Starting phenix.real_space_refine on Tue Feb 20 23:27:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i8e_35249/02_2024/8i8e_35249_updated.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.096 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 120 5.16 5 C 18564 2.51 5 N 4782 2.21 5 O 5580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "f GLU 41": "OE1" <-> "OE2" Residue "f GLU 48": "OE1" <-> "OE2" Residue "f GLU 49": "OE1" <-> "OE2" Residue "f ASP 51": "OD1" <-> "OD2" Residue "f GLU 57": "OE1" <-> "OE2" Residue "D ASP 7": "OD1" <-> "OD2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "D GLU 365": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D ASP 429": "OD1" <-> "OD2" Residue "D GLU 442": "OE1" <-> "OE2" Residue "D PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 7": "OD1" <-> "OD2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 418": "OE1" <-> "OE2" Residue "A ASP 429": "OD1" <-> "OD2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 7": "OD1" <-> "OD2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "F GLU 365": "OE1" <-> "OE2" Residue "F GLU 375": "OE1" <-> "OE2" Residue "F GLU 418": "OE1" <-> "OE2" Residue "F ASP 429": "OD1" <-> "OD2" Residue "F GLU 442": "OE1" <-> "OE2" Residue "F PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 7": "OD1" <-> "OD2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B ASP 429": "OD1" <-> "OD2" Residue "B GLU 442": "OE1" <-> "OE2" Residue "B PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 7": "OD1" <-> "OD2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 418": "OE1" <-> "OE2" Residue "C ASP 429": "OD1" <-> "OD2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 7": "OD1" <-> "OD2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "E GLU 365": "OE1" <-> "OE2" Residue "E GLU 375": "OE1" <-> "OE2" Residue "E GLU 418": "OE1" <-> "OE2" Residue "E ASP 429": "OD1" <-> "OD2" Residue "E GLU 442": "OE1" <-> "OE2" Residue "E PHE 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 41": "OE1" <-> "OE2" Residue "a GLU 48": "OE1" <-> "OE2" Residue "a GLU 49": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a GLU 57": "OE1" <-> "OE2" Residue "b GLU 41": "OE1" <-> "OE2" Residue "b GLU 48": "OE1" <-> "OE2" Residue "b GLU 49": "OE1" <-> "OE2" Residue "b ASP 51": "OD1" <-> "OD2" Residue "b GLU 57": "OE1" <-> "OE2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c GLU 48": "OE1" <-> "OE2" Residue "c GLU 49": "OE1" <-> "OE2" Residue "c ASP 51": "OD1" <-> "OD2" Residue "c GLU 57": "OE1" <-> "OE2" Residue "d GLU 41": "OE1" <-> "OE2" Residue "d GLU 48": "OE1" <-> "OE2" Residue "d GLU 49": "OE1" <-> "OE2" Residue "d ASP 51": "OD1" <-> "OD2" Residue "d GLU 57": "OE1" <-> "OE2" Residue "e GLU 41": "OE1" <-> "OE2" Residue "e GLU 48": "OE1" <-> "OE2" Residue "e GLU 49": "OE1" <-> "OE2" Residue "e ASP 51": "OD1" <-> "OD2" Residue "e GLU 57": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29058 Number of models: 1 Model: "" Number of chains: 24 Chain: "f" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "D" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 4220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4220 Classifications: {'peptide': 530} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 506} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "a" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "b" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "c" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "d" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "e" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 560 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 1, 'TRANS': 70} Chain: "f" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'OLA': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OLA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "b" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "c" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "d" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "e" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Time building chain proxies: 14.61, per 1000 atoms: 0.50 Number of scatterers: 29058 At special positions: 0 Unit cell: (189.618, 171.366, 92.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 12 15.00 O 5580 8.00 N 4782 7.00 C 18564 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 4.6 seconds 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 42 sheets defined 34.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.67 Creating SS restraints... Processing helix chain 'f' and resid 3 through 14 removed outlier: 3.634A pdb=" N LYS f 8 " --> pdb=" O GLU f 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS f 9 " --> pdb=" O GLU f 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE f 11 " --> pdb=" O VAL f 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY f 12 " --> pdb=" O LYS f 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN f 14 " --> pdb=" O ILE f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 30 through 32 No H-bonds generated for 'chain 'f' and resid 30 through 32' Processing helix chain 'f' and resid 36 through 50 removed outlier: 3.767A pdb=" N GLU f 47 " --> pdb=" O VAL f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 66 through 71 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 41 through 58 Processing helix chain 'D' and resid 74 through 86 removed outlier: 3.648A pdb=" N PHE D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE D 83 " --> pdb=" O CYS D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.517A pdb=" N LEU D 121 " --> pdb=" O GLU D 118 " (cutoff:3.500A) Proline residue: D 122 - end of helix removed outlier: 3.568A pdb=" N GLN D 126 " --> pdb=" O ILE D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 154 removed outlier: 3.762A pdb=" N GLN D 154 " --> pdb=" O ARG D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 229 through 239 Proline residue: D 233 - end of helix Processing helix chain 'D' and resid 251 through 261 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 280 through 282 No H-bonds generated for 'chain 'D' and resid 280 through 282' Processing helix chain 'D' and resid 301 through 309 Processing helix chain 'D' and resid 321 through 323 No H-bonds generated for 'chain 'D' and resid 321 through 323' Processing helix chain 'D' and resid 336 through 338 No H-bonds generated for 'chain 'D' and resid 336 through 338' Processing helix chain 'D' and resid 341 through 348 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 441 through 448 Processing helix chain 'D' and resid 484 through 492 Processing helix chain 'D' and resid 525 through 532 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 41 through 58 Processing helix chain 'A' and resid 74 through 86 removed outlier: 3.648A pdb=" N PHE A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 118 through 126 removed outlier: 3.517A pdb=" N LEU A 121 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Proline residue: A 122 - end of helix removed outlier: 3.568A pdb=" N GLN A 126 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 154 removed outlier: 3.762A pdb=" N GLN A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 229 through 239 Proline residue: A 233 - end of helix Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 321 through 323 No H-bonds generated for 'chain 'A' and resid 321 through 323' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 341 through 348 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 441 through 448 Processing helix chain 'A' and resid 484 through 492 Processing helix chain 'A' and resid 525 through 532 Processing helix chain 'F' and resid 15 through 20 Processing helix chain 'F' and resid 41 through 58 Processing helix chain 'F' and resid 74 through 86 removed outlier: 3.648A pdb=" N PHE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 83 " --> pdb=" O CYS F 79 " (cutoff:3.500A) Proline residue: F 84 - end of helix Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 118 through 126 removed outlier: 3.517A pdb=" N LEU F 121 " --> pdb=" O GLU F 118 " (cutoff:3.500A) Proline residue: F 122 - end of helix removed outlier: 3.568A pdb=" N GLN F 126 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 removed outlier: 3.763A pdb=" N GLN F 154 " --> pdb=" O ARG F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 204 Processing helix chain 'F' and resid 229 through 239 Proline