.44 % Allowed : 16.65 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 1978 helix: 1.48 (0.31), residues: 288 sheet: 0.62 (0.21), residues: 564 loop : -0.22 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 361 HIS 0.008 0.001 HIS H 189 PHE 0.015 0.002 PHE E 593 TYR 0.027 0.001 TYR E 214 ARG 0.006 0.000 ARG E 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 626 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7306 (mmm) cc_final: 0.7040 (mmm) REVERT: A 121 ILE cc_start: 0.7844 (tt) cc_final: 0.7298 (pt) REVERT: A 130 SER cc_start: 0.7551 (t) cc_final: 0.6634 (t) REVERT: A 152 ILE cc_start: 0.8324 (mt) cc_final: 0.8116 (mm) REVERT: A 154 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6757 (mt-10) REVERT: A 156 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6587 (mm-30) REVERT: A 293 ASP cc_start: 0.6529 (p0) cc_final: 0.5961 (p0) REVERT: A 315 MET cc_start: 0.6381 (mmm) cc_final: 0.5810 (mmm) REVERT: A 363 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7635 (ttp-110) REVERT: A 372 ARG cc_start: 0.7100 (ttp-110) cc_final: 0.6390 (ptm-80) REVERT: A 375 VAL cc_start: 0.8136 (t) cc_final: 0.7796 (p) REVERT: A 392 HIS cc_start: 0.7964 (m90) cc_final: 0.7728 (m-70) REVERT: A 428 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6453 (mt-10) REVERT: A 447 ASN cc_start: 0.7697 (m-40) cc_final: 0.7380 (m-40) REVERT: A 458 ARG cc_start: 0.8082 (mtm110) cc_final: 0.7703 (ttp80) REVERT: A 465 TYR cc_start: 0.7690 (m-80) cc_final: 0.7345 (m-80) REVERT: A 471 LEU cc_start: 0.8426 (tp) cc_final: 0.8197 (tp) REVERT: A 502 GLU cc_start: 0.6804 (mt-10) cc_final: 0.6495 (mt-10) REVERT: A 527 PHE cc_start: 0.7924 (p90) cc_final: 0.7428 (p90) REVERT: A 583 LYS cc_start: 0.7780 (tptt) cc_final: 0.7492 (tptt) REVERT: D 45 GLU cc_start: 0.7854 (tt0) cc_final: 0.7347 (tt0) REVERT: D 79 ILE cc_start: 0.7453 (mm) cc_final: 0.7090 (mt) REVERT: D 105 LYS cc_start: 0.8101 (mttt) cc_final: 0.7432 (mtmt) REVERT: D 141 ILE cc_start: 0.7907 (mt) cc_final: 0.7540 (mm) REVERT: D 142 SER cc_start: 0.8086 (t) cc_final: 0.7350 (p) REVERT: D 163 PHE cc_start: 0.6943 (m-80) cc_final: 0.6174 (m-80) REVERT: D 212 MET cc_start: 0.6114 (mmm) cc_final: 0.5769 (mmm) REVERT: D 244 ASP cc_start: 0.6891 (t70) cc_final: 0.6331 (t70) REVERT: D 252 ARG cc_start: 0.7486 (mtp180) cc_final: 0.6599 (mtp180) REVERT: D 285 ASP cc_start: 0.5837 (p0) cc_final: 0.5501 (p0) REVERT: D 287 THR cc_start: 0.7442 (t) cc_final: 0.6778 (m) REVERT: D 330 LEU cc_start: 0.7658 (mt) cc_final: 0.7141 (mt) REVERT: D 339 ARG cc_start: 0.6480 (mtt-85) cc_final: 0.6220 (mmt-90) REVERT: D 356 ASP cc_start: 0.6629 (m-30) cc_final: 0.6095 (m-30) REVERT: D 362 VAL cc_start: 0.7951 (t) cc_final: 0.7735 (p) REVERT: D 393 VAL cc_start: 0.7955 (t) cc_final: 0.7665 (p) REVERT: D 404 LEU cc_start: 0.7841 (mp) cc_final: 0.7540 (mt) REVERT: D 405 PHE cc_start: 0.7665 (m-10) cc_final: 0.7274 (m-80) REVERT: D 428 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6460 (mt-10) REVERT: D 445 LEU cc_start: 0.8218 (tp) cc_final: 0.7944 (mt) REVERT: D 446 GLU cc_start: 0.7163 (mt-10) cc_final: 0.6798 (mt-10) REVERT: D 487 HIS cc_start: 0.7733 (p-80) cc_final: 0.7484 (p-80) REVERT: D 502 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6630 (mt-10) REVERT: D 512 ASP cc_start: 0.7118 (t0) cc_final: 0.6872 (t0) REVERT: D 549 ARG cc_start: 0.8240 (mtp-110) cc_final: 0.8035 (mtp-110) REVERT: D 573 HIS cc_start: 0.7390 (m170) cc_final: 0.6926 (m170) REVERT: D 577 LYS cc_start: 0.7653 (mmtt) cc_final: 0.7329 (mmtt) REVERT: E 74 ARG cc_start: 0.7398 (mtt-85) cc_final: 0.6771 (mtt-85) REVERT: E 100 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: E 131 GLU cc_start: 0.7042 (mt-10) cc_final: 0.6480 (mt-10) REVERT: E 136 HIS cc_start: 0.7330 (m-70) cc_final: 0.6900 (m-70) REVERT: E 143 ILE cc_start: 0.8616 (mm) cc_final: 0.8338 (tp) REVERT: E 166 GLU cc_start: 0.6850 (tp30) cc_final: 0.6611 (tp30) REVERT: E 173 ASP cc_start: 0.7765 (m-30) cc_final: 0.7505 (t0) REVERT: E 182 GLN cc_start: 0.7315 (mm110) cc_final: 0.7111 (mm-40) REVERT: E 224 SER cc_start: 0.7024 (m) cc_final: 0.6538 (p) REVERT: E 234 GLU cc_start: 0.7368 (mp0) cc_final: 0.7088 (mp0) REVERT: E 241 GLN cc_start: 0.8032 (pp30) cc_final: 0.7621 (pp30) REVERT: E 256 MET cc_start: 0.7217 (ttp) cc_final: 0.6930 (ttp) REVERT: E 267 ASP cc_start: 0.6957 (t0) cc_final: 0.6330 (t0) REVERT: E 299 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6252 (mt-10) REVERT: E 315 MET cc_start: 0.7388 (mmm) cc_final: 0.7092 (mmm) REVERT: E 320 SER cc_start: 0.8326 (p) cc_final: 0.7890 (t) REVERT: E 326 GLU cc_start: 0.6273 (mt-10) cc_final: 0.5996 (mt-10) REVERT: E 351 THR cc_start: 0.7756 (p) cc_final: 0.7553 (p) REVERT: E 409 LYS cc_start: 0.8330 (mtpt) cc_final: 0.7691 (ttpp) REVERT: E 412 PRO cc_start: 0.8691 (Cg_endo) cc_final: 0.8286 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8016 (t80) cc_final: 0.7610 (t80) REVERT: E 518 ARG cc_start: 0.8207 (ttp-110) cc_final: 0.7817 (mtp-110) REVERT: E 521 MET cc_start: 0.7140 (mtp) cc_final: 0.6631 (mtp) REVERT: E 525 MET cc_start: 0.7278 (mmt) cc_final: 0.6963 (mmm) REVERT: E 530 SER cc_start: 0.8344 (t) cc_final: 0.7766 (p) REVERT: E 577 LYS cc_start: 0.8045 (mtpp) cc_final: 0.7704 (mtpp) REVERT: E 588 ILE cc_start: 0.8465 (mt) cc_final: 0.8032 (tp) REVERT: H 74 ARG cc_start: 0.7029 (mtt90) cc_final: 0.6646 (mtt-85) REVERT: H 76 THR cc_start: 0.7691 (m) cc_final: 0.7341 (p) REVERT: H 111 LYS cc_start: 0.7833 (pttt) cc_final: 0.7372 (pttt) REVERT: H 130 SER cc_start: 0.8487 (t) cc_final: 0.8002 (p) REVERT: H 140 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.6610 (m-40) REVERT: H 154 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6662 (mt-10) REVERT: H 166 GLU cc_start: 0.7221 (tp30) cc_final: 0.6662 (tp30) REVERT: H 212 MET cc_start: 0.6943 (mmm) cc_final: 0.6577 (mmm) REVERT: H 215 GLN cc_start: 0.7423 (mt0) cc_final: 0.7167 (mt0) REVERT: H 228 ILE cc_start: 0.8417 (mp) cc_final: 0.8193 (mp) REVERT: H 241 GLN cc_start: 0.7850 (pp30) cc_final: 0.7317 (pp30) REVERT: H 242 ARG cc_start: 0.7492 (mmm160) cc_final: 0.7275 (mmm160) REVERT: H 249 ASP cc_start: 0.6885 (m-30) cc_final: 0.6402 (m-30) REVERT: H 252 ARG cc_start: 0.7430 (ttm170) cc_final: 0.7145 (mtm-85) REVERT: H 256 MET cc_start: 0.7412 (ttp) cc_final: 0.6977 (ttp) REVERT: H 275 ASN cc_start: 0.7478 (p0) cc_final: 0.7217 (p0) REVERT: H 303 THR cc_start: 0.8293 (m) cc_final: 0.7663 (t) REVERT: H 314 PHE cc_start: 0.8538 (p90) cc_final: 0.8163 (p90) REVERT: H 315 MET cc_start: 0.7272 (mmm) cc_final: 0.6887 (mmm) REVERT: H 341 GLN cc_start: 0.7963 (tt0) cc_final: 0.7607 (tm-30) REVERT: H 350 MET cc_start: 0.7877 (ptp) cc_final: 0.7674 (ptp) REVERT: H 364 ARG cc_start: 0.7730 (ptp-170) cc_final: 0.7141 (ptm160) REVERT: H 381 GLN cc_start: 0.7185 (tp40) cc_final: 0.6697 (mm-40) REVERT: H 397 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6413 (mm-30) REVERT: H 404 LEU cc_start: 0.8483 (mp) cc_final: 0.8107 (mt) REVERT: H 482 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7426 (mt) REVERT: H 521 MET cc_start: 0.7393 (mtp) cc_final: 0.6855 (mtp) REVERT: H 522 SER cc_start: 0.8574 (p) cc_final: 0.8347 (p) REVERT: H 593 PHE cc_start: 0.8039 (t80) cc_final: 0.7553 (t80) outliers start: 62 outliers final: 41 residues processed: 650 average time/residue: 0.3256 time to fit residues: 304.0775 Evaluate side-chains 652 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 608 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 330 LEU Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 394 VAL Chi-restraints excluded: chain H residue 475 SER Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 563 ILE Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 163 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 146 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 HIS A 598 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 505 GLN H 177 ASN H 387 ASN H 474 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17259 Z= 0.303 Angle : 0.598 10.356 23366 Z= 0.321 Chirality : 0.045 0.238 2603 Planarity : 0.004 0.047 2976 Dihedral : 6.373 111.527 2856 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.33 % Allowed : 17.59 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 1978 helix: 1.34 (0.31), residues: 286 sheet: 0.41 (0.21), residues: 604 loop : -0.39 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 75 HIS 0.008 0.001 HIS H 189 PHE 0.027 0.002 PHE D 486 TYR 0.027 0.002 TYR E 214 ARG 0.013 0.001 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 629 time to evaluate : 1.