Starting phenix.real_space_refine on Mon Mar 18 02:12:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/03_2024/7rye_24735.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/03_2024/7rye_24735.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/03_2024/7rye_24735.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/03_2024/7rye_24735.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/03_2024/7rye_24735.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rye_24735/03_2024/7rye_24735.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 12445 2.51 5 N 3227 2.21 5 O 4006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 70": "OD1" <-> "OD2" Residue "B ASP 11": "OD1" <-> "OD2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "C ASP 10": "OD1" <-> "OD2" Residue "C PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 29": "OE1" <-> "OE2" Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "E ASP 10": "OD1" <-> "OD2" Residue "E ASP 11": "OD1" <-> "OD2" Residue "E ASP 17": "OD1" <-> "OD2" Residue "E GLU 53": "OE1" <-> "OE2" Residue "E PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 169": "OD1" <-> "OD2" Residue "F GLU 228": "OE1" <-> "OE2" Residue "F TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "F PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 17": "OD1" <-> "OD2" Residue "I ASP 32": "OD1" <-> "OD2" Residue "I TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 17": "OD1" <-> "OD2" Residue "J PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "K TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 17": "OD1" <-> "OD2" Residue "K ASP 21": "OD1" <-> "OD2" Residue "K GLU 29": "OE1" <-> "OE2" Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 72": "OD1" <-> "OD2" Residue "L ASP 21": "OD1" <-> "OD2" Residue "L PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 21": "OD1" <-> "OD2" Residue "M TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 32": "OD1" <-> "OD2" Residue "N TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 70": "OD1" <-> "OD2" Residue "N ASP 72": "OD1" <-> "OD2" Residue "O TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 162": "OD1" <-> "OD2" Residue "O TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 277": "OD1" <-> "OD2" Residue "O TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 11": "OD1" <-> "OD2" Residue "P GLU 53": "OE1" <-> "OE2" Residue "Q TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 133": "OE1" <-> "OE2" Residue "R TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 154": "OE1" <-> "OE2" Residue "R ASP 162": "OD1" <-> "OD2" Residue "R PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 283": "OD1" <-> "OD2" Residue "S ASP 17": "OD1" <-> "OD2" Residue "S ASP 21": "OD1" <-> "OD2" Residue "S ASP 32": "OD1" <-> "OD2" Residue "T ASP 10": "OD1" <-> "OD2" Residue "T ASP 21": "OD1" <-> "OD2" Residue "T ASP 72": "OD1" <-> "OD2" Residue "U TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "V TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 162": "OD1" <-> "OD2" Residue "V ASP 190": "OD1" <-> "OD2" Residue "V TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 267": "OD1" <-> "OD2" Residue "V ASP 269": "OD1" <-> "OD2" Residue "V TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 320": "OD1" <-> "OD2" Residue "W TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 11": "OD1" <-> "OD2" Residue "W ASP 32": "OD1" <-> "OD2" Residue "W ASP 40": "OD1" <-> "OD2" Residue "X GLU 154": "OE1" <-> "OE2" Residue "X ASP 183": "OD1" <-> "OD2" Residue "X PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 230": "OE1" <-> "OE2" Residue "X TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19708 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "B" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "D" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "E" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "H" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "I" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "J" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "K" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "L" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "M" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "N" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "O" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "P" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "Q" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "R" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 612 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 74} Chain: "T" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "U" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "V" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 604 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1627 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 206} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.50, per 1000 atoms: 0.48 Number of scatterers: 19708 At special positions: 0 Unit cell: (99.47, 96.04, 214.375, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 4006 8.00 N 3227 7.00 C 12445 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=0, symmetry=0 Time building additional restraints: 8.08 Conformation dependent library (CDL) restraints added in 3.2 seconds 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4854 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 10 sheets defined 79.4% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 40 through 77 removed outlier: 3.887A pdb=" N ALA A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 Processing helix chain 'B' and resid 22 through 37 Processing helix chain 'B' and resid 40 through 