residue: F 233 - end of helix Processing helix chain 'F' and resid 251 through 261 Processing helix chain 'F' and resid 270 through 278 Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 301 through 309 Processing helix chain 'F' and resid 321 through 323 No H-bonds generated for 'chain 'F' and resid 321 through 323' Processing helix chain 'F' and resid 336 through 338 No H-bonds generated for 'chain 'F' and resid 336 through 338' Processing helix chain 'F' and resid 341 through 348 Processing helix chain 'F' and resid 396 through 401 Processing helix chain 'F' and resid 403 through 405 No H-bonds generated for 'chain 'F' and resid 403 through 405' Processing helix chain 'F' and resid 441 through 448 Processing helix chain 'F' and resid 484 through 492 Processing helix chain 'F' and resid 525 through 532 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 41 through 58 Processing helix chain 'B' and resid 74 through 86 removed outlier: 3.648A pdb=" N PHE B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE B 83 " --> pdb=" O CYS B 79 " (cutoff:3.500A) Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 118 through 126 removed outlier: 3.517A pdb=" N LEU B 121 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Proline residue: B 122 - end of helix removed outlier: 3.568A pdb=" N GLN B 126 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 154 removed outlier: 3.763A pdb=" N GLN B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 229 through 239 Proline residue: B 233 - end of helix Processing helix chain 'B' and resid 251 through 261 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'B' and resid 341 through 348 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 41 through 58 Processing helix chain 'C' and resid 74 through 86 removed outlier: 3.648A pdb=" N PHE C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE C 83 " --> pdb=" O CYS C 79 " (cutoff:3.500A) Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 118 through 126 removed outlier: 3.517A pdb=" N LEU C 121 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Proline residue: C 122 - end of helix removed outlier: 3.568A pdb=" N GLN C 126 " --> pdb=" O ILE C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 154 removed outlier: 3.762A pdb=" N GLN C 154 " --> pdb=" O ARG C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 229 through 239 Proline residue: C 233 - end of helix Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 321 through 323 No H-bonds generated for 'chain 'C' and resid 321 through 323' Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 341 through 348 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 441 through 448 Processing helix chain 'C' and resid 484 through 492 Processing helix chain 'C' and resid 525 through 532 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 41 through 58 Processing helix chain 'E' and resid 74 through 86 removed outlier: 3.647A pdb=" N PHE E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 83 " --> pdb=" O CYS E 79 " (cutoff:3.500A) Proline residue: E 84 - end of helix Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.517A pdb=" N LEU E 121 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Proline residue: E 122 - end of helix removed outlier: 3.568A pdb=" N GLN E 126 " --> pdb=" O ILE E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 154 removed outlier: 3.763A pdb=" N GLN E 154 " --> pdb=" O ARG E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 204 Processing helix chain 'E' and resid 229 through 239 Proline residue: E 233 - end of helix Processing helix chain 'E' and resid 251 through 261 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 309 Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 441 through 448 Processing helix chain 'E' and resid 484 through 492 Processing helix chain 'E' and resid 525 through 532 Processing helix chain 'a' and resid 3 through 14 removed outlier: 3.634A pdb=" N LYS a 8 " --> pdb=" O GLU a 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS a 9 " --> pdb=" O GLU a 5 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE a 11 " --> pdb=" O VAL a 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN a 14 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 30 through 32 No H-bonds generated for 'chain 'a' and resid 30 through 32' Processing helix chain 'a' and resid 36 through 50 removed outlier: 3.767A pdb=" N GLU a 47 " --> pdb=" O VAL a 43 " (cutoff:3.500A) Processing helix chain 'a' and resid 66 through 71 Processing helix chain 'b' and resid 3 through 14 removed outlier: 3.634A pdb=" N LYS b 8 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE b 11 " --> pdb=" O VAL b 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY b 12 " --> pdb=" O LYS b 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN b 14 " --> pdb=" O ILE b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 32 No H-bonds generated for 'chain 'b' and resid 30 through 32' Processing helix chain 'b' and resid 36 through 50 removed outlier: 3.766A pdb=" N GLU b 47 " --> pdb=" O VAL b 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 71 Processing helix chain 'c' and resid 3 through 14 removed outlier: 3.634A pdb=" N LYS c 8 " --> pdb=" O GLU c 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS c 9 " --> pdb=" O GLU c 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE c 11 " --> pdb=" O VAL c 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY c 12 " --> pdb=" O LYS c 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN c 14 " --> pdb=" O ILE c 10 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 36 through 50 removed outlier: 3.766A pdb=" N GLU c 47 " --> pdb=" O VAL c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 66 through 71 Processing helix chain 'd' and resid 3 through 14 removed outlier: 3.634A pdb=" N LYS d 8 " --> pdb=" O GLU d 4 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS d 9 " --> pdb=" O GLU d 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE d 11 " --> pdb=" O VAL d 7 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN d 14 " --> pdb=" O ILE d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 32 No H-bonds generated for 'chain 'd' and resid 30 through 32' Processing helix chain 'd' and resid 36 through 50 removed outlier: 3.767A pdb=" N GLU d 47 " --> pdb=" O VAL d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 71 Processing helix chain 'e' and resid 3 through 14 removed outlier: 3.634A pdb=" N LYS e 8 " --> pdb=" O GLU e 4 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS e 9 " --> pdb=" O GLU e 5 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE e 11 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY e 12 " --> pdb=" O LYS e 8 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN e 14 " --> pdb=" O ILE e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 32 No H-bonds generated for 'chain 'e' and resid 30 through 32' Processing helix chain 'e' and resid 36 through 50 removed outlier: 3.767A pdb=" N GLU e 47 " --> pdb=" O VAL e 43 " (cutoff:3.500A) Processing helix chain 'e' and resid 66 through 71 Processing sheet with id= A, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.495A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS D 291 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS D 268 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL D 293 " --> pdb=" O CYS D 268 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE D 113 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS D 89 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL D 68 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS D 91 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR D 174 " --> pdb=" O LYS D 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS D 183 " --> pdb=" O TYR D 174 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 359 through 363 Processing sheet with id= D, first strand: chain 'D' and resid 431 through 433 Processing sheet with id= E, first strand: chain 'D' and resid 456 through 461 Processing sheet with id= F, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= G, first strand: chain 'D' and resid 411 through 415 removed outlier: 3.506A pdb=" N ASP D 425 " --> pdb=" O VAL D 412 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.495A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS A 291 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS A 268 