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7334 (mmm) cc_final: 0.6989 (mmm) REVERT: A 120 ILE cc_start: 0.8380 (mt) cc_final: 0.7963 (pt) REVERT: A 153 ILE cc_start: 0.8302 (mt) cc_final: 0.7797 (tp) REVERT: A 154 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6880 (mt-10) REVERT: A 156 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6533 (mm-30) REVERT: A 271 PHE cc_start: 0.8092 (m-10) cc_final: 0.7528 (m-10) REVERT: A 293 ASP cc_start: 0.6580 (p0) cc_final: 0.6013 (p0) REVERT: A 315 MET cc_start: 0.6295 (mmm) cc_final: 0.5702 (mmm) REVERT: A 363 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7796 (ttp-170) REVERT: A 372 ARG cc_start: 0.7146 (ttp-110) cc_final: 0.6611 (ptm-80) REVERT: A 375 VAL cc_start: 0.8123 (t) cc_final: 0.7750 (p) REVERT: A 376 LYS cc_start: 0.8042 (tttt) cc_final: 0.7574 (tttt) REVERT: A 428 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6479 (mt-10) REVERT: A 438 VAL cc_start: 0.8290 (t) cc_final: 0.7834 (p) REVERT: A 447 ASN cc_start: 0.7757 (m-40) cc_final: 0.7479 (m-40) REVERT: A 458 ARG cc_start: 0.8114 (mtm110) cc_final: 0.7805 (ttp80) REVERT: A 527 PHE cc_start: 0.7857 (p90) cc_final: 0.7310 (p90) REVERT: A 530 SER cc_start: 0.8392 (t) cc_final: 0.7965 (p) REVERT: A 560 PHE cc_start: 0.7691 (m-80) cc_final: 0.7471 (m-10) REVERT: A 583 LYS cc_start: 0.7750 (tptt) cc_final: 0.7502 (tptt) REVERT: D 45 GLU cc_start: 0.7922 (tt0) cc_final: 0.7419 (tt0) REVERT: D 59 ILE cc_start: 0.7592 (mt) cc_final: 0.7250 (mt) REVERT: D 79 ILE cc_start: 0.7505 (mm) cc_final: 0.7141 (mt) REVERT: D 85 ASP cc_start: 0.7473 (OUTLIER) cc_final: 0.7208 (t0) REVERT: D 95 ILE cc_start: 0.7961 (mt) cc_final: 0.7731 (mm) REVERT: D 101 MET cc_start: 0.7015 (mmm) cc_final: 0.6517 (mmm) REVERT: D 105 LYS cc_start: 0.8083 (mttt) cc_final: 0.7883 (mttp) REVERT: D 135 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6445 (mm-40) REVERT: D 141 ILE cc_start: 0.7876 (mt) cc_final: 0.7560 (mm) REVERT: D 142 SER cc_start: 0.8165 (t) cc_final: 0.7399 (p) REVERT: D 156 GLU cc_start: 0.6959 (mm-30) cc_final: 0.6464 (mm-30) REVERT: D 163 PHE cc_start: 0.6952 (m-80) cc_final: 0.6225 (m-80) REVERT: D 212 MET cc_start: 0.6166 (mmm) cc_final: 0.5904 (mmm) REVERT: D 244 ASP cc_start: 0.7015 (t70) cc_final: 0.6446 (t70) REVERT: D 252 ARG cc_start: 0.7565 (mtp180) cc_final: 0.6637 (mtp180) REVERT: D 287 THR cc_start: 0.7413 (t) cc_final: 0.6896 (m) REVERT: D 330 LEU cc_start: 0.7424 (mt) cc_final: 0.6933 (mt) REVERT: D 339 ARG cc_start: 0.6612 (mtt-85) cc_final: 0.6377 (mmt-90) REVERT: D 362 VAL cc_start: 0.8062 (t) cc_final: 0.7797 (p) REVERT: D 396 LYS cc_start: 0.7626 (mttt) cc_final: 0.7354 (mttt) REVERT: D 405 PHE cc_start: 0.7708 (m-10) cc_final: 0.7413 (m-10) REVERT: D 428 GLU cc_start: 0.6690 (mt-10) cc_final: 0.6452 (mt-10) REVERT: D 445 LEU cc_start: 0.8243 (tp) cc_final: 0.8017 (mt) REVERT: D 453 LYS cc_start: 0.7102 (pttt) cc_final: 0.6407 (pttt) REVERT: D 455 GLN cc_start: 0.7606 (mp10) cc_final: 0.6859 (mp10) REVERT: D 487 HIS cc_start: 0.7865 (p-80) cc_final: 0.7494 (p-80) REVERT: D 492 GLU cc_start: 0.6868 (pt0) cc_final: 0.6607 (pt0) REVERT: D 512 ASP cc_start: 0.7229 (t0) cc_final: 0.6972 (t0) REVERT: D 573 HIS cc_start: 0.7287 (m170) cc_final: 0.6739 (m170) REVERT: D 577 LYS cc_start: 0.7646 (mmtt) cc_final: 0.7339 (mmtt) REVERT: E 100 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7064 (tm-30) REVERT: E 131 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6556 (mt-10) REVERT: E 136 HIS cc_start: 0.7380 (m-70) cc_final: 0.6925 (m-70) REVERT: E 143 ILE cc_start: 0.8527 (mm) cc_final: 0.8261 (tp) REVERT: E 154 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6658 (mt-10) REVERT: E 166 GLU cc_start: 0.6881 (tp30) cc_final: 0.6436 (tp30) REVERT: E 173 ASP cc_start: 0.7746 (m-30) cc_final: 0.7511 (t0) REVERT: E 215 GLN cc_start: 0.7355 (mt0) cc_final: 0.6738 (mt0) REVERT: E 224 SER cc_start: 0.7179 (m) cc_final: 0.6736 (p) REVERT: E 234 GLU cc_start: 0.7475 (mp0) cc_final: 0.7196 (mp0) REVERT: E 241 GLN cc_start: 0.8082 (pp30) cc_final: 0.7611 (pp30) REVERT: E 267 ASP cc_start: 0.7002 (t0) cc_final: 0.6513 (t0) REVERT: E 268 HIS cc_start: 0.7578 (p-80) cc_final: 0.7253 (p-80) REVERT: E 299 GLU cc_start: 0.6682 (mt-10) cc_final: 0.6391 (mt-10) REVERT: E 320 SER cc_start: 0.8435 (p) cc_final: 0.7966 (t) REVERT: E 326 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6206 (tt0) REVERT: E 350 MET cc_start: 0.7293 (mtm) cc_final: 0.6843 (ptm) REVERT: E 381 GLN cc_start: 0.7545 (tp40) cc_final: 0.7250 (mm-40) REVERT: E 409 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7717 (ttpp) REVERT: E 412 PRO cc_start: 0.8730 (Cg_endo) cc_final: 0.8386 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8077 (t80) cc_final: 0.7656 (t80) REVERT: E 493 ASN cc_start: 0.8075 (m-40) cc_final: 0.7849 (m-40) REVERT: E 502 GLU cc_start: 0.7150 (mt-10) cc_final: 0.6745 (mt-10) REVERT: E 518 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7846 (mtp-110) REVERT: E 521 MET cc_start: 0.7215 (mtp) cc_final: 0.6687 (mtp) REVERT: E 525 MET cc_start: 0.7317 (mmt) cc_final: 0.7006 (mmm) REVERT: E 527 PHE cc_start: 0.7159 (p90) cc_final: 0.6810 (p90) REVERT: E 530 SER cc_start: 0.8450 (t) cc_final: 0.7921 (p) REVERT: E 568 SER cc_start: 0.8119 (p) cc_final: 0.7883 (t) REVERT: E 577 LYS cc_start: 0.8052 (mtpp) cc_final: 0.7703 (mtpp) REVERT: E 588 ILE cc_start: 0.8480 (mt) cc_final: 0.8003 (tt) REVERT: H 74 ARG cc_start: 0.7059 (mtt90) cc_final: 0.6699 (mtt-85) REVERT: H 76 THR cc_start: 0.7637 (m) cc_final: 0.7276 (p) REVERT: H 111 LYS cc_start: 0.7866 (pttt) cc_final: 0.7419 (pttt) REVERT: H 124 GLN cc_start: 0.7143 (tm-30) cc_final: 0.6546 (tm-30) REVERT: H 154 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6769 (mt-10) REVERT: H 166 GLU cc_start: 0.7312 (tp30) cc_final: 0.6762 (tp30) REVERT: H 200 THR cc_start: 0.6081 (OUTLIER) cc_final: 0.4575 (p) REVERT: H 212 MET cc_start: 0.6955 (mmm) cc_final: 0.6646 (mmm) REVERT: H 215 GLN cc_start: 0.7490 (mt0) cc_final: 0.7167 (mt0) REVERT: H 228 ILE cc_start: 0.8395 (mp) cc_final: 0.8167 (mp) REVERT: H 241 GLN cc_start: 0.7925 (pp30) cc_final: 0.7506 (pp30) REVERT: H 249 ASP cc_start: 0.6905 (m-30) cc_final: 0.6495 (m-30) REVERT: H 256 MET cc_start: 0.7466 (ttp) cc_final: 0.7107 (ttp) REVERT: H 275 ASN cc_start: 0.7511 (p0) cc_final: 0.7167 (p0) REVERT: H 303 THR cc_start: 0.8286 (m) cc_final: 0.7600 (t) REVERT: H 314 PHE cc_start: 0.8573 (p90) cc_final: 0.8164 (p90) REVERT: H 315 MET cc_start: 0.7269 (mmm) cc_final: 0.6845 (mmm) REVERT: H 364 ARG cc_start: 0.7824 (ptp-170) cc_final: 0.6943 (ptm160) REVERT: H 372 ARG cc_start: 0.7494 (mtp-110) cc_final: 0.7185 (mtm-85) REVERT: H 381 GLN cc_start: 0.7270 (tp40) cc_final: 0.6761 (mm-40) REVERT: H 397 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6173 (mm-30) REVERT: H 404 LEU cc_start: 0.8497 (mp) cc_final: 0.8141 (mt) REVERT: H 521 MET cc_start: 0.7434 (mtp) cc_final: 0.6722 (mtp) REVERT: H 522 SER cc_start: 0.8621 (p) cc_final: 