78 Processing helix chain 'C' and resid 7 through 20 Processing helix chain 'C' and resid 22 through 37 Processing helix chain 'C' and resid 40 through 78 removed outlier: 3.733A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 16 Processing helix chain 'D' and resid 17 through 21 removed outlier: 3.644A pdb=" N ASP D 21 " --> pdb=" O THR D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 37 Processing helix chain 'D' and resid 40 through 77 Processing helix chain 'E' and resid 8 through 16 Processing helix chain 'E' and resid 17 through 35 removed outlier: 3.918A pdb=" N ASN E 22 " --> pdb=" O THR E 18 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N THR E 25 " --> pdb=" O ASP E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 78 removed outlier: 4.047A pdb=" N LEU E 44 " --> pdb=" O ASP E 40 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N PHE E 68 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS E 69 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP E 72 " --> pdb=" O PHE E 68 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE E 75 " --> pdb=" O ILE E 71 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE E 76 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 131 through 147 removed outlier: 3.662A pdb=" N SER F 143 " --> pdb=" O SER F 139 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY F 146 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 147 " --> pdb=" O SER F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 175 Processing helix chain 'F' and resid 190 through 206 removed outlier: 3.894A pdb=" N LEU F 194 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.677A pdb=" N ALA F 231 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU F 237 " --> pdb=" O GLN F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 Processing helix chain 'F' and resid 283 through 311 Processing helix chain 'F' and resid 311 through 323 removed outlier: 4.591A pdb=" N SER F 317 " --> pdb=" O SER F 313 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU F 318 " --> pdb=" O ASN F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 332 through 340 removed outlier: 3.607A pdb=" N GLU F 335 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR F 336 " --> pdb=" O SER F 333 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 337 " --> pdb=" O LEU F 334 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 37 removed outlier: 3.976A pdb=" N PHE G 16 " --> pdb=" O VAL G 12 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP G 17 " --> pdb=" O SER G 13 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N THR G 18 " --> pdb=" O ALA G 14 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N GLY G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP G 21 " --> pdb=" O ASP G 17 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN G 22 " --> pdb=" O THR G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 78 removed outlier: 4.166A pdb=" N LEU G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASP G 72 " --> pdb=" O PHE G 68 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA G 74 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 37 removed outlier: 3.611A pdb=" N PHE H 16 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 18 " --> pdb=" O ALA H 14 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N GLY H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N THR H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU H 29 " --> pdb=" O THR H 25 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LYS H 33 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 78 removed outlier: 3.867A pdb=" N ALA H 45 " --> pdb=" O PRO H 41 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA H 46 " --> pdb=" O ALA H 42 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE H 68 " --> pdb=" O THR H 64 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LYS H 69 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP H 72 " --> pdb=" O PHE H 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 37 removed outlier: 4.192A pdb=" N GLY I 19 " --> pdb=" O LYS I 15 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN I 22 " --> pdb=" O THR I 18 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU I 23 " --> pdb=" O GLY I 19 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU I 29 " --> pdb=" O THR I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 78 removed outlier: 4.347A pdb=" N LEU I 44 " --> pdb=" O ASP I 40 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP I 72 " --> pdb=" O PHE I 68 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA I 74 " --> pdb=" O ASP I 70 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ILE I 75 " --> pdb=" O ILE I 71 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 43 through 79 Processing helix chain 'K' and resid 7 through 20 removed outlier: 3.514A pdb=" N VAL K 20 " --> pdb=" O PHE K 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 37 Processing helix chain 'K' and resid 40 through 77 Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 40 through 77 Processing helix chain 'M' and resid 7 through 20 Processing helix chain 'M' and resid 22 through 37 Processing helix chain 'M' and resid 40 through 78 Processing helix chain 'N' and resid 7 through 20 Processing helix chain 'N' and resid 22 through 37 Processing helix chain 'N' and resid 40 through 78 removed outlier: 3.709A pdb=" N ASN N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 149 removed outlier: 3.925A pdb=" N TRP O 135 " --> pdb=" O ASP O 131 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP O 136 " --> pdb=" O ALA O 132 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP O 147 " --> pdb=" O SER