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL A 293 " --> pdb=" O CYS A 268 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE A 113 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 89 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL A 68 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS A 91 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR A 174 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS A 183 " --> pdb=" O TYR A 174 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 359 through 363 Processing sheet with id= K, first strand: chain 'A' and resid 431 through 433 Processing sheet with id= L, first strand: chain 'A' and resid 456 through 461 Processing sheet with id= M, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= N, first strand: chain 'A' and resid 411 through 415 removed outlier: 3.505A pdb=" N ASP A 425 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 37 through 40 removed outlier: 6.496A pdb=" N GLN F 243 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE F 265 " --> pdb=" O MET F 219 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS F 291 " --> pdb=" O SER F 266 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N CYS F 268 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL F 293 " --> pdb=" O CYS F 268 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE F 113 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS F 89 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL F 68 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS F 91 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR F 174 " --> pdb=" O MET F 92 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE F 187 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR F 172 " --> pdb=" O VAL F 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL F 185 " --> pdb=" O THR F 172 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR F 174 " --> pdb=" O LYS F 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS F 183 " --> pdb=" O TYR F 174 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 359 through 363 Processing sheet with id= R, first strand: chain 'F' and resid 431 through 433 Processing sheet with id= S, first strand: chain 'F' and resid 456 through 461 Processing sheet with id= T, first strand: chain 'F' and resid 317 through 319 Processing sheet with id= U, first strand: chain 'F' and resid 411 through 415 removed outlier: 3.505A pdb=" N ASP F 425 " --> pdb=" O VAL F 412 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS F 414 " --> pdb=" O ILE F 423 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE F 423 " --> pdb=" O HIS F 414 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.495A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS B 291 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS B 268 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 293 " --> pdb=" O CYS B 268 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 136 through 140 removed outlier: 3.577A pdb=" N ILE B 113 " --> pdb=" O THR B 65 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LYS B 89 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL B 68 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N HIS B 91 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR B 174 " --> pdb=" O LYS B 183 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LYS B 183 " --> pdb=" O TYR B 174 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 359 through 363 Processing sheet with id= Y, first strand: chain 'B' and resid 431 through 433 Processing sheet with id= Z, first strand: chain 'B' and resid 456 through 461 Processing sheet with id= AA, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= AB, first strand: chain 'B' and resid 411 through 415 removed outlier: 3.506A pdb=" N ASP B 425 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.495A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LYS C 291 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N CYS C 268 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL C 293 " --> pdb=" O CYS C 268 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.576A pdb=" N ILE C 113 " --> pdb=" O THR C 65 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS C 89 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL C 68 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS C 91 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR C 174 " --> pdb=" O LYS C 183 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LYS C 183 " --> pdb=" O TYR C 174 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 359 through 363 Processing sheet with id= AF, first strand: chain 'C' and resid 431 through 433 Processing sheet with id= AG, first strand: chain 'C' and resid 456 through 461 Processing sheet with id= AH, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= AI, first strand: chain 'C' and resid 411 through 415 removed outlier: 3.506A pdb=" N ASP C 425 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'E' and resid 37 through 40 removed outlier: 6.495A pdb=" N GLN E 243 " --> pdb=" O VAL E 32 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N PHE E 265 " --> pdb=" O MET E 219 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N LYS E 291 " --> pdb=" O SER E 266 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N CYS E 268 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL E 293 " --> pdb=" O CYS E 268 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.576A pdb=" N ILE E 113 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS E 89 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N VAL E 68 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N HIS E 91 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR E 174 " --> pdb=" O MET E 92 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N PHE E 187 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N THR E 172 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 185 " --> pdb=" O THR E 172 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N TYR E 174 " --> pdb=" O LYS E 183 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LYS E 183 " --> pdb=" O TYR E 174 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'E' and resid 359 through 363 Processing sheet with id= AM, first strand: chain 'E' and resid 431 through 433 Processing sheet with id= AN, first strand: chain 'E' and resid 456 through 461 Processing sheet with id= AO, first strand: chain 'E' and resid 317 through 319 Processing sheet with id= AP, first strand: chain 'E' and resid 411 through 415 removed outlier: 3.506A pdb=" N ASP E 425 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS E 414 " --> pdb=" O ILE E 423 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ILE E 423 " --> pdb=" O HIS E 414 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2232 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: 9.57 Time building geometry restraints manager: 12.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4992 1.31 - 1.44: 7392 1.44 - 1.56: 17028 1.56 - 1.69: 18 1.69 - 1.82: 216 Bond restraints: 29646 Sorted by residual: bond pdb=" C2' AMP A 701 " pdb=" C3' AMP A 701 " ideal model delta sigma weight residual 1.523 1.344 0.179 1.50e-02 4.44e+03 1.43e+02 bond pdb=" C2' AMP F 701 " pdb=" C3' AMP F 701 " ideal model delta sigma weight residual 1.523 1.344 0.179 1.50e-02 4.44e+03 1.43e+02 bond pdb=" C2' AMP B 701 " pdb=" C3' AMP B 701 " ideal model delta sigma weight residual 1.523 1.344 0.179 1.50e-02 4.44e+03 1.42e+02 bond pdb=" C2' AMP C 701 " pdb=" C3' AMP C 701 " ideal model delta sigma weight residual 1.523 1.344 0.179 1.50e-02 4.44e+03 1.42e+02 bond pdb=" C2' AMP D 701 " pdb=" C3' AMP D 701 " ideal model delta sigma weight residual 1.523 1.345 0.178 1.50e-02 4.44e+03 1.41e+02 ... (remaining 29641 not shown) Histogram of bond angle deviations from ideal: 99.19 - 106.22: 747 106.22 - 113.26: 16437 113.26 - 120.29: 10767 120.29 - 127.33: 11908 127.33 - 134.36: 317 Bond angle restraints: 40176 Sorted by residual: angle pdb=" N GLN F 260 " pdb=" CA GLN F 260 " pdb=" C GLN F 260 " ideal model delta sigma weight residual 111.36 116.88 -5.52 1.09e+00 8.42e-01 2.56e+01 angle pdb=" N GLN A 260 " pdb=" CA GLN A 260 " pdb=" C GLN A 260 " ideal model delta sigma weight residual 111.36 116.86 -5.50 1.09e+00 8.42e-01 2.55e+01 angle pdb=" N GLN E 260 " pdb=" CA GLN E 260 " pdb=" C GLN E 260 " ideal model delta sigma weight