0.8384 (p) REVERT: H 593 PHE cc_start: 0.7948 (t80) cc_final: 0.7717 (t80) outliers start: 78 outliers final: 56 residues processed: 663 average time/residue: 0.3247 time to fit residues: 308.7520 Evaluate side-chains 666 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 607 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 374 LEU Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 292 GLN Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 368 THR Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 475 SER Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 563 ILE Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 66 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 38 optimal weight: 0.4980 chunk 115 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 196 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 165 HIS ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 215 GLN H 387 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17259 Z= 0.308 Angle : 0.613 11.482 23366 Z= 0.327 Chirality : 0.046 0.234 2603 Planarity : 0.004 0.053 2976 Dihedral : 6.316 108.652 2856 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.55 % Allowed : 18.76 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.18), residues: 1978 helix: 1.29 (0.30), residues: 285 sheet: 0.32 (0.21), residues: 599 loop : -0.52 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 75 HIS 0.007 0.001 HIS H 189 PHE 0.025 0.002 PHE D 486 TYR 0.036 0.002 TYR D 119 ARG 0.011 0.001 ARG D 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 642 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7336 (mmm) cc_final: 0.6988 (mmm) REVERT: A 120 ILE cc_start: 0.8405 (mt) cc_final: 0.7983 (pt) REVERT: A 121 ILE cc_start: 0.8006 (tt) cc_final: 0.7392 (pt) REVERT: A 152 ILE cc_start: 0.8301 (mt) cc_final: 0.8025 (mm) REVERT: A 153 ILE cc_start: 0.8291 (mt) cc_final: 0.7780 (tp) REVERT: A 154 GLU cc_start: 0.7193 (mt-10) cc_final: 0.6950 (mt-10) REVERT: A 156 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6595 (mm-30) REVERT: A 293 ASP cc_start: 0.6675 (p0) cc_final: 0.6428 (t0) REVERT: A 315 MET cc_start: 0.6244 (mmm) cc_final: 0.5898 (mmm) REVERT: A 330 LEU cc_start: 0.8054 (tp) cc_final: 0.7670 (tp) REVERT: A 363 ARG cc_start: 0.8093 (ttm170) cc_final: 0.7752 (ttp-170) REVERT: A 372 ARG cc_start: 0.7178 (ttp-110) cc_final: 0.6549 (ptm-80) REVERT: A 375 VAL cc_start: 0.8070 (t) cc_final: 0.7674 (p) REVERT: A 376 LYS cc_start: 0.8049 (tttt) cc_final: 0.7616 (tttt) REVERT: A 428 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6452 (mt-10) REVERT: A 438 VAL cc_start: 0.8303 (t) cc_final: 0.7876 (p) REVERT: A 447 ASN cc_start: 0.7790 (m-40) cc_final: 0.7556 (m-40) REVERT: A 458 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7833 (ttp80) REVERT: A 511 LEU cc_start: 0.8307 (tp) cc_final: 0.8081 (mp) REVERT: A 527 PHE cc_start: 0.7897 (p90) cc_final: 0.7359 (p90) REVERT: A 530 SER cc_start: 0.8377 (t) cc_final: 0.7960 (p) REVERT: A 583 LYS cc_start: 0.7754 (tptt) cc_final: 0.7417 (tptt) REVERT: A 585 ASP cc_start: 0.6635 (t70) cc_final: 0.6268 (t70) REVERT: D 45 GLU cc_start: 0.7936 (tt0) cc_final: 0.7419 (tt0) REVERT: D 59 ILE cc_start: 0.7745 (mt) cc_final: 0.7411 (mt) REVERT: D 85 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7251 (t0) REVERT: D 101 MET cc_start: 0.7118 (mmm) cc_final: 0.6536 (mmm) REVERT: D 135 GLN cc_start: 0.7061 (mm-40) cc_final: 0.6779 (mm-40) REVERT: D 141 ILE cc_start: 0.7879 (mt) cc_final: 0.7517 (mm) REVERT: D 142 SER cc_start: 0.8116 (t) cc_final: 0.7330 (p) REVERT: D 156 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6499 (mm-30) REVERT: D 163 PHE cc_start: 0.6991 (m-80) cc_final: 0.6166 (m-80) REVERT: D 212 MET cc_start: 0.6174 (mmm) cc_final: 0.5893 (mmm) REVERT: D 252 ARG cc_start: 0.7555 (mtp180) cc_final: 0.6742 (mtp180) REVERT: D 287 THR cc_start: 0.7367 (t) cc_final: 0.7041 (m) REVERT: D 330 LEU cc_start: 0.7666 (mt) cc_final: 0.7200 (mt) REVERT: D 339 ARG cc_start: 0.6767 (mtt180) cc_final: 0.6476 (mmt-90) REVERT: D 362 VAL cc_start: 0.8031 (t) cc_final: 0.7819 (m) REVERT: D 396 LYS cc_start: 0.7644 (mttt) cc_final: 0.7382 (mttt) REVERT: D 404 LEU cc_start: 0.7846 (mp) cc_final: 0.7594 (mt) REVERT: D 405 PHE cc_start: 0.7671 (m-10) cc_final: 0.7386 (m-10) REVERT: D 428 GLU cc_start: 0.6710 (mt-10) cc_final: 0.6471 (mt-10) REVERT: D 441 PHE cc_start: 0.8569 (t80) cc_final: 0.7939 (t80) REVERT: D 445 LEU cc_start: 0.8268 (tp) cc_final: 0.8063 (mt) REVERT: D 453 LYS cc_start: 0.7303 (pttt) cc_final: 0.6906 (pttt) REVERT: D 486 PHE cc_start: 0.7995 (t80) cc_final: 0.7784 (t80) REVERT: D 487 HIS cc_start: 0.7861 (p-80) cc_final: 0.7533 (p-80) REVERT: D 492 GLU cc_start: 0.6891 (pt0) cc_final: 0.6683 (pt0) REVERT: D 512 ASP cc_start: 0.7268 (t0) cc_final: 0.7055 (t0) REVERT: D 544 TRP cc_start: 0.8113 (m100) cc_final: 0.7745 (m100) REVERT: D 573 HIS cc_start: 0.7347 (m170) cc_final: 0.6781 (m170) REVERT: D 577 LYS cc_start: 0.7707 (mmtt) cc_final: 0.7363 (mmtt) REVERT: E 74 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.7187 (mtt-85) REVERT: E 100 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: E 136 HIS cc_start: 0.7328 (m-70) cc_final: 0.6914 (m-70) REVERT: E 143 ILE cc_start: 0.8501 (mm) cc_final: 0.8200 (tp) REVERT: E 154 GLU cc_start: 0.6959 (mt-10) cc_final: 0.6646 (mt-10) REVERT: E 173 ASP cc_start: 0.7730 (m-30) cc_final: 0.7474 (t0) REVERT: E 180 TRP cc_start: 0.8430 (m100) cc_final: 0.8068 (m100) REVERT: E 209 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6856 (tt0) REVERT: E 215 GLN cc_start: 0.7427 (mt0) cc_final: 0.6807 (mt0) REVERT: E 224 SER cc_start: 0.7353 (m) cc_final: 0.6997 (p) REVERT: E 241 GLN cc_start: 0.8130 (pp30) cc_final: 0.7676 (pp30) REVERT: E 256 MET cc_start: 0.7306 (OUTLIER) cc_final: 0.6813 (tpp) REVERT: E 267 ASP cc_start: 0.7001 (t0) cc_final: 0.6496 (t0) REVERT: E 299 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6389 (mt-10) REVERT: E 326 GLU cc_start: 0.6660 (mt-10) cc_final: 0.6276 (tt0) REVERT: E 329 LEU cc_start: 0.7958 (mt) cc_final: 0.7751 (tp) REVERT: E 356 ASP cc_start: 0.6842 (m-30) cc_final: 0.6641 (m-30) REVERT: E 409 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7772 (ttpp) REVERT: E 412 PRO cc_start: 0.8739 (Cg_endo) cc_final: 0.8444 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8115 (t80) cc_final: 0.7728 (t80) REVERT: E 493 ASN cc_start: 0.8034 (m-40) cc_final: 0.7804 (m-40) REVERT: E 502 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6787 (mt-10) REVERT: E 518 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7833 (mtp-110) REVERT: E 521 MET cc_start: 0.7209 (mtp) cc_final: 0.6680 (mtp) REVERT: E 525 MET cc_start: 0.7291 (mmt) cc_final: 0.7015 (mmm) REVERT: E 527 PHE cc_start: 0.7155 (p90) cc_final: 0.6730 (p90) REVERT: E 530 SER cc_start: 0.8521 (t) cc_final: 0.8029 (p) REVERT: E 568 SER cc_start: 0.8141 (p) cc_final: 0.7922 (t) REVERT: E 577 LYS cc_start: 0.8065 (mtpp) cc_final: 0.7725 (mtpp) REVERT: E 588 ILE cc_start: 0.8459 (mt) cc_final: 0.8044 (tp) REVERT: H 74 ARG cc_start: 0.7069 (mtt90) cc_final: 0.6602 (mtt-85) REVERT: H 76 THR cc_start: 0.7616 (m) cc_final: 0.7267 (p) REVERT: H 86 ASN cc_start: 0.8520 (p0) cc_final: 0.8314 (p0) REVERT: H 111 LYS cc_start: 0.7843 (pttt) cc_final: 0.7459 (pttt) REVERT: H 124 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6749 (tm-30) REVERT: H 154 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6738 (mt-10) REVERT: H 166 GLU cc_start: 0.7345 (tp30) cc_final: 0.6856 (tp30) REVERT: H 200 THR cc_start: 0.5978 (OUTLIER) cc_final: 0.4382 (p) REVERT: H 212 MET cc_start: 0.6901 (mmm) cc_final: 0.6576 (mmm) REVERT: H 215 GLN cc_start: 0.7590 (mt0) cc_final: 0.7215 (mt0) REVERT: H 228 ILE cc_start: 0.8384 (mp) cc_final: 0.8011 (mm) REVERT: H 241 GLN