O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 174 removed outlier: 3.541A pdb=" N TYR O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 207 removed outlier: 3.852A pdb=" N GLN O 207 " --> pdb=" O ASN O 203 " (cutoff:3.500A) Processing helix chain 'O' and resid 227 through 239 removed outlier: 3.766A pdb=" N GLU O 237 " --> pdb=" O GLN O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 258 through 269 removed outlier: 3.817A pdb=" N ASP O 269 " --> pdb=" O VAL O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 272 No H-bonds generated for 'chain 'O' and resid 270 through 272' Processing helix chain 'O' and resid 283 through 311 Processing helix chain 'O' and resid 311 through 323 removed outlier: 4.351A pdb=" N SER O 317 " --> pdb=" O SER O 313 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU O 318 " --> pdb=" O ASN O 314 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN O 321 " --> pdb=" O SER O 317 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 331 Processing helix chain 'O' and resid 333 through 340 removed outlier: 3.881A pdb=" N THR O 336 " --> pdb=" O SER O 333 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA O 337 " --> pdb=" O LEU O 334 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 22 through 37 Processing helix chain 'P' and resid 40 through 78 removed outlier: 3.711A pdb=" N ASN P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.637A pdb=" N VAL Q 20 " --> pdb=" O PHE Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 37 removed outlier: 4.128A pdb=" N THR Q 28 " --> pdb=" O GLN Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 79 Processing helix chain 'R' and resid 131 through 145 removed outlier: 4.193A pdb=" N SER R 143 " --> pdb=" O SER R 139 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE R 145 " --> pdb=" O ASN R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 175 removed outlier: 3.588A pdb=" N TYR R 153 " --> pdb=" O TYR R 149 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY R 175 " --> pdb=" O LEU R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 205 removed outlier: 3.575A pdb=" N LEU R 194 " --> pdb=" O ASP R 190 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 239 removed outlier: 3.529A pdb=" N ALA R 231 " --> pdb=" O THR R 227 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU R 237 " --> pdb=" O GLN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 268 Processing helix chain 'R' and resid 269 through 272 removed outlier: 3.722A pdb=" N GLY R 272 " --> pdb=" O ASP R 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 269 through 272' Processing helix chain 'R' and resid 283 through 323 removed outlier: 4.117A pdb=" N ALA R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N TYR R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER R 313 " --> pdb=" O THR R 309 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU R 318 " --> pdb=" O ASN R 314 " (cutoff:3.500A) Processing helix chain 'R' and resid 326 through 334 removed outlier: 4.193A pdb=" N SER R 332 " --> pdb=" O SER R 328 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 340 Processing helix chain 'S' and resid 7 through 20 removed outlier: 3.638A pdb=" N PHE S 16 " --> pdb=" O VAL S 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 37 removed outlier: 3.963A pdb=" N THR S 28 " --> pdb=" O GLN S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 40 through 80 removed outlier: 3.745A pdb=" N ARG S 80 " --> pdb=" O ILE S 76 " (cutoff:3.500A) Processing helix chain 'T' and resid 7 through 37 removed outlier: 3.593A pdb=" N PHE T 16 " --> pdb=" O VAL T 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY T 19 " --> pdb=" O LYS T 15 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN T 22 " --> pdb=" O THR T 18 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR T 28 " --> pdb=" O GLN T 24 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU T 29 " --> pdb=" O THR T 25 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS T 33 " --> pdb=" O GLU T 29 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 78 removed outlier: 4.033A pdb=" N LEU T 44 " --> pdb=" O ASP T 40 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LYS T 66 " --> pdb=" O SER T 62 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE T 68 " --> pdb=" O THR T 64 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 20 Processing helix chain 'U' and resid 22 through 37 removed outlier: 4.283A pdb=" N THR U 28 " --> pdb=" O GLN U 24 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS U 37 " --> pdb=" O LYS U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 80 Processing helix chain 'V' and resid 132 through 147 removed outlier: 3.527A pdb=" N ASP V 136 " --> pdb=" O ALA V 132 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP V 147 " --> pdb=" O SER V 143 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 175 removed outlier: 3.521A pdb=" N TYR V 153 " --> pdb=" O TYR V 149 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY V 175 " --> pdb=" O LEU V 171 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 206 Processing helix chain 'V' and resid 227 through 239 Processing helix chain 'V' and resid 258 through 268 Processing helix chain 'V' and resid 269 through 272 Processing helix chain 'V' and resid 283 through 323 removed outlier: 4.133A pdb=" N TYR V 312 " --> pdb=" O LEU V 308 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER V 313 " --> pdb=" O THR V 309 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN V 314 " --> pdb=" O GLN V 310 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N SER V 317 " --> pdb=" O SER V 313 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU V 318 " --> pdb=" O ASN V 314 " (cutoff:3.500A) Processing helix chain 'V' and resid 326 through 331 Processing helix chain 'V' and resid 335 through 340 Processing helix chain 'W' and resid 7 through 37 removed outlier: 4.215A pdb=" N GLY W 19 " --> pdb=" O LYS W 15 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN W 22 " --> pdb=" O THR W 18 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 78 removed outlier: 3.775A pdb=" N LEU W 44 " --> pdb=" O ASP W 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE W 71 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP W 72 " --> pdb=" O PHE W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 147 removed outlier: 3.949A pdb=" N ASP X 136 " --> pdb=" O ALA X 132 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASP X 147 " --> pdb=" O SER X 143 " (cutoff:3.500A) Processing helix chain 'X' and resid 149 through 175 removed outlier: 3.759A pdb=" N GLY X 175 " --> pdb=" O LEU X 171 " (cutoff:3.500A) Processing helix chain 'X' and resid 191 through 206 Processing helix chain 'X' and resid 227 through 239 Processing helix chain 'X' and resid 258 through 269 Processing helix chain 'X' and resid 270 through 272 No H-bonds generated for 'chain 'X' and resid 270 through 272' Processing helix chain 'X' and resid 283 through 311 removed outlier: 3.708A pdb=" N ALA X 289 " --> pdb=" O ALA X 285 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 323 Processing helix chain 'X' and resid 326 through 334 removed outlier: 3.794A pdb=" N SER X 332 " --> pdb=" O SER X 328 " (cutoff:3.500A) Processing helix chain 'X' and resid 335 through 340 Processing sheet with id=AA1, first strand: chain 'F' and resid 178 through 180 removed outlier: 3.636A pdb=" N LEU F 179 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 245 through 248 removed outlier: 3.916A pdb=" N GLY F 251 " --> pdb=" O TYR F 248 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'O' and resid 178 through 181 removed outlier: 3.785A pdb=" N THR O 186 " --> pdb=" O GLY O 181 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'O' and resid 213 through 215 removed outlier: 3.897A pdb=" N PHE O 215 " --> pdb=" O VAL O 254 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 178 through 180 removed outlier: 3.920A pdb=" N LEU R 179 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 245 through 248 removed outlier: 4.025A pdb=" N GLY R 251 " --> pdb=" O TYR R 248 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'V' and resid 178 through 180 removed outlier: 3.614A pdb=" N LEU V 179 " --> pdb=" O LYS V 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 245 through 246 Processing sheet with id=AA9, first strand: chain 'X' and resid 178 through 181 removed outlier: 3.623A pdb=" N LEU X 179 " --> pdb=" O LYS X 188 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR X 186 " --> pdb=" O GLY X 181 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 245 through 248 removed outlier: 4.033A pdb=" N GLY X 251 " --> pdb=" O TYR X 248 " (cutoff:3.500A) 1524 hydrogen bonds defined for protein. 4512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.82 Time building geometry restraints manager: 8.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6046 1.34 - 1.45: 2762 1.45 - 1.57: 11189 1.57 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 20052 Sorted by residual: bond pdb=" CA LYS K 37 " pdb=" CB LYS K 37 " ideal model delta sigma weight residual 1.526 1.540 -0.013 9.30e-03 1.16e+04 2.05e+00 bond pdb=" CG1 ILE G 71 " pdb=" CD1 ILE G 71 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.62e+00 bond pdb=" CA LYS O 311 " pdb=" C LYS O 311 " ideal model delta sigma weight residual 1.523 1.539 -0.016 1.34e-02 5.57e+03 1.44e+00 bond pdb=" CG1 ILE A 71 " pdb=" CD1 ILE A 71 " ideal model delta sigma weight residual 1.513 1.467 0.046 3.90e-02 6.57e+02 1.40e+00 bond pdb=" CB ASN W 63 " pdb=" CG ASN W 63 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.28e+00 ... (remaining 20047 not shown) Histogram of bond angle deviations from ideal: 98.41 - 106.14: 318 106.14 - 113.86: 11470 113.86 - 121.58: 11502 121.58 - 129.31: 3869 129.31 - 137.03: 84 Bond angle restraints: 27243 Sorted by residual: angle pdb=" C PHE R 215 " pdb=" N PRO R 216 " pdb=" CA PRO R 216 " ideal model delta sigma weight residual 127.00 137.03 -10.03 2.40e+00 1.74e-01 1.75e+01 angle pdb=" N LEU J 43 " pdb=" CA LEU J 43 " pdb=" C LEU J 43 " ideal model delta sigma weight residual 114.04 108.93 5.11 1.24e+00 6.50e-01 1.70e+01 angle pdb=" C PHE R 215 " pdb=" N PRO R 216 " pdb=" CD PRO R 216 " ideal model delta sigma weight residual 120.60 112.51 8.09 2.20e+00 2.07e-01 1.35e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 114.92 111.15 3.77 1.19e+00 7.06e-01 1.00e+01 angle pdb=" N VAL R 325 " pdb=" CA VAL R 325 " pdb=" C VAL R 325 " ideal model delta sigma weight residual 112.04 107.62 4.42 1.40e+00 5.10e-01 9.98e+00 ... (remaining 27238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 10932 17.96 - 35.91: 944 35.91 - 53.87: 176 53.87 - 71.83: 44 71.83 - 89.78: 17 Dihedral angle restraints: 12113 sinusoidal: 4622 harmonic: 7491 Sorted by residual: dihedral pdb=" CA LYS O 311 " pdb=" C LYS O 311 " pdb=" N TYR O 312 " pdb=" CA TYR O 312 " ideal model delta harmonic sigma weight residual 180.00 159.80 20.20 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA GLU V 281 " pdb=" C GLU V 281 " pdb=" N MET V 282 " pdb=" CA MET V 282 " ideal model delta harmonic sigma weight residual 180.00 -160.02 -19.98 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA GLU F 228 " pdb=" C GLU F 228 " pdb=" N ALA F 229 " pdb=" CA ALA F 229 " ideal model delta harmonic sigma weight residual -180.00 -162.47 -17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 12110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2054 0.035 - 0.070: 794 0.070 - 0.104: 224 0.104 - 0.139: 41 0.139 - 0.174: 6 Chirality restraints: 3119 Sorted by residual: chirality pdb=" CA GLU P 29 " pdb=" N GLU P 29 " pdb=" C GLU P 29 " pdb=" CB GLU P 29 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA GLN O 266 " pdb=" N GLN O 266 " pdb=" C GLN O 266 " pdb=" CB GLN O 266 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA GLU L 29 " pdb=" N GLU L 29 " pdb=" C GLU L 29 " pdb=" CB GLU L 29 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 3116 not shown) Planarity restraints: 3524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 177 " 0.018 2.00e-02 2.50e+03 1.58e-02 6.24e+00 pdb=" CG TRP X 177 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP X 177 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP X 177 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP X 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 177 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 177 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP X 177 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR P 25 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.43e+00 pdb=" C THR P 25 " 0.036 2.00e-02 2.50e+03 pdb=" O THR P 25 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN P 26 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 164 " 0.021 2.00e-02 2.50e+03 1.38e-02 3.79e+00 pdb=" CG TYR V 164 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR V 164 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR V 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR V 164 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR V 164 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR V 164 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR V 164 " 0.003 2.00e-02 2.50e+03 ... (remaining 3521 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 310 2.65 - 3.21: 20461 3.21 - 3.78: 33044 3.78 - 4.34: 41246 4.34 - 4.90: 67330 Nonbonded interactions: 162391 Sorted by model distance: nonbonded pdb=" OD1 ASP D 17 " pdb=" OH TYR D 57 " model vdw 2.090 2.440 nonbonded pdb=" O SER O 328 " pdb=" OG SER O 332 " model vdw 2.095 2.440 nonbonded pdb=" OH TYR I 54 " pdb=" OD2 ASP V 131 " model vdw 2.136 2.440 nonbonded pdb=" O SER R 328 " pdb=" OG SER R 332 " model vdw 2.159 2.440 nonbonded pdb=" OD1 ASN V 314 " pdb=" ND2 ASN X 316 " model vdw 2.176 2.520 ... (remaining 162386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'B' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'C' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'D' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = (chain 'J' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'K' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'L' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'M' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'N' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'P' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'Q' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = (chain 'S' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'T' selection = (chain 'U' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)))) selection = chain 'W' } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'R' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.450 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 50.600 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6931 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 : 0.003 0.050 20052 Z= 0.221 Angle : 0.649 10.032 27243 Z= 0.359 Chirality : 0.040 0.174 3119 Planarity : 0.003 0.040 3524 Dihedral : 14.566 89.782 7259 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.07 (0.17), residues: 2487 helix: 1.59 (0.12), residues: 1813 sheet: -1.31 (0.58), residues: 75 loop : -1.76 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP X 177 PHE 0.025 0.002 PHE P 16 TYR 0.032 0.002 TYR V 164 ARG 0.009 0.001 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 866 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 VAL cc_start: 0.9280 (t) cc_final: 0.8823 (p) REVERT: A 31 LEU cc_start: 0.9182 (mt) cc_final: 0.8968 (mm) REVERT: A 48 GLN cc_start: 0.7157 (tm-30) cc_final: 0.6837 (tm-30) REVERT: B 28 THR cc_start: 0.8683 (m) cc_final: 0.8376 (p) REVERT: B 58 ARG cc_start: 0.8420 (mmt180) cc_final: 0.8025 (mmt90) REVERT: C 70 ASP cc_start: 0.7141 (m-30) cc_final: 0.6932 (m-30) REVERT: D 16 PHE cc_start: 0.8560 (t80) cc_final: 0.7892 (t80) REVERT: E 22 ASN cc_start: 0.7932 (p0) cc_final: 0.7152 (t0) REVERT: E 26 GLN cc_start: 0.8128 (mt0) cc_final: 0.6962 (mt0) REVERT: F 215 PHE cc_start: 0.7062 (t80) cc_final: 0.6521 (t80) REVERT: F 266 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7605 (pp30) REVERT: G 20 VAL cc_start: 0.8241 (t) cc_final: 0.7948 (t) REVERT: G 69 LYS cc_start: 0.7819 (tmtt) cc_final: 0.7472 (tptm) REVERT: H 32 ASP cc_start: 0.7165 (p0) cc_final: 0.6871 (p0) REVERT: I 17 ASP cc_start: 0.7440 (m-30) cc_final: 0.5992 (t70) REVERT: I 31 LEU cc_start: 0.7570 (tp) cc_final: 0.6907 (tp) REVERT: I 68 PHE cc_start: 0.7625 (m-80) cc_final: 0.6949 (m-10) REVERT: J 5 TRP cc_start: 0.8384 (t60) cc_final: 0.8178 (t60) REVERT: J 66 LYS cc_start: 0.8110 (tptm) cc_final: 0.7307 (tptm) REVERT: J 69 LYS cc_start: 0.8480 (tmtt) cc_final: 0.8120 (tptt) REVERT: K 72 ASP cc_start: 0.7319 (m-30) cc_final: 0.6512 (m-30) REVERT: K 79 PHE cc_start: 0.7069 (m-10) cc_final: 0.6811 (m-10) REVERT: L 11 ASP cc_start: 0.8012 (t0) cc_final: 0.7601 (m-30) REVERT: L 21 ASP cc_start: 0.5444 (p0) cc_final: 0.5193 (p0) REVERT: L 22 ASN cc_start: 0.8077 (p0) cc_final: 