residual 111.36 116.83 -5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N GLN D 260 " pdb=" CA GLN D 260 " pdb=" C GLN D 260 " ideal model delta sigma weight residual 111.36 116.83 -5.47 1.09e+00 8.42e-01 2.52e+01 angle pdb=" N GLN C 260 " pdb=" CA GLN C 260 " pdb=" C GLN C 260 " ideal model delta sigma weight residual 111.36 116.83 -5.47 1.09e+00 8.42e-01 2.52e+01 ... (remaining 40171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 15295 17.59 - 35.18: 1781 35.18 - 52.76: 591 52.76 - 70.35: 110 70.35 - 87.94: 43 Dihedral angle restraints: 17820 sinusoidal: 7290 harmonic: 10530 Sorted by residual: dihedral pdb=" C5' AMP A 701 " pdb=" O5' AMP A 701 " pdb=" P AMP A 701 " pdb=" O3P AMP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 11.97 -71.96 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" C5' AMP E 701 " pdb=" O5' AMP E 701 " pdb=" P AMP E 701 " pdb=" O3P AMP E 701 " ideal model delta sinusoidal sigma weight residual -60.00 11.92 -71.92 1 2.00e+01 2.50e-03 1.66e+01 dihedral pdb=" C5' AMP C 701 " pdb=" O5' AMP C 701 " pdb=" P AMP C 701 " pdb=" O3P AMP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 11.89 -71.89 1 2.00e+01 2.50e-03 1.65e+01 ... (remaining 17817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3850 0.067 - 0.133: 670 0.133 - 0.200: 46 0.200 - 0.267: 0 0.267 - 0.333: 6 Chirality restraints: 4572 Sorted by residual: chirality pdb=" C2' AMP F 701 " pdb=" C1' AMP F 701 " pdb=" C3' AMP F 701 " pdb=" O2' AMP F 701 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C2' AMP A 701 " pdb=" C1' AMP A 701 " pdb=" C3' AMP A 701 " pdb=" O2' AMP A 701 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" C2' AMP C 701 " pdb=" C1' AMP C 701 " pdb=" C3' AMP C 701 " pdb=" O2' AMP C 701 " both_signs ideal model delta sigma weight residual False -2.75 -2.42 -0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 4569 not shown) Planarity restraints: 5106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 333 " -0.055 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO E 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 334 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 334 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 333 " -0.055 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO C 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 334 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 334 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 333 " -0.055 5.00e-02 4.00e+02 8.16e-02 1.06e+01 pdb=" N PRO A 334 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 334 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 334 " -0.045 5.00e-02 4.00e+02 ... (remaining 5103 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3339 2.75 - 3.29: 27597 3.29 - 3.82: 48953 3.82 - 4.36: 61743 4.36 - 4.90: 101007 Nonbonded interactions: 242639 Sorted by model distance: nonbonded pdb=" O TYR B 41 " pdb=" ND1 HIS B 45 " model vdw 2.212 2.520 nonbonded pdb=" O TYR E 41 " pdb=" ND1 HIS E 45 " model vdw 2.213 2.520 nonbonded pdb=" O TYR D 41 " pdb=" ND1 HIS D 45 " model vdw 2.213 2.520 nonbonded pdb=" O TYR A 41 " pdb=" ND1 HIS A 45 " model vdw 2.213 2.520 nonbonded pdb=" O TYR C 41 " pdb=" ND1 HIS C 45 " model vdw 2.213 2.520 ... (remaining 242634 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 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: 0.040 Extract box with map and model: 8.600 Check model and map are aligned: 0.450 Set scattering table: 0.290 Process input model: 73.360 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 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 : 0.007 0.179 29646 Z= 0.454 Angle : 0.728 11.182 40176 Z= 0.397 Chirality : 0.049 0.333 4572 Planarity : 0.006 0.082 5106 Dihedral : 17.466 87.941 11028 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.19 % Favored : 91.64 % Rotamer: Outliers : 0.76 % Allowed : 21.76 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.93 (0.14), residues: 3588 helix: 0.69 (0.15), residues: 1212 sheet: 0.18 (0.20), residues: 624 loop : -1.94 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 230 HIS 0.007 0.001 HIS F 228 PHE 0.013 0.002 PHE b 28 TYR 0.013 0.001 TYR A 245 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 276 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 MET cc_start: 0.8710 (mtp) cc_final: 0.8362 (mtp) REVERT: D 96 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7728 (mpt-90) REVERT: D 256 ASN cc_start: 0.8089 (t0) cc_final: 0.7740 (t0) REVERT: A 252 ASP cc_start: 0.7243 (m-30) cc_final: 0.7040 (m-30) REVERT: F 69 MET cc_start: 0.8723 (mtp) cc_final: 0.8191 (mtp) REVERT: F 96 ARG cc_start: 0.8080 (mmt90) cc_final: 0.7848 (mpt-90) REVERT: F 145 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7341 (tt0) REVERT: F 320 MET cc_start: 0.8919 (ptp) cc_final: 0.8661 (ptm) REVERT: F 331 GLN cc_start: 0.7873 (mm110) cc_final: 0.7579 (mm110) REVERT: F 461 MET cc_start: 0.1849 (OUTLIER) cc_final: 0.1361 (mpp) REVERT: C 7 ASP cc_start: 0.7063 (t0) cc_final: 0.6846 (t0) REVERT: C 69 MET cc_start: 0.8759 (mtp) cc_final: 0.8260 (mtp) REVERT: C 96 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7791 (mpt-90) REVERT: C 125 ASP cc_start: 0.7439 (m-30) cc_final: 0.7160 (m-30) REVERT: C 145 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7260 (tt0) REVERT: C 320 MET cc_start: 0.8934 (ptp) cc_final: 0.8561 (ptp) REVERT: C 331 GLN cc_start: 0.7821 (mm110) cc_final: 0.7531 (mm110) REVERT: E 69 MET cc_start: 0.8689 (mtp) cc_final: 0.8348 (mtp) REVERT: E 256 ASN cc_start: 0.8140 (t0) cc_final: 0.7793 (t0) REVERT: E 396 LYS cc_start: 0.8517 (mttp) cc_final: 0.8285 (mttm) outliers start: 24 outliers final: 10 residues processed: 294 average time/residue: 1.5330 time to fit residues: 522.9086 Evaluate side-chains 246 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 235 time to evaluate : 2.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 461 MET Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain b residue 69 ILE Chi-restraints excluded: chain c residue 69 ILE Chi-restraints excluded: chain d residue 69 ILE Chi-restraints excluded: chain e residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.9980 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 20.0000 chunk 171 optimal weight: 5.9990 chunk 210 optimal weight: 0.7980 chunk 326 optimal weight: 30.0000 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 19 GLN f 24 ASN D 154 GLN A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN E 226 HIS a 19 GLN a 24 ASN b 19 GLN ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 19 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 GLN ** e 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29646 Z= 0.196 Angle : 0.561 7.594 40176 Z= 0.290 Chirality : 0.045 0.170 4572 Planarity : 0.004 0.051 5106 Dihedral : 8.319 57.160 4079 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.25 % Favored : 92.59 % Rotamer: Outliers : 3.21 % Allowed : 20.10 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.99 (0.14), residues: 3588 helix: 0.46 (0.15), residues: 1290 sheet: -0.02 (0.21), residues: 606 loop : -1.82 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 437 HIS 0.007 0.001 HIS E 228 PHE 0.015 0.001 PHE D 225 TYR 0.013 0.001 TYR E 245 ARG 0.003 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 242 time to evaluate : 3.044 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: f 58 GLU cc_start: 0.1376 (OUTLIER) cc_final: 0.0694 (tt0) REVERT: D 69 MET cc_start: 0.8749 (mtp) cc_final: 0.8454 (mtp) REVERT: D 96 ARG cc_start: 0.7982 (mmt90) cc_final: 0.7771 (mpt-90) REVERT: D 238 MET cc_start: 0.9160 (tpt) cc_final: 0.8835 (tpt) REVERT: D 252 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: D 256 ASN cc_start: 0.8061 (t0) cc_final: 0.7726 (t0) REVERT: A 119 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 152 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8413 (tp) REVERT: A 283 LYS cc_start: 0.8374 (mptt) cc_final: 0.8163 (mmtt) REVERT: F 96 ARG cc_start: 0.8068 (mmt90) cc_final: 0.7789 (mpt-90) REVERT: F 145 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7453 (tt0) REVERT: F 320 MET cc_start: 0.8782 (ptp) cc_final: 0.8485 (ptm) REVERT: F 513 ASP cc_start: 0.3472 (OUTLIER) cc_final: 0.2617 (p0) REVERT: B 152 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8414 (tp) REVERT: B 224 MET cc_start: 0.8581 (ttt) cc_final: 0.8225 (ttt) REVERT: B 461 MET cc_start: 