cc_start: 0.7939 (pp30) cc_final: 0.7615 (pp30) REVERT: H 249 ASP cc_start: 0.6917 (m-30) cc_final: 0.6494 (m-30) REVERT: H 256 MET cc_start: 0.7474 (ttp) cc_final: 0.6777 (ttp) REVERT: H 275 ASN cc_start: 0.7532 (p0) cc_final: 0.7205 (p0) REVERT: H 303 THR cc_start: 0.8290 (m) cc_final: 0.7528 (t) REVERT: H 314 PHE cc_start: 0.8592 (p90) cc_final: 0.8176 (p90) REVERT: H 315 MET cc_start: 0.7251 (mmm) cc_final: 0.6837 (mmm) REVERT: H 373 LYS cc_start: 0.7973 (ttpp) cc_final: 0.7397 (ttpp) REVERT: H 381 GLN cc_start: 0.7388 (tp40) cc_final: 0.6842 (mm-40) REVERT: H 397 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6298 (mm-30) REVERT: H 404 LEU cc_start: 0.8520 (mp) cc_final: 0.8197 (mt) REVERT: H 409 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8727 (mttm) REVERT: H 502 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: H 522 SER cc_start: 0.8575 (p) cc_final: 0.8207 (p) REVERT: H 543 ILE cc_start: 0.7899 (mt) cc_final: 0.7660 (mt) REVERT: H 584 ASN cc_start: 0.7925 (t0) cc_final: 0.7597 (t0) REVERT: H 593 PHE cc_start: 0.7964 (t80) cc_final: 0.7569 (t80) outliers start: 82 outliers final: 60 residues processed: 673 average time/residue: 0.3358 time to fit residues: 326.3503 Evaluate side-chains 684 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 619 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 576 LEU Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 256 MET Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 292 GLN Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 563 ILE Chi-restraints excluded: chain H residue 564 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 189 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 ASN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 HIS H 189 HIS H 302 HIS H 503 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17259 Z= 0.276 Angle : 0.618 13.252 23366 Z= 0.325 Chirality : 0.046 0.239 2603 Planarity : 0.004 0.052 2976 Dihedral : 6.179 106.709 2856 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.44 % Allowed : 19.98 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 1978 helix: 1.27 (0.30), residues: 285 sheet: 0.26 (0.21), residues: 590 loop : -0.51 (0.18), residues: 1103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 361 HIS 0.007 0.001 HIS H 189 PHE 0.024 0.002 PHE D 110 TYR 0.020 0.002 TYR H 553 ARG 0.008 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 631 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8016 (tt) cc_final: 0.7388 (pt) REVERT: A 153 ILE cc_start: 0.8197 (mt) cc_final: 0.7675 (tp) REVERT: A 154 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6888 (mt-10) REVERT: A 156 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6585 (mm-30) REVERT: A 212 MET cc_start: 0.6857 (mmm) cc_final: 0.6545 (mmm) REVERT: A 271 PHE cc_start: 0.8029 (m-10) cc_final: 0.7484 (m-10) REVERT: A 293 ASP cc_start: 0.6705 (p0) cc_final: 0.6435 (t0) REVERT: A 315 MET cc_start: 0.6184 (mmm) cc_final: 0.5983 (mmm) REVERT: A 330 LEU cc_start: 0.8043 (tp) cc_final: 0.7664 (tp) REVERT: A 363 ARG cc_start: 0.8124 (ttm170) cc_final: 0.7891 (ttm170) REVERT: A 375 VAL cc_start: 0.8021 (t) cc_final: 0.7622 (p) REVERT: A 428 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6452 (mt-10) REVERT: A 438 VAL cc_start: 0.8309 (t) cc_final: 0.7896 (p) REVERT: A 447 ASN cc_start: 0.7776 (m-40) cc_final: 0.7542 (m-40) REVERT: A 458 ARG cc_start: 0.8093 (mtm110) cc_final: 0.7821 (ttp80) REVERT: A 511 LEU cc_start: 0.8313 (tp) cc_final: 0.8063 (mp) REVERT: A 527 PHE cc_start: 0.7787 (p90) cc_final: 0.7199 (p90) REVERT: A 530 SER cc_start: 0.8351 (t) cc_final: 0.7916 (p) REVERT: A 583 LYS cc_start: 0.7765 (tptt) cc_final: 0.7518 (tptt) REVERT: A 585 ASP cc_start: 0.6617 (t70) cc_final: 0.6369 (t70) REVERT: D 45 GLU cc_start: 0.7937 (tt0) cc_final: 0.7418 (tt0) REVERT: D 59 ILE cc_start: 0.7748 (mt) cc_final: 0.7494 (mt) REVERT: D 85 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7256 (t0) REVERT: D 101 MET cc_start: 0.7281 (mmm) cc_final: 0.6950 (mmm) REVERT: D 135 GLN cc_start: 0.7112 (mm-40) cc_final: 0.6782 (mm-40) REVERT: D 141 ILE cc_start: 0.7894 (mt) cc_final: 0.7564 (mm) REVERT: D 142 SER cc_start: 0.8152 (t) cc_final: 0.7381 (p) REVERT: D 156 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6413 (mm-30) REVERT: D 163 PHE cc_start: 0.7062 (m-80) cc_final: 0.6101 (m-80) REVERT: D 212 MET cc_start: 0.6129 (mmm) cc_final: 0.5838 (mmm) REVERT: D 252 ARG cc_start: 0.7505 (mtp180) cc_final: 0.6645 (ttp-170) REVERT: D 272 GLU cc_start: 0.5075 (mm-30) cc_final: 0.4798 (mm-30) REVERT: D 287 THR cc_start: 0.7393 (t) cc_final: 0.6996 (m) REVERT: D 330 LEU cc_start: 0.7665 (mt) cc_final: 0.7158 (mt) REVERT: D 339 ARG cc_start: 0.6786 (mtt180) cc_final: 0.6529 (mmt-90) REVERT: D 362 VAL cc_start: 0.8057 (t) cc_final: 0.7815 (p) REVERT: D 389 LYS cc_start: 0.8069 (mttm) cc_final: 0.7718 (mttp) REVERT: D 396 LYS cc_start: 0.7666 (mttt) cc_final: 0.7389 (mttt) REVERT: D 404 LEU cc_start: 0.7872 (mp) cc_final: 0.7634 (mt) REVERT: D 405 PHE cc_start: 0.7679 (m-10) cc_final: 0.7358 (m-80) REVERT: D 428 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6454 (mt-10) REVERT: D 441 PHE cc_start: 0.8556 (t80) cc_final: 0.8186 (t80) REVERT: D 445 LEU cc_start: 0.8338 (tp) cc_final: 0.8097 (mt) REVERT: D 453 LYS cc_start: 0.7393 (pttt) cc_final: 0.6996 (pttt) REVERT: D 487 HIS cc_start: 0.7860 (p-80) cc_final: 0.7536 (p-80) REVERT: D 504 ARG cc_start: 0.7415 (mpt180) cc_final: 0.7193 (mpt180) REVERT: D 544 TRP cc_start: 0.8125 (m100) cc_final: 0.7730 (m100) REVERT: D 577 LYS cc_start: 0.7733 (mmtt) cc_final: 0.7350 (mmtt) REVERT: E 74 ARG cc_start: 0.7373 (mtt-85) cc_final: 0.7049 (mtt-85) REVERT: E 100 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: E 131 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6469 (mt-10) REVERT: E 136 HIS cc_start: 0.7298 (m-70) cc_final: 0.6986 (m-70) REVERT: E 143 ILE cc_start: 0.8483 (mm) cc_final: 0.8035 (tp) REVERT: E 173 ASP cc_start: 0.7721 (m-30) cc_final: 0.7497 (t0) REVERT: E 180 TRP cc_start: 0.8438 (m100) cc_final: 0.8049 (m100) REVERT: E 209 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6853 (tt0) REVERT: E 215 GLN cc_start: 0.7353 (mt0) cc_final: 0.6730 (mt0) REVERT: E 224 SER cc_start: 0.7401 (m) cc_final: 0.7056 (p) REVERT: E 241 GLN cc_start: 0.8153 (pp30) cc_final: 0.7702 (pp30) REVERT: E 256 MET cc_start: 0.7315 (ttp) cc_final: 0.6755 (tpp) REVERT: E 267 ASP cc_start: 0.7093 (t0) cc_final: 0.6517 (t0) REVERT: E 287 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7854 (m) REVERT: E 299 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6398 (mt-10) REVERT: E 326 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6422 (tt0) REVERT: E 350 MET cc_start: 0.7283 (mtm) cc_final: 0.6902 (ptm) REVERT: E 409 LYS cc_start: 0.8333 (mtpt) cc_final: 0.7795 (ttpp) REVERT: E 412 PRO cc_start: 0.8737 (Cg_endo) cc_final: 0.8441 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8122 (t80) cc_final: 0.7707 (t80) REVERT: E 502 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6771 (mt-10) REVERT: E 518 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7815 (mtp-110) REVERT: E 521 MET cc_start: 0.7241 (mtp) cc_final: 0.6710 (mtp) REVERT: E 525 MET cc_start: 0.7353 (mmt) cc_final: 0.7090 (mmm) REVERT: E 527 PHE cc_start: 0.7221 (p90) cc_final: 0.6766 (p90) REVERT: E 530 SER cc_start: 0.8521 (t) cc_final: 0.8049 (p) REVERT: E 568 SER cc_start: 0.8182 (p) cc_final: 0.7978 (t) REVERT: E 577 LYS cc_start: 0.8149 (mtpp) cc_final: 0.7794 (mtpp) REVERT: E 588 ILE cc_start: 0.8432 (mt) cc_final: 0.8027 (tp) REVERT: H 74 ARG cc_start: 0.7099 (mtt90) cc_final: 0.6668 (mtt-85) REVERT: H 76 THR cc_start: 0.7617 (m) cc_final: 0.7265 (p) REVERT: H 111 LYS cc_start: 0.7855 (pttt) cc_final: 0.7468 (pttt) REVERT: H 154 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6772 (mt-10) REVERT: H 166 GLU cc_start: 0.7200 (tp30) cc_final: 0.6655 (tp30) REVERT: H 200 THR cc_start: 0.5932 (OUTLIER) cc_final: 0.4352 (p) REVERT: H 212 MET cc_start: 0.6894 (mmm) cc_final: 0.6521 (mmm) REVERT: H 228 ILE cc_start: 0.8395 (mp) cc_final: 0.8152 (mp) REVERT: H 241 GLN cc_start: 0.7959 (pp30) cc_final: 0.7689 (pp30) REVERT: H 249 ASP cc_start: 0.6888 (m-30) cc_final: 0.6490 (m-30) REVERT: H 256 MET cc_start: 0.7479 (ttp) cc_final: 0.6629 (ttp) REVERT: H 273 LYS cc_start: 0.7550 (tttt) cc_final: 0.7325 (tptt) REVERT: H 275 ASN cc_start: 0.7489 (p0) cc_final: 0.7162 (p0) REVERT: H 303 THR cc_start: 0.8319 (m) cc_final: 0.7542 (t) REVERT: H 314 PHE cc_start: 0.8576 (p90) cc_final: 0.8202 (p90) REVERT: H 315 MET cc_start: 0.7254 (mmm) cc_final: 0.6858 (mmm) REVERT: H 330 LEU cc_start: 0.8160 (tp) cc_final: 0.7801 (tt) REVERT: H 338 LYS cc_start: 0.8057 (mttt) cc_final: 0.7841 (mttt) REVERT: H 373 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7518 (ttpp) REVERT: H 397 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6297 (mm-30) REVERT: H 404 LEU cc_start: 0.8486 (mp) cc_final: 0.8168 (mt) REVERT: H 455 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7436 (pt0) REVERT: H 502 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: H 521 MET cc_start: 0.7526 (mtp) cc_final: 0.6897 (mtp) REVERT: H 522 SER cc_start: 0.8620 (p) cc_final: 0.8245 (p) REVERT: H 543 ILE cc_start: 0.7914 (mt) cc_final: 0.7687 (mt) REVERT: H 584 ASN cc_start: 0.7908 (t0) cc_final: 0.7557 (t0) REVERT: H 593 PHE cc_start: 0.7896 (t80) cc_final: 0.7667 (t80) outliers start: 80 outliers final: 61 residues processed: 671 average time/residue: 0.3152 time to fit residues: 305.0778 Evaluate side-chains 679 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 612 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 131 GLU Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 293 ASP Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 261 THR Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain E residue 599 LEU Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 292 GLN Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 563 ILE Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 302 HIS D 573 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS E 574 GLN H 190 ASN H 302 HIS H 574 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17259 Z= 0.224 Angle : 0.589 9.297 23366 Z= 0.312 Chirality : 0.044 0.242 2603 Planarity : 0.004 0.049 2976 Dihedral : 5.984 104.279 2856 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.83 % Allowed : 21.53 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1978 helix: 1.32 (0.31), residues: 286 sheet: 0.31 (0.21), residues: 588 loop : -0.52 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 361 HIS 0.008 0.001 HIS H 189 PHE 0.024 0.002 PHE D 486 TYR 0.021 0.002 TYR H 553 ARG 0.011 0.001 ARG D 74 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 619 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.8006 (tt) cc_final: 0.7378 (pt) REVERT: A 153 ILE cc_start: 0.8193 (mt) cc_final: 0.7705 (tp) REVERT: A 154 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6824 (mt-10) REVERT: A 156 GLU cc_start: 0.6906 (mm-30) cc_final: 0.6614 (mm-30) REVERT: A 188 GLN cc_start: 0.7625 (pm20) cc_final: 0.7348 (pm20) REVERT: A 271 PHE cc_start: 0.8069 (m-10) cc_final: 0.7642 (m-80) REVERT: A 293 ASP cc_start: 0.6719 (p0) cc_final: 0.6443 (t0) REVERT: A 330 LEU cc_start: 0.8036 (tp) cc_final: 0.7668 (tp) REVERT: A 363 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7864 (ttm170) REVERT: A 375 VAL cc_start: 0.8102 (t) cc_final: 0.7732 (p) REVERT: A 383 ASP cc_start: 0.7300 (p0) cc_final: 0.6962 (p0) REVERT: A 428 GLU cc_start: 0.6822 (mt-10) cc_final: 0.6448 (mt-10) REVERT: A 438 VAL cc_start: 0.8340 (t) cc_final: 0.7904 (p) REVERT: A 493 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7509 (m-40) REVERT: A 527 PHE cc_start: 0.7773 (p90) cc_final: 0.7182 (p90) REVERT: A 530 SER cc_start: 0.8297 (t) cc_final: 0.7822 (p) REVERT: A 583 LYS cc_start: 0.7756 (tptt) cc_final: 0.7501 (tptt) REVERT: A 585 ASP cc_start: 0.6654 (t70) cc_final: 0.6389 (t70) REVERT: D 45 GLU cc_start: 0.7910 (tt0) cc_final: 0.7360 (tt0) REVERT: D 101 MET cc_start: 0.7149 (mmm) cc_final: 0.6888 (mmm) REVERT: D 135 GLN cc_start: 0.7047 (mm-40) cc_final: 0.6694 (mm-40) REVERT: D 141 ILE cc_start: 0.7867 (mt) cc_final: 0.7360 (mm) REVERT: D 142 SER cc_start: 0.8119 (t) cc_final: 0.7367 (p) REVERT: D 156 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6423 (mm-30) REVERT: D 163 PHE cc_start: 0.7036 (m-80) cc_final: 0.6018 (m-80) REVERT: D 212 MET cc_start: 0.6072 (mmm) cc_final: 0.5761 (mmm) REVERT: D 252 ARG cc_start: 0.7495 (mtp180) cc_final: 0.6643 (ttp-170) REVERT: D 272 GLU cc_start: 0.5109 (mm-30) cc_final: 0.4807 (mm-30) REVERT: D 287 THR cc_start: 0.7357 (t) cc_final: 0.7037 (m) REVERT: D 330 LEU cc_start: 0.7694 (mt) cc_final: 0.7251 (mt) REVERT: D 362 VAL cc_start: 0.8027 (t) cc_final: 0.7791 (p) REVERT: D 389 LYS cc_start: 0.8022 (mttm) cc_final: 0.7698 (mttp) REVERT: D 396 LYS cc_start: 0.7606 (mttt) cc_final: 0.7321 (mttt) REVERT: D 404 LEU cc_start: 0.7886 (mp) cc_final: 0.7616 (mt) REVERT: D 405 PHE cc_start: 0.7664 (m-10) cc_final: 0.7343 (m-80) REVERT: D 428 GLU cc_start: 0.6670 (mt-10) cc_final: 0.6424 (mt-10) REVERT: D 441 PHE cc_start: 0.8679 (t80) cc_final: 0.8115 (t80) REVERT: D 445 LEU cc_start: 0.8316 (tp) cc_final: 0.8103 (mt) REVERT: D 453 LYS cc_start: 0.7412 (pttt) cc_final: 0.6506 (pttt) REVERT: D 455 GLN cc_start: 0.7576 (mp10) cc_final: 0.7023 (mp10) REVERT: D 487 HIS cc_start: 0.7856 (p-80) cc_final: 0.7655 (p-80) REVERT: D 544 TRP cc_start: 0.8143 (m100) cc_final: 0.7692 (m100) REVERT: D 577 LYS cc_start: 0.7726 (mmtt) cc_final: 0.7339 (mmtt) REVERT: E 48 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8217 (tt) REVERT: E 74 ARG cc_start: 0.7383 (mtt-85) cc_final: 0.7107 (mtt-85) REVERT: E 92 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7763 (mtmm) REVERT: E 100 GLU cc_start: 0.7331 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: E 126 ASP cc_start: 0.8117 (m-30) cc_final: 0.7846 (m-30) REVERT: E 131 GLU cc_start: 0.7021 (mt-10) cc_final: 0.6441 (mt-10) REVERT: E 136 HIS cc_start: 0.6887 (m-70) cc_final: 0.6612 (m-70) REVERT: E 143 ILE cc_start: 0.8460 (mm) cc_final: 0.8010 (tp) REVERT: E 154 GLU cc_start: 0.6869 (mt-10) cc_final: 0.6599 (mt-10) REVERT: E 173 ASP cc_start: 0.7660 (m-30) cc_final: 0.7434 (t0) REVERT: E 180 TRP cc_start: 0.8445 (m100) cc_final: 0.8066 (m100) REVERT: E 209 GLU cc_start: 0.7095 (mt-10) cc_final: 0.6855 (tt0) REVERT: E 224 SER cc_start: 0.7452 (m) cc_final: 0.7094 (p) REVERT: E 245 PHE cc_start: 0.7142 (m-80) cc_final: 0.6871 (m-10) REVERT: E 249 ASP cc_start: 0.6771 (m-30) cc_final: 0.6143 (m-30) REVERT: E 251 GLU cc_start: 0.7276 (tp30) cc_final: 0.6533 (tp30) REVERT: E 256 MET cc_start: 0.7308 (ttp) cc_final: 0.6796 (tpp) REVERT: E 267 ASP cc_start: 0.7055 (t0) cc_final: 0.6433 (t0) REVERT: E 287 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7828 (m) REVERT: E 299 GLU cc_start: 0.6640 (mt-10) cc_final: 0.6394 (mt-10) REVERT: E 315 MET cc_start: 0.7189 (mmm) cc_final: 0.6874 (mmm) REVERT: E 326 GLU cc_start: 0.6580 (mt-10) cc_final: 0.6369 (tt0) REVERT: E 339 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7620 (mmm-85) REVERT: E 350 MET cc_start: 0.7265 (mtm) cc_final: 0.6828 (ptm) REVERT: E 356 ASP cc_start: 0.6815 (m-30) cc_final: 0.6532 (m-30) REVERT: E 392 HIS cc_start: 0.8314 (m90) cc_final: 0.8041 (m-70) REVERT: E 409 LYS cc_start: 0.8342 (mtpt) cc_final: 0.7774 (ttpp) REVERT: E 412 PRO cc_start: 0.8699 (Cg_endo) cc_final: 0.8413 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8094 (t80) cc_final: 0.7694 (t80) REVERT: E 502 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6726 (mt-10) REVERT: E 518 ARG cc_start: 0.8224 (ttp-110) cc_final: 0.7845 (mtp85) REVERT: E 521 MET cc_start: 0.7200 (mtp) cc_final: 0.6683 (mtp) REVERT: E 525 MET cc_start: 0.7327 (mmt) cc_final: 0.6922 (mmt) REVERT: E 530 SER cc_start: 0.8523 (t) cc_final: 0.8034 (p) REVERT: E 577 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7842 (mtpp) REVERT: E 588 ILE cc_start: 0.8451 (mt) cc_final: 0.8048 (tp) REVERT: H 74 ARG cc_start: 0.7081 (mtt90) cc_final: 0.6568 (mtt-85) REVERT: H 76 THR cc_start: 0.7619 (m) cc_final: 0.7267 (p) REVERT: H 111 LYS cc_start: 0.7852 (pttt) cc_final: 0.7466 (pttt) REVERT: H 154 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6767 (mt-10) REVERT: H 166 GLU cc_start: 0.7037 (tp30) cc_final: 0.6423 (tp30) REVERT: H 200 THR cc_start: 0.5980 (OUTLIER) cc_final: 0.4397 (p) REVERT: H 212 MET cc_start: 0.6882 (mmm) cc_final: 0.6484 (mmm) REVERT: H 228 ILE cc_start: 0.8374 (mp) cc_final: 0.8143 (mp) REVERT: H 241 GLN cc_start: 0.7976 (pp30) cc_final: 0.7691 (pp30) REVERT: H 249 ASP cc_start: 0.6909 (m-30) cc_final: 0.6532 (m-30) REVERT: H 256 MET cc_start: 0.7465 (ttp) cc_final: 0.6509 (ttp) REVERT: H 273 LYS cc_start: 0.7563 (tttt) cc_final: 0.7330 (tptt) REVERT: H 275 ASN cc_start: 0.7499 (p0) cc_final: 0.7173 (p0) REVERT: H 293 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7109 (p0) REVERT: H 303 THR cc_start: 0.8332 (m) cc_final: 0.7526 (t) REVERT: H 314 PHE cc_start: 0.8561 (p90) cc_final: 0.8178 (p90) REVERT: H 315 MET cc_start: 0.7227 (mmm) cc_final: 0.6834 (mmm) REVERT: H 330 LEU cc_start: 0.8145 (tp) cc_final: 0.7847 (tt) REVERT: H 364 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.6808 (ptm160) REVERT: H 373 LYS cc_start: 0.7942 (ttpp) cc_final: 0.7517 (ttpp) REVERT: H 397 GLU cc_start: 0.6823 (mm-30) cc_final: 0.6118 (mm-30) REVERT: H 404 LEU cc_start: 0.8519 (mp) cc_final: 0.8229 (mt) REVERT: H 455 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: H 463 GLU cc_start: 0.7333 (mt-10) cc_final: 0.7060 (mt-10) REVERT: H 502 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6895 (mm-30) REVERT: H 521 MET cc_start: 0.7545 (mtp) cc_final: 0.6867 (mtp) REVERT: H 522 SER cc_start: 0.8567 (p) cc_final: 0.8193 (p) REVERT: H 543 ILE cc_start: 0.7873 (mt) cc_final: 0.7615 (mt) REVERT: H 593 PHE cc_start: 0.7868 (t80) cc_final: 0.7636 (t80) outliers start: 69 outliers final: 57 residues processed: 649 average time/residue: 0.3255 time to fit residues: 304.2103 Evaluate side-chains 675 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 610 time to evaluate : 1.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 461 ASN Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 90 ASN Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 314 PHE Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 139 GLN Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 376 LYS Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 221 LYS Chi-restraints excluded: chain H residue 292 GLN Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 187 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 chunk 182 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 0.1980 chunk 143 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 181 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN ** E 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS H 190 ASN H 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.4984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17259 Z= 0.171 Angle : 0.586 14.837 23366 Z= 0.306 Chirality : 0.044 0.246 2603 Planarity : 0.004 0.048 2976 Dihedral : 5.709 101.238 2856 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.33 % Allowed : 22.75 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.19), residues: 1978 helix: 1.49 (0.32), residues: 286 sheet: 0.39 (0.21), residues: 580 loop : -0.46 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 361 HIS 0.008 0.001 HIS H 189 PHE 0.027 0.002 PHE E 55 TYR 0.019 0.001 TYR H 553 ARG 0.012 0.001 ARG D 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 620 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 ILE cc_start: 0.7999 (tt) cc_final: 0.7379 (pt) REVERT: A 153 ILE cc_start: 0.8154 (mt) cc_final: 0.7661 (tp) REVERT: A 154 GLU cc_start: 0.7067 (mt-10) cc_final: 0.6795 (mt-10) REVERT: A 156 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6591 (mm-30) REVERT: A 188 GLN cc_start: 0.7502 (pm20) cc_final: 0.7227 (pm20) REVERT: A 293 ASP cc_start: 0.6630 (p0) cc_final: 0.6387 (t0) REVERT: A 330 LEU cc_start: 0.8037 (tp) cc_final: 0.7643 (tp) REVERT: A 363 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7679 (ttp-110) REVERT: A 375 VAL cc_start: 0.8125 (t) cc_final: 0.7728 (p) REVERT: A 383 ASP cc_start: 0.7327 (p0) cc_final: 0.6976 (p0) REVERT: A 428 GLU cc_start: 0.6817 (mt-10) cc_final: 0.6419 (mt-10) REVERT: A 458 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7873 (ttp80) REVERT: A 493 ASN cc_start: 0.7879 (OUTLIER) cc_final: 0.7531 (m-40) REVERT: A 527 PHE cc_start: 0.7715 (p90) cc_final: 0.7112 (p90) REVERT: A 530 SER cc_start: 0.8276 (t) cc_final: 0.7813 (p) REVERT: A 583 LYS cc_start: 0.7764 (tptt) cc_final: 0.7502 (tptt) REVERT: A 585 ASP cc_start: 0.6622 (t70) cc_final: 0.6288 (t70) REVERT: D 45 GLU cc_start: 0.7885 (tt0) cc_final: 0.7333 (tt0) REVERT: D 96 LEU cc_start: 0.8144 (mt) cc_final: 0.7791 (mp) REVERT: D 101 MET cc_start: 0.7058 (mmm) cc_final: 0.6829 (mmm) REVERT: D 135 GLN cc_start: 0.7050 (mm-40) cc_final: 0.6724 (mm-40) REVERT: D 141 ILE cc_start: 0.7789 (mt) cc_final: 0.7477 (mm) REVERT: D 142 SER cc_start: 0.8132 (t) cc_final: 0.7396 (p) REVERT: D 155 HIS cc_start: 0.7577 (t70) cc_final: 0.7294 (t70) REVERT: D 156 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6668 (mm-30) REVERT: D 215 GLN cc_start: 0.7585 (mt0) cc_final: 0.7372 (mt0) REVERT: D 252 ARG cc_start: 0.7432 (mtp180) cc_final: 0.7181 (ttp-170) REVERT: D 272 GLU cc_start: 0.5159 (mm-30) cc_final: 0.4844 (mm-30) REVERT: D 287 THR cc_start: 0.7341 (t) cc_final: 0.6902 (m) REVERT: D 301 ASP cc_start: 0.7154 (p0) cc_final: 0.6355 (p0) REVERT: D 330 LEU cc_start: 0.7815 (mt) cc_final: 0.6943 (mt) REVERT: D 339 ARG cc_start: 0.6898 (mmt-90) cc_final: 0.6640 (mmt-90) REVERT: D 362 VAL cc_start: 0.8052 (t) cc_final: 0.7813 (p) REVERT: D 389 LYS cc_start: 0.8061 (mttm) cc_final: 0.7713 (mttp) REVERT: D 404 LEU cc_start: 0.7872 (mp) cc_final: 0.7533 (mt) REVERT: D 405 PHE cc_start: 0.7658 (m-10) cc_final: 0.7322 (m-80) REVERT: D 428 GLU cc_start: 0.6646 (mt-10) cc_final: 0.6385 (mt-10) REVERT: D 441 PHE cc_start: 0.8669 (t80) cc_final: 0.8171 (t80) REVERT: D 445 LEU cc_start: 0.8302 (tp) cc_final: 0.8040 (mt) REVERT: D 453 LYS cc_start: 0.7392 (pttt) cc_final: 0.6965 (pttt) REVERT: D 483 ARG cc_start: 0.7281 (ttt90) cc_final: 0.6849 (tpt170) REVERT: D 487 HIS cc_start: 0.7817 (p-80) cc_final: 0.7597 (p-80) REVERT: D 544 TRP cc_start: 0.8141 (m100) cc_final: 0.7694 (m100) REVERT: D 577 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7310 (mmtt) REVERT: E 74 ARG cc_start: 0.7323 (mtt-85) cc_final: 0.7051 (mtt-85) REVERT: E 100 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6944 (tm-30) REVERT: E 126 ASP cc_start: 0.8188 (m-30) cc_final: 0.7482 (m-30) REVERT: E 131 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6384 (mt-10) REVERT: E 136 HIS cc_start: 0.6921 (m-70) cc_final: 0.6661 (m-70) REVERT: E 143 ILE cc_start: 0.8439 (mm) cc_final: 0.7962 (tp) REVERT: E 154 GLU cc_start: 0.6914 (mt-10) cc_final: 0.6633 (mt-10) REVERT: E 173 ASP cc_start: 0.7620 (m-30) cc_final: 0.7404 (t0) REVERT: E 209 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6849 (tt0) REVERT: E 224 