0.1192 (mmm) cc_final: 0.0817 (mtt) REVERT: C 7 ASP cc_start: 0.6931 (t0) cc_final: 0.6726 (t0) REVERT: C 69 MET cc_start: 0.8816 (mtp) cc_final: 0.8439 (mtp) REVERT: C 96 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7764 (mpt-90) REVERT: C 125 ASP cc_start: 0.7367 (m-30) cc_final: 0.7044 (m-30) REVERT: C 145 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7325 (tt0) REVERT: C 226 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.7051 (m170) REVERT: C 320 MET cc_start: 0.8778 (ptp) cc_final: 0.8476 (ptm) REVERT: E 226 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.7077 (m170) REVERT: E 238 MET cc_start: 0.9167 (tpt) cc_final: 0.8841 (tpt) REVERT: E 252 ASP cc_start: 0.7046 (OUTLIER) cc_final: 0.6711 (m-30) REVERT: E 256 ASN cc_start: 0.8158 (t0) cc_final: 0.7832 (t0) REVERT: E 311 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.6976 (t70) REVERT: a 48 GLU cc_start: 0.2501 (OUTLIER) cc_final: 0.1925 (pp20) outliers start: 101 outliers final: 39 residues processed: 326 average time/residue: 1.5689 time to fit residues: 589.9710 Evaluate side-chains 285 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 235 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain F residue 513 ASP Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 226 HIS Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 48 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 327 optimal weight: 0.0060 chunk 353 optimal weight: 40.0000 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 chunk 262 optimal weight: 10.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29646 Z= 0.153 Angle : 0.529 7.363 40176 Z= 0.271 Chirality : 0.044 0.157 4572 Planarity : 0.004 0.046 5106 Dihedral : 7.891 59.251 4062 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.11 % Favored : 92.67 % Rotamer: Outliers : 3.72 % Allowed : 19.82 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.85 (0.14), residues: 3588 helix: 0.55 (0.15), residues: 1290 sheet: -0.06 (0.22), residues: 534 loop : -1.60 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 437 HIS 0.014 0.001 HIS E 226 PHE 0.012 0.001 PHE D 225 TYR 0.009 0.001 TYR E 245 ARG 0.007 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 244 time to evaluate : 3.282 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: f 5 GLU cc_start: 0.5196 (mm-30) cc_final: 0.3903 (mt-10) REVERT: f 58 GLU cc_start: 0.1327 (OUTLIER) cc_final: 0.0646 (tt0) REVERT: D 69 MET cc_start: 0.8749 (mtp) cc_final: 0.8479 (mtp) REVERT: D 96 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7760 (mpt-90) REVERT: D 226 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6997 (m170) REVERT: D 232 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8619 (mm) REVERT: D 238 MET cc_start: 0.9139 (tpt) cc_final: 0.8892 (tpt) REVERT: D 252 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6779 (m-30) REVERT: D 256 ASN cc_start: 0.8063 (t0) cc_final: 0.7751 (t0) REVERT: D 461 MET cc_start: 0.0899 (mtt) cc_final: 0.0373 (mmm) REVERT: A 119 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7989 (mt-10) REVERT: A 125 ASP cc_start: 0.7264 (m-30) cc_final: 0.7051 (m-30) REVERT: F 69 MET cc_start: 0.8793 (mtp) cc_final: 0.8419 (mtp) REVERT: F 96 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7802 (mpt-90) REVERT: F 145 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7392 (tt0) REVERT: F 320 MET cc_start: 0.8763 (ptp) cc_final: 0.8502 (ptm) REVERT: F 331 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.7085 (mt0) REVERT: B 62 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.8137 (tmmt) REVERT: B 224 MET cc_start: 0.8490 (ttt) cc_final: 0.8133 (ttt) REVERT: B 461 MET cc_start: 0.1097 (mmm) cc_final: 0.0724 (mtt) REVERT: C 7 ASP cc_start: 0.6871 (t0) cc_final: 0.6633 (t0) REVERT: C 69 MET cc_start: 0.8827 (mtp) cc_final: 0.8464 (mtp) REVERT: C 96 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7745 (mpt-90) REVERT: C 125 ASP cc_start: 0.7353 (m-30) cc_final: 0.7112 (m-30) REVERT: C 145 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7364 (tt0) REVERT: C 320 MET cc_start: 0.8771 (ptp) cc_final: 0.8470 (ptm) REVERT: C 331 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.6963 (mt0) REVERT: C 461 MET cc_start: 0.1677 (mmm) cc_final: 0.1399 (mtp) REVERT: E 62 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8113 (tmtt) REVERT: E 69 MET cc_start: 0.8832 (mtm) cc_final: 0.8412 (mtp) REVERT: E 232 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8618 (mm) REVERT: E 238 MET cc_start: 0.9183 (tpt) cc_final: 0.8862 (tpt) REVERT: E 256 ASN cc_start: 0.8138 (t0) cc_final: 0.7803 (t0) REVERT: E 311 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6963 (t70) outliers start: 117 outliers final: 61 residues processed: 343 average time/residue: 1.5254 time to fit residues: 608.2951 Evaluate side-chains 311 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 239 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain B residue 62 LYS Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 58 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 40.0000 chunk 246 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 0.0570 chunk 219 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 347 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN E 226 HIS ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29646 Z= 0.265 Angle : 0.584 7.745 40176 Z= 0.301 Chirality : 0.046 0.182 4572 Planarity : 0.004 0.044 5106 Dihedral : 7.947 59.595 4062 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.36 % Favored : 92.42 % Rotamer: Outliers : 4.52 % Allowed : 19.40 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.14), residues: 3588 helix: 0.42 (0.15), residues: 1290 sheet: -0.25 (0.20), residues: 618 loop : -1.70 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 290 HIS 0.012 0.001 HIS D 226 PHE 0.016 0.002 PHE E 225 TYR 0.016 0.001 TYR E 245 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 240 time to evaluate : 3.307 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: f 25 ASN cc_start: 0.3392 (OUTLIER) cc_final: 0.3138 (t0) REVERT: f 58 GLU cc_start: 0.1323 (OUTLIER) cc_final: 0.0552 (tt0) REVERT: D 69 MET cc_start: 0.8775 (mtp) cc_final: 0.8471 (mtp) REVERT: D 232 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8776 (mm) REVERT: D 238 MET cc_start: 0.9138 (tpt) cc_final: 0.8877 (tpt) REVERT: D 252 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6791 (m-30) REVERT: D 256 ASN cc_start: 0.8070 (t0) cc_final: 0.7729 (t0) REVERT: D 331 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7168 (mt0) REVERT: A 119 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: A 461 MET cc_start: 0.1739 (mmm) cc_final: 0.1246 (mtt) REVERT: F 62 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.7465 (ttpt) REVERT: F 96 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7796 (mpt-90) REVERT: F 145 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7412 (tt0) REVERT: F 320 MET cc_start: 0.8847 (ptp) cc_final: 0.8588 (ptm) REVERT: F 331 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7189 (mt0) REVERT: B 461 MET cc_start: 0.1230 (mmm) cc_final: 0.0876 (mtt) REVERT: C 7 ASP cc_start: 0.6970 (t0) cc_final: 0.6761 (t0) REVERT: C 69 MET cc_start: 0.8827 (mtp) cc_final: 0.8446 (mtp) REVERT: C 96 ARG cc_start: 0.8059 (mmt90) cc_final: 0.7753 (mpt-90) REVERT: C 145 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7367 (tt0) REVERT: C 320 MET cc_start: 0.8845 (ptp) cc_final: 0.8544 (ptm) REVERT: C 331 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7151 (mt0) REVERT: C 461 MET cc_start: 0.1544 (mmm) cc_final: 0.1259 (mtp) REVERT: E 62 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.8136 (tmtt) REVERT: E 232 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8766 (mm) REVERT: E 238 MET cc_start: 0.9155 (tpt) cc_final: 0.8892 (tpt) REVERT: E 252 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: E 256 ASN cc_start: 0.8159 (t0) cc_final: 0.7801 (t0) REVERT: E 311 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7010 (t70) REVERT: E 331 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7149 (mt0) REVERT: E 461 MET cc_start: 0.0308 (mtt) cc_final: -0.0573 (mmm) REVERT: e 30 GLU cc_start: 0.3811 (OUTLIER) cc_final: 0.3428 (tm-30) outliers start: 142 outliers final: 74 residues processed: 355 average time/residue: 1.4340 time to fit residues: 594.2114 Evaluate side-chains 330 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 241 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 163 ASP Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 62 LYS Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 132 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain F residue 453 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 285 MET Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.0070 chunk 197 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 0 optimal weight: 40.0000 chunk 177 optimal weight: 3.9990 chunk 312 optimal weight: 7.9990 chunk 87 optimal weight: 0.2980 overall best weight: 1.