SER cc_start: 0.7532 (m) cc_final: 0.7163 (p) REVERT: E 241 GLN cc_start: 0.8092 (pp30) cc_final: 0.7873 (pp30) REVERT: E 245 PHE cc_start: 0.7109 (m-80) cc_final: 0.6784 (m-10) REVERT: E 249 ASP cc_start: 0.6754 (m-30) cc_final: 0.6090 (m-30) REVERT: E 256 MET cc_start: 0.7243 (ttp) cc_final: 0.6674 (tpp) REVERT: E 267 ASP cc_start: 0.6996 (t0) cc_final: 0.6388 (t0) REVERT: E 287 THR cc_start: 0.8103 (OUTLIER) cc_final: 0.7813 (m) REVERT: E 299 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6380 (mt-10) REVERT: E 315 MET cc_start: 0.7224 (mmm) cc_final: 0.6884 (mmm) REVERT: E 326 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6260 (tt0) REVERT: E 339 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.7684 (mmm-85) REVERT: E 340 LYS cc_start: 0.8196 (mttt) cc_final: 0.7978 (mttt) REVERT: E 350 MET cc_start: 0.7217 (mtm) cc_final: 0.6820 (ptm) REVERT: E 409 LYS cc_start: 0.8309 (mtpt) cc_final: 0.7752 (ttpp) REVERT: E 412 PRO cc_start: 0.8671 (Cg_endo) cc_final: 0.8377 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8055 (t80) cc_final: 0.7651 (t80) REVERT: E 502 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6723 (mt-10) REVERT: E 518 ARG cc_start: 0.8210 (ttp-110) cc_final: 0.7863 (mtp85) REVERT: E 521 MET cc_start: 0.7171 (mtp) cc_final: 0.6729 (mtp) REVERT: E 525 MET cc_start: 0.7318 (mmt) cc_final: 0.7056 (mmm) REVERT: E 530 SER cc_start: 0.8507 (t) cc_final: 0.8025 (p) REVERT: E 577 LYS cc_start: 0.8152 (mtpp) cc_final: 0.7819 (mtpp) REVERT: E 588 ILE cc_start: 0.8440 (mt) cc_final: 0.8030 (tp) REVERT: H 74 ARG cc_start: 0.7058 (mtt90) cc_final: 0.6670 (mtt-85) REVERT: H 76 THR cc_start: 0.7638 (m) cc_final: 0.7290 (p) REVERT: H 111 LYS cc_start: 0.7842 (pttt) cc_final: 0.7441 (pttt) REVERT: H 124 GLN cc_start: 0.7134 (tm-30) cc_final: 0.6912 (tm-30) REVERT: H 140 ASN cc_start: 0.7890 (OUTLIER) cc_final: 0.6929 (m-40) REVERT: H 154 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6699 (mt-10) REVERT: H 200 THR cc_start: 0.5826 (OUTLIER) cc_final: 0.4231 (p) REVERT: H 212 MET cc_start: 0.6852 (mmm) cc_final: 0.6439 (mmm) REVERT: H 228 ILE cc_start: 0.8389 (mp) cc_final: 0.8147 (mp) REVERT: H 241 GLN cc_start: 0.7955 (pp30) cc_final: 0.7701 (pp30) REVERT: H 249 ASP cc_start: 0.6871 (m-30) cc_final: 0.6513 (m-30) REVERT: H 256 MET cc_start: 0.7441 (ttp) cc_final: 0.6951 (ttp) REVERT: H 273 LYS cc_start: 0.7544 (tttt) cc_final: 0.7337 (tptt) REVERT: H 275 ASN cc_start: 0.7476 (p0) cc_final: 0.7235 (p0) REVERT: H 293 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7091 (p0) REVERT: H 303 THR cc_start: 0.8345 (m) cc_final: 0.7615 (t) REVERT: H 314 PHE cc_start: 0.8547 (p90) cc_final: 0.8219 (p90) REVERT: H 315 MET cc_start: 0.7234 (mmm) cc_final: 0.6950 (mmm) REVERT: H 330 LEU cc_start: 0.8153 (tp) cc_final: 0.7848 (tt) REVERT: H 364 ARG cc_start: 0.7802 (ptp-170) cc_final: 0.6727 (ptm160) REVERT: H 365 ASP cc_start: 0.6631 (t0) cc_final: 0.6394 (t0) REVERT: H 373 LYS cc_start: 0.7945 (ttpp) cc_final: 0.7385 (ttpp) REVERT: H 397 GLU cc_start: 0.6785 (mm-30) cc_final: 0.6062 (mm-30) REVERT: H 404 LEU cc_start: 0.8480 (mp) cc_final: 0.8178 (mt) REVERT: H 409 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8660 (mttm) REVERT: H 455 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7552 (pt0) REVERT: H 463 GLU cc_start: 0.7338 (mt-10) cc_final: 0.7084 (mt-10) REVERT: H 502 GLU cc_start: 0.7192 (OUTLIER) cc_final: 0.6895 (mm-30) REVERT: H 521 MET cc_start: 0.7544 (mtp) cc_final: 0.6871 (mtp) REVERT: H 522 SER cc_start: 0.8567 (p) cc_final: 0.8210 (p) REVERT: H 543 ILE cc_start: 0.7890 (mt) cc_final: 0.7617 (mt) REVERT: H 564 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6943 (t70) outliers start: 60 outliers final: 47 residues processed: 649 average time/residue: 0.3184 time to fit residues: 299.0539 Evaluate side-chains 662 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 606 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 446 GLU Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 280 ILE Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 381 GLN Chi-restraints excluded: chain E residue 404 LEU Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 564 ASP Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 192 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 161 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 127 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 HIS ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 HIS H 190 ASN H 302 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.5098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17259 Z= 0.175 Angle : 0.596 12.647 23366 Z= 0.310 Chirality : 0.044 0.246 2603 Planarity : 0.004 0.055 2976 Dihedral : 5.594 98.411 2856 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.11 % Allowed : 23.47 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1978 helix: 1.56 (0.32), residues: 286 sheet: 0.49 (0.22), residues: 563 loop : -0.42 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 289 HIS 0.008 0.001 HIS H 189 PHE 0.036 0.002 PHE E 55 TYR 0.018 0.001 TYR H 553 ARG 0.015 0.001 ARG D 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3956 Ramachandran restraints generated. 1978 Oldfield, 0 Emsley, 1978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 600 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 MET cc_start: 0.7299 (mmm) cc_final: 0.6969 (mmm) REVERT: A 121 ILE cc_start: 0.7981 (tt) cc_final: 0.7359 (pt) REVERT: A 153 ILE cc_start: 0.8154 (mt) cc_final: 0.7681 (tp) REVERT: A 154 GLU cc_start: 0.7061 (mt-10) cc_final: 0.6844 (mt-10) REVERT: A 156 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6630 (mm-30) REVERT: A 293 ASP cc_start: 0.6596 (p0) cc_final: 0.6358 (t0) REVERT: A 330 LEU cc_start: 0.8051 (tp) cc_final: 0.7663 (tp) REVERT: A 363 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7677 (ttp-110) REVERT: A 375 VAL cc_start: 0.8115 (t) cc_final: 0.7749 (p) REVERT: A 383 ASP cc_start: 0.7338 (p0) cc_final: 0.6984 (p0) REVERT: A 428 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6426 (mt-10) REVERT: A 438 VAL cc_start: 0.8348 (t) cc_final: 0.7929 (p) REVERT: A 493 ASN cc_start: 0.7928 (OUTLIER) cc_final: 0.7584 (m-40) REVERT: A 527 PHE cc_start: 0.7696 (p90) cc_final: 0.7071 (p90) REVERT: A 530 SER cc_start: 0.8279 (t) cc_final: 0.7819 (p) REVERT: A 583 LYS cc_start: 0.7757 (tptt) cc_final: 0.7515 (tptt) REVERT: A 585 ASP cc_start: 0.6651 (t70) cc_final: 0.6331 (t70) REVERT: D 45 GLU cc_start: 0.7862 (tt0) cc_final: 0.7318 (tt0) REVERT: D 96 LEU cc_start: 0.8158 (mt) cc_final: 0.7809 (mp) REVERT: D 101 MET cc_start: 0.7079 (mmm) cc_final: 0.6859 (mmm) REVERT: D 131 GLU cc_start: 0.6043 (mt-10) cc_final: 0.5824 (mt-10) REVERT: D 135 GLN cc_start: 0.7094 (mm-40) cc_final: 0.6857 (mm-40) REVERT: D 141 ILE cc_start: 0.7813 (mt) cc_final: 0.7457 (mm) REVERT: D 142 SER cc_start: 0.8145 (t) cc_final: 0.7421 (p) REVERT: D 156 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6463 (mm-30) REVERT: D 215 GLN cc_start: 0.7589 (mt0) cc_final: 0.7334 (mt0) REVERT: D 252 ARG cc_start: 0.7437 (mtp180) cc_final: 0.7192 (ttp-170) REVERT: D 272 GLU cc_start: 0.5041 (mm-30) cc_final: 0.4788 (mm-30) REVERT: D 301 ASP cc_start: 0.7143 (p0) cc_final: 0.6374 (p0) REVERT: D 315 MET cc_start: 0.6446 (mmm) cc_final: 0.6202 (mmm) REVERT: D 330 LEU cc_start: 0.7699 (mt) cc_final: 0.7342 (mt) REVERT: D 339 ARG cc_start: 0.6927 (mmt-90) cc_final: 0.6718 (mmt-90) REVERT: D 362 VAL cc_start: 0.8089 (t) cc_final: 0.7835 (p) REVERT: D 389 LYS cc_start: 0.8062 (mttm) cc_final: 0.7724 (mttp) REVERT: D 404 LEU cc_start: 0.7840 (mp) cc_final: 0.7559 (mt) REVERT: D 405 PHE cc_start: 0.7656 (m-10) cc_final: 0.7373 (m-10) REVERT: D 428 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6356 (mt-10) REVERT: D 441 PHE cc_start: 0.8676 (t80) cc_final: 0.8212 (t80) REVERT: D 453 LYS cc_start: 0.7384 (pttt) cc_final: 0.6973 (pttt) REVERT: D 483 ARG cc_start: 0.7269 (ttt90) cc_final: 0.6878 (tpt170) REVERT: D 487 HIS cc_start: 0.7797 (p-80) cc_final: 0.7579 (p-80) REVERT: D 544 TRP cc_start: 0.8152 (m100) cc_final: 0.7684 (m100) REVERT: D 573 HIS cc_start: 0.7794 (m170) cc_final: 0.7432 (m90) REVERT: D 577 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7340 (mmtt) REVERT: E 74 ARG cc_start: 0.7319 (mtt-85) cc_final: 0.6967 (mtt-85) REVERT: E 100 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6990 (tm-30) REVERT: E 131 GLU cc_start: 0.7048 (mt-10) cc_final: 0.6493 (mt-10) REVERT: E 136 HIS cc_start: 0.6875 (m-70) cc_final: 0.6657 (m-70) REVERT: E 143 ILE cc_start: 0.8431 (mm) cc_final: 0.7945 (tp) REVERT: E 154 GLU cc_start: 0.6910 (mt-10) cc_final: 0.6667 (mt-10) REVERT: E 173 ASP cc_start: 0.7597 (m-30) cc_final: 0.7370 (t0) REVERT: E 209 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6810 (tt0) REVERT: E 224 SER cc_start: 0.7573 (m) cc_final: 0.7181 (p) REVERT: E 241 GLN cc_start: 0.8143 (pp30) cc_final: 0.7858 (pp30) REVERT: E 249 ASP cc_start: 0.6828 (m-30) cc_final: 0.6151 (m-30) REVERT: E 256 MET cc_start: 0.7263 (ttp) cc_final: 0.6632 (tpp) REVERT: E 267 ASP cc_start: 0.6997 (t0) cc_final: 0.6410 (t0) REVERT: E 299 GLU cc_start: 0.6618 (mt-10) cc_final: 0.6348 (mt-10) REVERT: E 315 MET cc_start: 0.7225 (mmm) cc_final: 0.6906 (tpp) REVERT: E 326 GLU cc_start: 0.6480 (mt-10) cc_final: 0.6062 (tt0) REVERT: E 340 LYS cc_start: 0.8213 (mttt) cc_final: 0.7986 (mttt) REVERT: E 350 MET cc_start: 0.7160 (mtm) cc_final: 0.6802 (ptm) REVERT: E 392 HIS cc_start: 0.8279 (m90) cc_final: 0.8010 (m-70) REVERT: E 409 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7749 (ttpp) REVERT: E 412 PRO cc_start: 0.8651 (Cg_endo) cc_final: 0.8352 (Cg_exo) REVERT: E 486 PHE cc_start: 0.8063 (t80) cc_final: 0.7655 (t80) REVERT: E 502 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6741 (mt-10) REVERT: E 518 ARG cc_start: 0.8212 (ttp-110) cc_final: 0.7857 (mtp-110) REVERT: E 521 MET cc_start: 0.7165 (mtp) cc_final: 0.6686 (mtp) REVERT: E 525 MET cc_start: 0.7321 (mmt) cc_final: 0.6912 (mmt) REVERT: E 530 SER cc_start: 0.8513 (t) cc_final: 0.8018 (p) REVERT: E 577 LYS cc_start: 0.8142 (mtpp) cc_final: 0.7811 (mtpp) REVERT: E 588 ILE cc_start: 0.8428 (mt) cc_final: 0.8014 (tp) REVERT: H 74 ARG cc_start: 0.7059 (mtt90) cc_final: 0.6683 (mtt-85) REVERT: H 76 THR cc_start: 0.7648 (m) cc_final: 0.7305 (p) REVERT: H 111 LYS cc_start: 0.7844 (pttt) cc_final: 0.7447 (pttt) REVERT: H 124 GLN cc_start: 0.7151 (tm-30) cc_final: 0.6929 (tm-30) REVERT: H 140 ASN cc_start: 0.7907 (OUTLIER) cc_final: 0.6958 (m-40) REVERT: H 154 GLU cc_start: 0.7015 (mt-10) cc_final: 0.6732 (mt-10) REVERT: H 200 THR cc_start: 0.5907 (OUTLIER) cc_final: 0.4338 (p) REVERT: H 212 MET cc_start: 0.6792 (mmm) cc_final: 0.6384 (mmm) REVERT: H 228 ILE cc_start: 0.8391 (mp) cc_final: 0.8131 (mp) REVERT: H 241 GLN cc_start: 0.7969 (pp30) cc_final: 0.7696 (pp30) REVERT: H 249 ASP cc_start: 0.6862 (m-30) cc_final: 0.6491 (m-30) REVERT: H 256 MET cc_start: 0.7433 (ttp) cc_final: 0.6969 (ttp) REVERT: H 273 LYS cc_start: 0.7548 (tttt) cc_final: 0.7347 (tptt) REVERT: H 275 ASN cc_start: 0.7475 (p0) cc_final: 0.7221 (p0) REVERT: H 293 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7147 (p0) REVERT: H 303 THR cc_start: 0.8346 (m) cc_final: 0.7634 (t) REVERT: H 314 PHE cc_start: 0.8563 (p90) cc_final: 0.8241 (p90) REVERT: H 315 MET cc_start: 0.7257 (mmm) cc_final: 0.6937 (mmm) REVERT: H 330 LEU cc_start: 0.8207 (tp) cc_final: 0.7896 (tt) REVERT: H 362 VAL cc_start: 0.8397 (t) cc_final: 0.8085 (p) REVERT: H 364 ARG cc_start: 0.7793 (ptp-170) cc_final: 0.6718 (ptm160) REVERT: H 365 ASP cc_start: 0.6618 (t0) cc_final: 0.6357 (t0) REVERT: H 373 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7395 (ttpp) REVERT: H 397 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6099 (mm-30) REVERT: H 404 LEU cc_start: 0.8464 (mp) cc_final: 0.8157 (mt) REVERT: H 455 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: H 467 PHE cc_start: 0.8145 (p90) cc_final: 0.7918 (p90) REVERT: H 502 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6904 (mm-30) REVERT: H 521 MET cc_start: 0.7546 (mtp) cc_final: 0.6877 (mtp) REVERT: H 522 SER cc_start: 0.8567 (p) cc_final: 0.8337 (p) REVERT: H 543 ILE cc_start: 0.7892 (mt) cc_final: 0.7602 (mt) outliers start: 56 outliers final: 45 residues processed: 622 average time/residue: 0.3223 time to fit residues: 288.1970 Evaluate side-chains 644 residues out of total 1820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 592 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 PHE Chi-restraints excluded: chain A residue 104 LEU Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 128 CYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 HIS Chi-restraints excluded: chain A residue 269 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 LYS Chi-restraints excluded: chain A residue 456 SER Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 VAL Chi-restraints excluded: chain A residue 572 SER Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain D residue 189 HIS Chi-restraints excluded: chain D residue 340 LYS Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 422 ASP Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 519 ASN Chi-restraints excluded: chain E residue 100 GLU Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 171 ASP Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 287 THR Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 425 THR Chi-restraints excluded: chain E residue 463 GLU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 501 VAL Chi-restraints excluded: chain E residue 524 SER Chi-restraints excluded: chain E residue 526 VAL Chi-restraints excluded: chain E residue 542 VAL Chi-restraints excluded: chain E residue 571 ILE Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain H residue 140 ASN Chi-restraints excluded: chain H residue 200 THR Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 293 ASP Chi-restraints excluded: chain H residue 375 VAL Chi-restraints excluded: chain H residue 395 LEU Chi-restraints excluded: chain H residue 455 GLN Chi-restraints excluded: chain H residue 502 GLU Chi-restraints excluded: chain H residue 572 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 203 random chunks: chunk 171 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 148 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 HIS ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 381 GLN E 487 HIS H 189 HIS H 190 ASN H 302 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.138247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.120513 restraints weight = 26310.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124914 restraints weight = 13273.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127818 restraints weight = 8114.312| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17259 Z= 0.300 Angle : 0.639 10.804 23366 Z= 0.337 Chirality : 0.046 0.250 2603 Planarity : 0.004 0.050 2976 Dihedral : 5.808 96.531 2856 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.66 % Allowed : 23.42 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.90 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.19), residues: 1978 helix: 1.35 (0.31), residues: 286 sheet: 0.35 (0.21), residues: 590 loop : -0.57 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 75 HIS 0.008 0.001 HIS H 189 PHE 0.039 0.002 PHE E 55 TYR 0.019 0.002 TYR D 553 ARG 0.016 0.001 ARG D 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5061.91 seconds wall clock time: 91 minutes 20.46 seconds (5480.46 seconds total)