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 HIS D 464 ASN A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 226 HIS ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29646 Z= 0.189 Angle : 0.542 8.329 40176 Z= 0.278 Chirality : 0.045 0.193 4572 Planarity : 0.004 0.042 5106 Dihedral : 7.643 57.254 4062 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.74 % Favored : 92.92 % Rotamer: Outliers : 4.10 % Allowed : 20.20 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.89 (0.14), residues: 3588 helix: 0.51 (0.15), residues: 1290 sheet: -0.28 (0.22), residues: 546 loop : -1.55 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 230 HIS 0.008 0.001 HIS E 532 PHE 0.014 0.001 PHE E 225 TYR 0.011 0.001 TYR E 245 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 249 time to evaluate : 3.502 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: f 5 GLU cc_start: 0.5074 (mm-30) cc_final: 0.4226 (mt-10) REVERT: f 25 ASN cc_start: 0.3344 (OUTLIER) cc_final: 0.3138 (t0) REVERT: f 30 GLU cc_start: 0.3791 (pm20) cc_final: 0.3416 (pm20) REVERT: f 58 GLU cc_start: 0.1111 (OUTLIER) cc_final: 0.0574 (tt0) REVERT: D 69 MET cc_start: 0.8715 (mtp) cc_final: 0.8441 (mtp) REVERT: D 232 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8745 (mm) REVERT: D 238 MET cc_start: 0.9142 (tpt) cc_final: 0.8864 (tpt) REVERT: D 252 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: D 256 ASN cc_start: 0.8054 (t0) cc_final: 0.7743 (t0) REVERT: D 331 GLN cc_start: 0.7964 (OUTLIER) cc_final: 0.7090 (mt0) REVERT: A 31 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 119 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: A 152 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8310 (tp) REVERT: A 461 MET cc_start: 0.1785 (mmm) cc_final: 0.1412 (mtt) REVERT: F 96 ARG cc_start: 0.8089 (mmt90) cc_final: 0.7809 (mpt-90) REVERT: F 145 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7450 (tt0) REVERT: F 320 MET cc_start: 0.8790 (ptp) cc_final: 0.8553 (ptm) REVERT: F 331 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7171 (mt0) REVERT: B 31 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8641 (mm) REVERT: B 152 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8339 (tp) REVERT: B 224 MET cc_start: 0.8475 (ttt) cc_final: 0.8247 (ttt) REVERT: B 283 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7844 (mmmm) REVERT: B 311 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7267 (t70) REVERT: B 461 MET cc_start: 0.1361 (mmm) cc_final: 0.0816 (mtt) REVERT: C 7 ASP cc_start: 0.6908 (t0) cc_final: 0.6691 (t0) REVERT: C 69 MET cc_start: 0.8797 (mtp) cc_final: 0.8428 (mtp) REVERT: C 96 ARG cc_start: 0.8058 (mmt90) cc_final: 0.7738 (mpt-90) REVERT: C 145 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7374 (tt0) REVERT: C 320 MET cc_start: 0.8800 (ptp) cc_final: 0.8500 (ptm) REVERT: C 331 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7145 (mt0) REVERT: C 461 MET cc_start: 0.2054 (mmm) cc_final: 0.1181 (mtp) REVERT: E 62 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8112 (tmtt) REVERT: E 232 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8726 (mm) REVERT: E 238 MET cc_start: 0.9180 (tpt) cc_final: 0.8880 (tpt) REVERT: E 252 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: E 256 ASN cc_start: 0.8144 (t0) cc_final: 0.7790 (t0) REVERT: E 418 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: E 461 MET cc_start: 0.0107 (mtt) cc_final: -0.0289 (mmm) REVERT: e 30 GLU cc_start: 0.3743 (OUTLIER) cc_final: 0.3450 (tm-30) outliers start: 129 outliers final: 69 residues processed: 353 average time/residue: 1.4601 time to fit residues: 601.7793 Evaluate side-chains 330 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 243 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 331 GLN Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 453 VAL Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9980 chunk 313 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 348 optimal weight: 9.9990 chunk 289 optimal weight: 0.0030 chunk 161 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 226 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 226 HIS ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29646 Z= 0.137 Angle : 0.511 7.712 40176 Z= 0.259 Chirality : 0.043 0.176 4572 Planarity : 0.004 0.041 5106 Dihedral : 7.236 58.164 4062 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.47 % Favored : 93.20 % Rotamer: Outliers : 3.21 % Allowed : 21.34 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.70 (0.14), residues: 3588 helix: 0.62 (0.15), residues: 1308 sheet: -0.11 (0.22), residues: 540 loop : -1.43 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 290 HIS 0.006 0.001 HIS C 228 PHE 0.011 0.001 PHE D 225 TYR 0.009 0.001 TYR E 148 ARG 0.004 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 248 time to evaluate : 3.265 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: f 25 ASN cc_start: 0.3300 (OUTLIER) cc_final: 0.3049 (t0) REVERT: f 58 GLU cc_start: 0.1114 (OUTLIER) cc_final: 0.0610 (tt0) REVERT: D 69 MET cc_start: 0.8711 (mtp) cc_final: 0.8454 (mtp) REVERT: D 238 MET cc_start: 0.9140 (tpt) cc_final: 0.8830 (tpt) REVERT: D 256 ASN cc_start: 0.8047 (t0) cc_final: 0.7726 (t0) REVERT: D 461 MET cc_start: 0.1472 (OUTLIER) cc_final: 0.0978 (ttm) REVERT: A 119 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7968 (mt-10) REVERT: A 461 MET cc_start: 0.1716 (mmm) cc_final: 0.1296 (mtt) REVERT: F 96 ARG cc_start: 0.8090 (mmt90) cc_final: 0.7847 (mpt-90) REVERT: F 145 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7479 (tt0) REVERT: F 320 MET cc_start: 0.8719 (ptp) cc_final: 0.8506 (ptm) REVERT: B 152 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8402 (tp) REVERT: B 283 LYS cc_start: 0.8308 (mmtt) cc_final: 0.7854 (mmmm) REVERT: B 311 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7236 (t70) REVERT: C 69 MET cc_start: 0.8789 (mtp) cc_final: 0.8480 (mtp) REVERT: C 96 ARG cc_start: 0.8076 (mmt90) cc_final: 0.7793 (mpt-90) REVERT: C 145 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7413 (tt0) REVERT: C 320 MET cc_start: 0.8776 (ptp) cc_final: 0.8499 (ptm) REVERT: C 461 MET cc_start: 0.2026 (mmm) cc_final: 0.1131 (mtp) REVERT: E 62 LYS cc_start: 0.8328 (OUTLIER) cc_final: 0.8114 (tmtt) REVERT: E 69 MET cc_start: 0.8812 (mtm) cc_final: 0.8400 (mtp) REVERT: E 238 MET cc_start: 0.9183 (tpt) cc_final: 0.8853 (tpt) REVERT: E 252 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6794 (m-30) REVERT: E 256 ASN cc_start: 0.8128 (t0) cc_final: 0.7759 (t0) REVERT: E 396 LYS cc_start: 0.8475 (mttp) cc_final: 0.8227 (mmtp) REVERT: E 418 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6589 (pp20) outliers start: 101 outliers final: 48 residues processed: 333 average time/residue: 1.4984 time to fit residues: 579.9308 Evaluate side-chains 302 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 245 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 25 ASN Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 58 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 chunk 198 optimal weight: 0.9980 chunk 254 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 194 optimal weight: 0.0370 chunk 346 optimal weight: 30.0000 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 0.0060 chunk 160 optimal weight: 10.0000 overall best weight: 0.6076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 226 HIS A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN E 226 HIS ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 29646 Z= 0.134 Angle : 0.509 7.196 40176 Z= 0.257 Chirality : 0.043 0.175 4572 Planarity : 0.004 0.040 5106 Dihedral : 7.010 57.918 4062 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.61 % Favored : 93.06 % Rotamer: Outliers : 2.86 % Allowed : 21.56 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.65 (0.14), residues: 3588 helix: 0.70 (0.15), residues: 1284 sheet: -0.37 (0.24), residues: 450 loop : -1.27 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 230 HIS 0.006 0.001 HIS C 228 PHE 0.012 0.001 PHE B 225 TYR 0.008 0.001 TYR D 148 ARG 0.004 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 250 time to evaluate : 3.371 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: f 5 GLU cc_start: 0.4830 (mm-30) cc_final: 0.4185 (mt-10) REVERT: D 69 MET cc_start: 0.8700 (mtp) cc_final: 0.8435 (mtp) REVERT: D 86 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8621 (pt) REVERT: D 96 ARG cc_start: 0.8097 (mmt90) cc_final: 0.7830 (mpt-90) REVERT: D 238 MET cc_start: 0.9129 (tpt) cc_final: 0.8832 (tpt) REVERT: D 252 ASP cc_start: 0.7131 (OUTLIER) cc_final: 0.6814 (m-30) REVERT: D 256 ASN cc_start: 0.8040 (t0) cc_final: 0.7722 (t0) REVERT: D 461 MET cc_start: 0.1583 (mpp) cc_final: 0.1061 (ttm) REVERT: A 119 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: A 152 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8397 (tp) REVERT: F 69 MET cc_start: 0.8936 (mtm) cc_final: 0.8573 (mtp) REVERT: F 96 ARG cc_start: 0.8104 (mmt90) cc_final: 0.7861 (mpt-90) REVERT: F 145 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7494 (tt0) REVERT: B 31 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8645 (mm) REVERT: B 152 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8429 (tp) REVERT: B 283 LYS cc_start: 0.8287 (mmtt) cc_final: 0.7860 (mmmm) REVERT: B 311 ASP cc_start: 0.7833 (OUTLIER) cc_final: 0.7191 (t70) REVERT: B 461 MET cc_start: 0.1845 (mmm) cc_final: 0.1382 (mtt) REVERT: C 69 MET cc_start: 0.8763 (mtp) cc_final: 0.8456 (mtp) REVERT: C 96 ARG cc_start: 0.8108 (mmt90) cc_final: 0.7802 (mpt-90) REVERT: C 145 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7424 (tt0) REVERT: C 224 MET cc_start: 0.8162 (ttt) cc_final: 0.7830 (ttt) REVERT: C 235 MET cc_start: 0.8938 (mtp) cc_final: 0.8705 (mtt) REVERT: C 311 ASP cc_start: 0.7796 (OUTLIER) cc_final: 0.7100 (t70) REVERT: C 320 MET cc_start: 0.8784 (ptp) cc_final: 0.8495 (ptm) REVERT: C 461 MET cc_start: 0.2137 (mmm) cc_final: 0.1138 (mtp) REVERT: E 62 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8131 (tmtt) REVERT: E 69 MET cc_start: 0.8814 (mtm) cc_final: 0.8452 (mtp) REVERT: E 238 MET cc_start: 0.9136 (tpt) cc_final: 0.8830 (tpt) REVERT: E 252 ASP cc_start: 0.7071 (OUTLIER) cc_final: 0.6775 (m-30) REVERT: E 256 ASN cc_start: 0.8097 (t0) cc_final: 0.7733 (t0) REVERT: E 396 LYS cc_start: 0.8470 (mttp) cc_final: 0.8230 (mmtp) REVERT: E 418 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6564 (pp20) outliers start: 90 outliers final: 53 residues processed: 327 average time/residue: 1.5842 time to fit residues: 601.9410 Evaluate side-chains 315 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 251 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 359 GLU Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 359 GLU Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 220 optimal weight: 0.1980 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN E 390 ASN ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 24 ASN d 24 ASN e 24 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29646 Z= 0.205 Angle : 0.554 7.540 40176 Z= 0.282 Chirality : 0.045 0.167 4572 Planarity : 0.004 0.040 5106 Dihedral : 7.187 57.835 4062 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.69 % Favored : 92.98 % Rotamer: Outliers : 3.28 % Allowed : 21.25 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.70 (0.14), residues: 3588 helix: 0.61 (0.15), residues: 1314 sheet: -0.14 (0.22), residues: 540 loop : -1.42 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 290 HIS 0.007 0.001 HIS F 228 PHE 0.015 0.001 PHE E 225 TYR 0.013 0.001 TYR D 245 ARG 0.004 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 250 time to evaluate : 3.568 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: f 5 GLU cc_start: 0.4762 (mm-30) cc_final: 0.4088 (mt-10) REVERT: f 57 GLU cc_start: 0.3375 (mm-30) cc_final: 0.3070 (mp0) REVERT: D 69 MET cc_start: 0.8740 (mtp) cc_final: 0.8477 (mtp) REVERT: D 158 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7793 (mp0) REVERT: D 226 HIS cc_start: 0.7375 (OUTLIER) cc_final: 0.7045 (m170) REVERT: D 238 MET cc_start: 0.9144 (tpt) cc_final: 0.8845 (tpt) REVERT: D 252 ASP cc_start: 0.7122 (OUTLIER) cc_final: 0.6806 (m-30) REVERT: D 256 ASN cc_start: 0.8057 (t0) cc_final: 0.7737 (t0) REVERT: D 337 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.8037 (mm) REVERT: D 346 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: D 461 MET cc_start: 0.1496 (mpp) cc_final: 0.1011 (ttm) REVERT: A 31 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 119 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7974 (mt-10) REVERT: F 96 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7848 (mpt-90) REVERT: F 145 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7474 (tt0) REVERT: F 331 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7143 (mt0) REVERT: B 31 ILE cc_start: 0.8984 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 283 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7851 (mmmm) REVERT: B 311 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7260 (t70) REVERT: B 328 SER cc_start: 0.9276 (OUTLIER) cc_final: 0.9064 (m) REVERT: C 69 MET cc_start: 0.8802 (mtp) cc_final: 0.8595 (mtm) REVERT: C 96 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7814 (mpt-90) REVERT: C 145 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7405 (tt0) REVERT: C 224 MET cc_start: 0.8410 (ttt) cc_final: 0.7959 (ttt) REVERT: C 320 MET cc_start: 0.8850 (ptp) cc_final: 0.8561 (ptm) REVERT: C 331 GLN cc_start: 0.7864 (OUTLIER) cc_final: 0.7081 (mt0) REVERT: C 461 MET cc_start: 0.2148 (mmm) cc_final: 0.1164 (mtp) REVERT: E 62 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8128 (tmtt) REVERT: E 69 MET cc_start: 0.8811 (mtm) cc_final: 0.8413 (mtp) REVERT: E 226 HIS cc_start: 0.7400 (OUTLIER) cc_final: 0.7087 (m170) REVERT: E 238 MET cc_start: 0.9137 (tpt) cc_final: 0.8880 (tpt) REVERT: E 252 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6802 (m-30) REVERT: E 256 ASN cc_start: 0.8145 (t0) cc_final: 0.7813 (t0) REVERT: E 337 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.7976 (mm) REVERT: E 338 GLU cc_start: 0.7830 (mp0) cc_final: 0.7481 (mp0) REVERT: E 396 LYS cc_start: 0.8510 (mttp) cc_final: 0.8252 (mmtp) REVERT: E 418 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6656 (pp20) outliers start: 103 outliers final: 57 residues processed: 334 average time/residue: 1.4707 time to fit residues: 571.2267 Evaluate side-chains 325 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 251 time to evaluate : 3.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 GLU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 53 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 8.9990 chunk 332 optimal weight: 40.0000 chunk 303 optimal weight: 1.9990 chunk 323 optimal weight: 6.9990 chunk 194 optimal weight: 0.4980 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 292 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 chunk 322 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN D 390 ASN A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29646 Z= 0.223 Angle : 0.574 8.386 40176 Z= 0.291 Chirality : 0.045 0.174 4572 Planarity : 0.004 0.040 5106 Dihedral : 7.309 58.280 4062 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.63 % Favored : 93.03 % Rotamer: Outliers : 2.80 % Allowed : 21.79 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.82 (0.14), residues: 3588 helix: 0.54 (0.15), residues: 1314 sheet: -0.27 (0.20), residues: 618 loop : -1.53 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 290 HIS 0.007 0.001 HIS A 228 PHE 0.015 0.001 PHE E 225 TYR 0.013 0.001 TYR E 245 ARG 0.004 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 252 time to evaluate : 3.607 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: D 69 MET cc_start: 0.8755 (mtp) cc_final: 0.8461 (mtp) REVERT: D 158 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: D 226 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.7019 (m170) REVERT: D 238 MET cc_start: 0.9125 (tpt) cc_final: 0.8830 (tpt) REVERT: D 252 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6790 (m-30) REVERT: D 256 ASN cc_start: 0.8078 (t0) cc_final: 0.7757 (t0) REVERT: D 337 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8043 (mm) REVERT: D 461 MET cc_start: 0.1574 (mpp) cc_final: 0.1057 (ttm) REVERT: A 119 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: F 96 ARG cc_start: 0.8129 (mmt90) cc_final: 0.7840 (mpt-90) REVERT: F 331 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7159 (mt0) REVERT: B 31 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8680 (mm) REVERT: B 283 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7806 (mmmm) REVERT: B 311 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7300 (t70) REVERT: B 328 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.9058 (m) REVERT: C 69 MET cc_start: 0.8807 (mtp) cc_final: 0.8404 (mtp) REVERT: C 96 ARG cc_start: 0.8109 (mmt90) cc_final: 0.7786 (mpt-90) REVERT: C 145 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7386 (tt0) REVERT: C 224 MET cc_start: 0.8419 (ttt) cc_final: 0.8064 (ttt) REVERT: C 320 MET cc_start: 0.8852 (ptp) cc_final: 0.8577 (ptm) REVERT: C 331 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7120 (mt0) REVERT: C 461 MET cc_start: 0.2378 (mmm) cc_final: 0.1327 (mtp) REVERT: E 62 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8184 (tmtt) REVERT: E 69 MET cc_start: 0.8828 (mtm) cc_final: 0.8426 (mtp) REVERT: E 226 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6969 (m170) REVERT: E 238 MET cc_start: 0.9164 (tpt) cc_final: 0.8840 (tpt) REVERT: E 252 ASP cc_start: 0.7107 (OUTLIER) cc_final: 0.6810 (m-30) REVERT: E 256 ASN cc_start: 0.8157 (t0) cc_final: 0.7809 (t0) REVERT: E 337 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8085 (mm) REVERT: E 418 GLU cc_start: 0.7125 (OUTLIER) cc_final: 0.6665 (pp20) REVERT: e 30 GLU cc_start: 0.3948 (OUTLIER) cc_final: 0.3643 (tm-30) outliers start: 88 outliers final: 58 residues processed: 322 average time/residue: 1.5387 time to fit residues: 577.4875 Evaluate side-chains 320 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 246 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 158 GLU Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 226 HIS Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 252 ASP Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain F residue 331 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 111 ASP Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 252 ASP Chi-restraints excluded: chain B residue 260 GLN Chi-restraints excluded: chain B residue 311 ASP Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 328 SER Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 252 ASP Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 311 ASP Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 331 GLN Chi-restraints excluded: chain E residue 62 LYS Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain E residue 222 THR Chi-restraints excluded: chain E residue 226 HIS Chi-restraints excluded: chain E residue 252 ASP Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 30 GLU Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 20.0000 chunk 341 optimal weight: 0.1980 chunk 208 optimal weight: 5.9990 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 358 optimal weight: 0.0170 chunk 330 optimal weight: 40.0000 chunk 285 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 220 optimal weight: 0.5980 chunk 175 optimal weight: 0.0370 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN A 154 GLN A 226 HIS F 154 GLN F 226 HIS B 154 GLN B 226 HIS C 226 HIS E 154 GLN b 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29646 Z= 0.121 Angle : 0.510 8.845 40176 Z= 0.255 Chirality : 0.043 0.167 4572 Planarity : 0.004 0.040 5106 Dihedral : 6.813 59.173 4062 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.94 % Favored : 93.73 % Rotamer: Outliers : 1.84 % Allowed : 22.74 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.14), residues: 3588 helix: 0.79 (0.15), residues: 1284 sheet: -0.07 (0.23), residues: 534 loop : -1.33 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 290 HIS 0.005 0.001 HIS E 228 PHE 0.009 0.001 PHE B 225 TYR 0.009 0.001 TYR B 234 ARG 0.004 0.000 ARG E 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7176 Ramachandran restraints generated. 3588 Oldfield, 0 Emsley, 3588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 262 time to evaluate : 3.510 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: D 69 MET cc_start: 0.8710 (mtp) cc_final: 0.8460 (mtp) REVERT: D 96 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7820 (mpt-90) REVERT: D 238 MET cc_start: 0.9120 (tpt) cc_final: 0.8821 (tpt) REVERT: D 256 ASN cc_start: 0.8044 (t0) cc_final: 0.7726 (t0) REVERT: D 338 GLU cc_start: 0.7939 (mp0) cc_final: 0.7589 (mp0) REVERT: D 461 MET cc_start: 0.1518 (mpp) cc_final: 0.1102 (ttm) REVERT: A 224 MET cc_start: 0.8227 (ttt) cc_final: 0.7856 (ttt) REVERT: A 311 ASP cc_start: 0.7747 (t70) cc_final: 0.7134 (t0) REVERT: F 69 MET cc_start: 0.8902 (mtm) cc_final: 0.8533 (mtp) REVERT: F 96 ARG cc_start: 0.8145 (mmt90) cc_final: 0.7872 (mpt-90) REVERT: B 224 MET cc_start: 0.8218 (ttt) cc_final: 0.7855 (ttt) REVERT: B 283 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7800 (mmmm) REVERT: C 69 MET cc_start: 0.8732 (mtp) cc_final: 0.8424 (mtp) REVERT: C 96 ARG cc_start: 0.8107 (mmt90) cc_final: 0.7816 (mpt-90) REVERT: C 145 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7436 (tt0) REVERT: C 224 MET cc_start: 0.7931 (ttt) cc_final: 0.7588 (ttt) REVERT: C 320 MET cc_start: 0.8743 (ptp) cc_final: 0.8468 (ptm) REVERT: C 461 MET cc_start: 0.2236 (mmm) cc_final: 0.1274 (mtp) REVERT: E 238 MET cc_start: 0.9147 (tpt) cc_final: 0.8845 (tpt) REVERT: E 256 ASN cc_start: 0.8088 (t0) cc_final: 0.7755 (t0) REVERT: E 338 GLU cc_start: 0.7830 (mp0) cc_final: 0.7491 (mp0) REVERT: E 396 LYS cc_start: 0.8457 (mttp) cc_final: 0.8234 (mmtp) REVERT: E 418 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6617 (pp20) outliers start: 58 outliers final: 37 residues processed: 313 average time/residue: 1.5715 time to fit residues: 576.5056 Evaluate side-chains 301 residues out of total 3168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 263 time to evaluate : 3.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain f residue 53 GLU Chi-restraints excluded: chain f residue 63 THR Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 359 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain F residue 76 TYR Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain E residue 359 GLU Chi-restraints excluded: chain E residue 418 GLU Chi-restraints excluded: chain E residue 509 VAL Chi-restraints excluded: chain a residue 53 GLU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain b residue 17 VAL Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 58 GLU Chi-restraints excluded: chain b residue 63 THR Chi-restraints excluded: chain c residue 17 VAL Chi-restraints excluded: chain c residue 48 GLU Chi-restraints excluded: chain c residue 53 GLU Chi-restraints excluded: chain c residue 63 THR Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 53 GLU Chi-restraints excluded: chain d residue 63 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 48 GLU Chi-restraints excluded: chain e residue 63 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 293 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN A 154 GLN A 226 HIS F 154 GLN B 154 GLN B 226 HIS E 154 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.192248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126911 restraints weight = 30293.761| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.38 r_work: 0.3106 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 29646 Z= 0.367 Angle : 0.650 8.287 40176 Z= 0.332 Chirality : 0.049 0.207 4572 Planarity : 0.005 0.042 5106 Dihedral : 7.524 58.029 4062 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.72 % Favored : 92.95 % Rotamer: Outliers : 2.45 % Allowed : 22.04 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: -0.90 (0.14), residues: 3588 helix: 0.48 (0.15), residues: 1308 sheet: -0.32 (0.20), residues: 618 loop : -1.58 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP F 290 HIS 0.009 0.002 HIS F 228 PHE 0.019 0.002 PHE E 225 TYR 0.020 0.002 TYR E 245 ARG 0.010 0.001 ARG D 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10192.50 seconds wall clock time: 182 minutes 35.07 seconds (10955.07 seconds total)