0.7593 (p0) REVERT: L 25 THR cc_start: 0.8822 (m) cc_final: 0.8432 (m) REVERT: L 63 ASN cc_start: 0.7515 (m-40) cc_final: 0.7249 (m110) REVERT: M 10 ASP cc_start: 0.7794 (t0) cc_final: 0.7530 (t70) REVERT: N 5 TRP cc_start: 0.3194 (t60) cc_final: 0.2703 (p90) REVERT: N 17 ASP cc_start: 0.7345 (m-30) cc_final: 0.6909 (m-30) REVERT: N 31 LEU cc_start: 0.9302 (tp) cc_final: 0.9054 (tp) REVERT: N 58 ARG cc_start: 0.4283 (mtt180) cc_final: 0.3385 (mmt180) REVERT: N 59 ASN cc_start: 0.8082 (t0) cc_final: 0.7843 (t0) REVERT: N 62 SER cc_start: 0.8948 (t) cc_final: 0.8704 (t) REVERT: N 66 LYS cc_start: 0.8215 (tmtt) cc_final: 0.7786 (ttpp) REVERT: O 147 ASP cc_start: 0.7028 (p0) cc_final: 0.6710 (t0) REVERT: O 260 PRO cc_start: 0.9254 (Cg_exo) cc_final: 0.8703 (Cg_endo) REVERT: O 287 TYR cc_start: 0.7868 (t80) cc_final: 0.7442 (t80) REVERT: O 288 GLN cc_start: 0.7700 (mm110) cc_final: 0.7335 (pt0) REVERT: O 326 LEU cc_start: 0.7731 (pp) cc_final: 0.7090 (mt) REVERT: P 24 GLN cc_start: 0.8427 (pm20) cc_final: 0.8123 (mp10) REVERT: P 28 THR cc_start: 0.8833 (m) cc_final: 0.8271 (m) REVERT: P 47 TYR cc_start: 0.8143 (t80) cc_final: 0.7523 (t80) REVERT: P 54 TYR cc_start: 0.7292 (t80) cc_final: 0.6974 (t80) REVERT: P 66 LYS cc_start: 0.7849 (tptm) cc_final: 0.6756 (tptt) REVERT: P 70 ASP cc_start: 0.7271 (m-30) cc_final: 0.6999 (m-30) REVERT: Q 10 ASP cc_start: 0.7731 (m-30) cc_final: 0.7459 (m-30) REVERT: Q 17 ASP cc_start: 0.7905 (t0) cc_final: 0.7554 (t0) REVERT: Q 34 LEU cc_start: 0.8829 (tp) cc_final: 0.8624 (tp) REVERT: Q 57 TYR cc_start: 0.6781 (t80) cc_final: 0.6578 (t80) REVERT: Q 67 VAL cc_start: 0.8971 (p) cc_final: 0.8684 (m) REVERT: R 171 LEU cc_start: 0.7924 (tp) cc_final: 0.7723 (tt) REVERT: R 267 ASP cc_start: 0.7780 (m-30) cc_final: 0.7527 (t0) REVERT: T 23 LEU cc_start: 0.8113 (mt) cc_final: 0.7861 (mp) REVERT: T 47 TYR cc_start: 0.7774 (t80) cc_final: 0.7552 (t80) REVERT: T 52 SER cc_start: 0.9050 (t) cc_final: 0.8474 (p) REVERT: U 15 LYS cc_start: 0.7569 (tptp) cc_final: 0.7018 (tmtt) REVERT: V 171 LEU cc_start: 0.7861 (tt) cc_final: 0.7656 (tt) REVERT: V 214 LEU cc_start: 0.6710 (mt) cc_final: 0.6400 (mt) REVERT: V 269 ASP cc_start: 0.7588 (t0) cc_final: 0.7276 (t0) REVERT: W 28 THR cc_start: 0.6176 (m) cc_final: 0.5123 (p) REVERT: W 71 ILE cc_start: 0.9113 (pt) cc_final: 0.8678 (pt) REVERT: X 260 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: X 291 GLN cc_start: 0.8069 (mm-40) cc_final: 0.7769 (mm-40) REVERT: X 308 LEU cc_start: 0.7467 (mm) cc_final: 0.5676 (tp) outliers start: 0 outliers final: 0 residues processed: 866 average time/residue: 0.2914 time to fit residues: 385.9842 Evaluate side-chains 518 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 518 time to evaluate : 2.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.7980 chunk 180 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 186 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 ASN B 78 ASN ** D 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 59 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 63 ASN N 24 GLN ** N 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 ASN ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 77 GLN Q 48 GLN R 196 ASN ** R 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 233 GLN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 199 ASN ** V 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20052 Z= 0.203 Angle : 0.640 11.541 27243 Z= 0.327 Chirality : 0.041 0.222 3119 Planarity : 0.004 0.058 3524 Dihedral : 4.354 27.160 2693 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.29 % Allowed : 17.06 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.20 (0.17), residues: 2487 helix: 1.58 (0.12), residues: 1859 sheet: -1.31 (0.58), residues: 75 loop : -1.60 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 234 PHE 0.018 0.001 PHE F 215 TYR 0.036 0.002 TYR J 57 ARG 0.007 0.001 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 580 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8551 (tmmt) cc_final: 0.8260 (ttpt) REVERT: A 72 ASP cc_start: 0.7696 (OUTLIER) cc_final: 0.7404 (t0) REVERT: B 28 THR cc_start: 0.8668 (m) cc_final: 0.8378 (p) REVERT: B 33 LYS cc_start: 0.9002 (tppt) cc_final: 0.8704 (mtmt) REVERT: B 54 TYR cc_start: 0.8472 (t80) cc_final: 0.8101 (t80) REVERT: C 53 GLU cc_start: 0.7147 (tt0) cc_final: 0.6776 (mt-10) REVERT: C 66 LYS cc_start: 0.8349 (tptp) cc_final: 0.7545 (tptm) REVERT: C 70 ASP cc_start: 0.7547 (m-30) cc_final: 0.7024 (m-30) REVERT: C 71 ILE cc_start: 0.9022 (mt) cc_final: 0.8769 (mt) REVERT: D 61 GLN cc_start: 0.8224 (pp30) cc_final: 0.7757 (pp30) REVERT: E 11 ASP cc_start: 0.8716 (m-30) cc_final: 0.7472 (m-30) REVERT: F 214 LEU cc_start: 0.8048 (mt) cc_final: 0.7835 (mt) REVERT: F 215 PHE cc_start: 0.7159 (t80) cc_final: 0.6632 (t80) REVERT: G 20 VAL cc_start: 0.8099 (t) cc_final: 0.7851 (t) REVERT: G 69 LYS cc_start: 0.8036 (tmtt) cc_final: 0.7709 (tptm) REVERT: H 76 ILE cc_start: 0.8094 (pt) cc_final: 0.7754 (pt) REVERT: I 17 ASP cc_start: 0.7423 (m-30) cc_final: 0.5595 (t70) REVERT: J 59 ASN cc_start: 0.8261 (m110) cc_final: 0.7671 (m110) REVERT: J 66 LYS cc_start: 0.8051 (tptm) cc_final: 0.7264 (tppt) REVERT: J 69 LYS cc_start: 0.8479 (tmtt) cc_final: 0.7985 (tppt) REVERT: J 70 ASP cc_start: 0.7415 (m-30) cc_final: 0.6785 (m-30) REVERT: K 61 GLN cc_start: 0.9082 (tt0) cc_final: 0.8627 (tp40) REVERT: L 11 ASP cc_start: 0.8143 (t0) cc_final: 0.7743 (m-30) REVERT: L 21 ASP cc_start: 0.6837 (p0) cc_final: 0.6284 (p0) REVERT: L 25 THR cc_start: 0.8880 (m) cc_final: 0.8618 (m) REVERT: M 10 ASP cc_start: 0.7679 (t0) cc_final: 0.7469 (t0) REVERT: M 31 LEU cc_start: 0.8484 (tp) cc_final: 0.8229 (mt) REVERT: N 59 ASN cc_start: 0.7818 (t0) cc_final: 0.7580 (t0) REVERT: N 66 LYS cc_start: 0.7909 (tmtt) cc_final: 0.7618 (tmtt) REVERT: O 288 GLN cc_start: 0.7676 (mm110) cc_final: 0.7325 (pt0) REVERT: O 294 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5977 (t80) REVERT: O 301 MET cc_start: 0.6949 (mmp) cc_final: 0.6559 (mmt) REVERT: O 316 ASN cc_start: 0.8085 (m-40) cc_final: 0.7592 (m-40) REVERT: P 10 ASP cc_start: 0.8143 (t0) cc_final: 0.7887 (t0) REVERT: P 27 VAL cc_start: 0.9283 (m) cc_final: 0.9021 (m) REVERT: P 48 GLN cc_start: 0.7516 (pp30) cc_final: 0.7192 (pp30) REVERT: P 70 ASP cc_start: 0.7591 (m-30) cc_final: 0.7381 (m-30) REVERT: P 72 ASP cc_start: 0.8060 (m-30) cc_final: 0.6998 (t0) REVERT: Q 16 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7504 (t80) REVERT: Q 61 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7222 (mt0) REVERT: Q 67 VAL cc_start: 0.8959 (p) cc_final: 0.8727 (m) REVERT: Q 75 ILE cc_start: 0.7416 (tt) cc_final: 0.7093 (tp) REVERT: R 145 ILE cc_start: 0.9118 (pt) cc_final: 0.8899 (mt) REVERT: R 267 ASP cc_start: 0.7799 (m-30) cc_final: 0.7389 (t0) REVERT: T 52 SER cc_start: 0.8436 (t) cc_final: 0.8155 (p) REVERT: U 15 LYS cc_start: 0.7553 (tptp) cc_final: 0.7011 (tmtt) REVERT: U 16 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7687 (t80) REVERT: V 214 LEU cc_start: 0.6923 (mt) cc_final: 0.6561 (mt) REVERT: V 282 MET cc_start: 0.6040 (tpp) cc_final: 0.5696 (tpp) REVERT: W 28 THR cc_start: 0.6234 (m) cc_final: 0.5790 (p) REVERT: X 277 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6378 (m-30) REVERT: X 298 GLU cc_start: 0.7317 (tm-30) cc_final: 0.7003 (tm-30) outliers start: 71 outliers final: 37 residues processed: 614 average time/residue: 0.2788 time to fit residues: 271.1019 Evaluate side-chains 523 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 480 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASP Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain O residue 142 ILE Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 16 PHE Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain W residue 61 GLN Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 277 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.3980 chunk 67 optimal weight: 2.9990 chunk 179 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 216 optimal weight: 0.5980 chunk 233 optimal weight: 3.9990 chunk 192 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 26 GLN ** D 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN I 55 ASN ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 239 ASN ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 141 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20052 Z= 0.208 Angle : 0.607 9.753 27243 Z= 0.315 Chirality : 0.041 0.164 3119 Planarity : 0.004 0.040 3524 Dihedral : 4.258 25.327 2693 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.45 % Allowed : 18.82 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.27 (0.17), residues: 2487 helix: 1.55 (0.12), residues: 1917 sheet: -1.60 (0.78), residues: 50 loop : -1.53 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 234 PHE 0.024 0.002 PHE V 167 TYR 0.029 0.002 TYR H 54 ARG 0.007 0.000 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 555 time to evaluate : 3.083 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: A 16 PHE cc_start: 0.8371 (OUTLIER) cc_final: 0.7143 (t80) REVERT: A 48 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7834 (tm-30) REVERT: A 66 LYS cc_start: 0.8635 (tmmt) cc_final: 0.8088 (ttpt) REVERT: A 72 ASP cc_start: 0.7900 (OUTLIER) cc_final: 0.7565 (t0) REVERT: B 16 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6649 (m-80) REVERT: B 28 THR cc_start: 0.8552 (m) cc_final: 0.8340 (p) REVERT: B 33 LYS cc_start: 0.9001 (tppt) cc_final: 0.8610 (mtpt) REVERT: B 54 TYR cc_start: 0.8660 (t80) cc_final: 0.8354 (t80) REVERT: C 34 LEU cc_start: 0.8170 (tp) cc_final: 0.7879 (tt) REVERT: C 53 GLU cc_start: 0.7701 (tt0) cc_final: 0.7296 (mt-10) REVERT: C 66 LYS cc_start: 0.8502 (tptp) cc_final: 0.7939 (tptm) REVERT: C 70 ASP cc_start: 0.7668 (m-30) cc_final: 0.7190 (m-30) REVERT: C 78 ASN cc_start: 0.8068 (m110) cc_final: 0.7861 (m-40) REVERT: D 20 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8262 (p) REVERT: D 61 GLN cc_start: 0.8049 (pp30) cc_final: 0.7820 (pp30) REVERT: D 66 LYS cc_start: 0.8590 (tmmt) cc_final: 0.8298 (ttpp) REVERT: D 69 LYS cc_start: 0.8587 (tptt) cc_final: 0.8146 (tptt) REVERT: D 72 ASP cc_start: 0.8300 (m-30) cc_final: 0.8064 (m-30) REVERT: E 11 ASP cc_start: 0.8863 (m-30) cc_final: 0.7532 (m-30) REVERT: E 23 LEU cc_start: 0.8868 (tt) cc_final: 0.7746 (tt) REVERT: E 26 GLN cc_start: 0.8397 (mt0) cc_final: 0.7584 (mp10) REVERT: E 53 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7623 (tm-30) REVERT: F 214 LEU cc_start: 0.8290 (mt) cc_final: 0.8052 (mt) REVERT: F 215 PHE cc_start: 0.7390 (t80) cc_final: 0.7071 (t80) REVERT: F 287 TYR cc_start: 0.6485 (t80) cc_final: 0.6282 (t80) REVERT: G 69 LYS cc_start: 0.8386 (tmtt) cc_final: 0.8150 (tptm) REVERT: G 76 ILE cc_start: 0.7521 (mm) cc_final: 0.7175 (mm) REVERT: I 17 ASP cc_start: 0.7736 (m-30) cc_final: 0.5827 (t70) REVERT: J 59 ASN cc_start: 0.8177 (m110) cc_final: 0.7843 (m110) REVERT: J 66 LYS cc_start: 0.8183 (tptm) cc_final: 0.7057 (tppt) REVERT: J 69 LYS cc_start: 0.8610 (tmtt) cc_final: 0.8033 (tppt) REVERT: J 70 ASP cc_start: 0.7556 (m-30) cc_final: 0.6790 (m-30) REVERT: L 21 ASP cc_start: 0.7384 (p0) cc_final: 0.7055 (p0) REVERT: M 10 ASP cc_start: 0.7936 (t0) cc_final: 0.7595 (t0) REVERT: M 32 ASP cc_start: 0.8166 (t0) cc_final: 0.7922 (t70) REVERT: M 51 LEU cc_start: 0.8873 (tt) cc_final: 0.8588 (tt) REVERT: M 65 VAL cc_start: 0.8580 (t) cc_final: 0.8237 (p) REVERT: N 17 ASP cc_start: 0.8164 (m-30) cc_final: 0.7711 (m-30) REVERT: N 24 GLN cc_start: 0.7775 (pm20) cc_final: 0.7377 (tp40) REVERT: N 59 ASN cc_start: 0.8045 (t0) cc_final: 0.7774 (t0) REVERT: N 66 LYS cc_start: 0.8097 (tmtt) cc_final: 0.7740 (tmtt) REVERT: O 169 ASP cc_start: 0.7623 (t0) cc_final: 0.7233 (m-30) REVERT: O 261 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (mp) REVERT: O 288 GLN cc_start: 0.7722 (mm110) cc_final: 0.7364 (pt0) REVERT: O 301 MET cc_start: 0.7143 (mmp) cc_final: 0.6805 (mmt) REVERT: O 316 ASN cc_start: 0.8181 (m-40) cc_final: 0.7686 (m-40) REVERT: P 27 VAL cc_start: 0.9284 (m) cc_final: 0.8998 (m) REVERT: P 47 TYR cc_start: 0.7015 (t80) cc_final: 0.6335 (t80) REVERT: P 48 GLN cc_start: 0.7780 (pp30) cc_final: 0.7319 (pp30) REVERT: P 54 TYR cc_start: 0.7699 (t80) cc_final: 0.7436 (t80) REVERT: P 66 LYS cc_start: 0.7753 (tptm) cc_final: 0.6593 (tptt) REVERT: P 72 ASP cc_start: 0.8048 (m-30) cc_final: 0.7677 (m-30) REVERT: Q 17 ASP cc_start: 0.7280 (t0) cc_final: 0.7060 (t0) REVERT: R 160 TYR cc_start: 0.5149 (t80) cc_final: 0.4808 (t80) REVERT: R 267 ASP cc_start: 0.8077 (m-30) cc_final: 0.7539 (t0) REVERT: T 11 ASP cc_start: 0.7063 (m-30) cc_final: 0.6729 (m-30) REVERT: T 23 LEU cc_start: 0.8012 (mp) cc_final: 0.7477 (mt) REVERT: T 52 SER cc_start: 0.8958 (t) cc_final: 0.8592 (p) REVERT: U 15 LYS cc_start: 0.7454 (tptp) cc_final: 0.6851 (tmtt) REVERT: U 16 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7409 (t80) REVERT: U 43 LEU cc_start: 0.7689 (mt) cc_final: 0.7282 (mt) REVERT: V 150 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7599 (mp) REVERT: V 215 PHE cc_start: 0.7605 (t80) cc_final: 0.7357 (t80) REVERT: V 269 ASP cc_start: 0.8328 (t0) cc_final: 0.7968 (t0) REVERT: V 282 MET cc_start: 0.6606 (tpp) cc_final: 0.6191 (tpp) REVERT: V 300 ASN cc_start: 0.7793 (OUTLIER) cc_final: 0.7433 (t0) REVERT: X 189 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8272 (pp) REVERT: X 298 GLU cc_start: 0.7737 (tm-30) cc_final: 0.7215 (tm-30) outliers start: 96 outliers final: 52 residues processed: 609 average time/residue: 0.2818 time to fit residues: 271.5656 Evaluate side-chains 553 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 492 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 155 ASN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 291 GLN Chi-restraints excluded: chain P residue 13 SER Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 32 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 153 TYR Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 189 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 10.0000 chunk 162 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 0.9990 chunk 230 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 GLN F 141 ASN ** F 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** K 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 48 GLN Q 63 ASN ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 284 ASN V 300 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 297 GLN ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20052 Z= 0.186 Angle : 0.587 9.624 27243 Z= 0.299 Chirality : 0.040 0.215 3119 Planarity : 0.003 0.046 3524 Dihedral : 4.122 21.851 2693 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 4.40 % Allowed : 21.74 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.49 (0.17), residues: 2487 helix: 1.77 (0.12), residues: 1899 sheet: -1.77 (0.76), residues: 50 loop : -1.58 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP X 177 PHE 0.015 0.001 PHE R 215 TYR 0.026 0.002 TYR H 54 ARG 0.006 0.000 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 552 time to evaluate : 2.271 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: A 16 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7767 (t80) REVERT: A 66 LYS cc_start: 0.8786 (tmmt) cc_final: 0.8131 (tptp) REVERT: A 72 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8210 (t0) REVERT: B 11 ASP cc_start: 0.8798 (m-30) cc_final: 0.8572 (m-30) REVERT: B 16 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: B 28 THR cc_start: 0.8581 (m) cc_final: 0.7191 (p) REVERT: B 33 LYS cc_start: 0.8906 (tppt) cc_final: 0.8573 (mtpt) REVERT: C 34 LEU cc_start: 0.8166 (tp) cc_final: 0.7911 (tt) REVERT: C 53 GLU cc_start: 0.7719 (tt0) cc_final: 0.7344 (mt-10) REVERT: C 66 LYS cc_start: 0.8621 (tptp) cc_final: 0.7962 (tppt) REVERT: C 70 ASP cc_start: 0.7682 (m-30) cc_final: 0.7190 (m-30) REVERT: D 69 LYS cc_start: 0.8817 (tptt) cc_final: 0.8316 (tptt) REVERT: E 11 ASP cc_start: 0.8898 (m-30) cc_final: 0.7798 (m-30) REVERT: E 23 LEU cc_start: 0.8860 (tt) cc_final: 0.8397 (tt) REVERT: E 26 GLN cc_start: 0.8429 (mt0) cc_final: 0.7570 (mp10) REVERT: E 53 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 68 PHE cc_start: 0.8740 (m-10) cc_final: 0.8498 (m-10) REVERT: F 141 ASN cc_start: 0.8035 (OUTLIER) cc_final: 0.7507 (m-40) REVERT: F 214 LEU cc_start: 0.7950 (mt) cc_final: 0.7690 (mt) REVERT: F 215 PHE cc_start: 0.7403 (t80) cc_final: 0.7188 (t80) REVERT: F 334 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9177 (tt) REVERT: G 69 LYS cc_start: 0.8433 (tmtt) cc_final: 0.7930 (tptm) REVERT: G 72 ASP cc_start: 0.8886 (OUTLIER) cc_final: 0.7770 (p0) REVERT: I 17 ASP cc_start: 0.7714 (m-30) cc_final: 0.5852 (t70) REVERT: I 76 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8044 (tp) REVERT: J 59 ASN cc_start: 0.8409 (m-40) cc_final: 0.8031 (m110) REVERT: J 66 LYS cc_start: 0.8397 (tptm) cc_final: 0.6845 (tppt) REVERT: J 69 LYS cc_start: 0.8789 (tmtt) cc_final: 0.8190 (tppt) REVERT: J 70 ASP cc_start: 0.7579 (m-30) cc_final: 0.6744 (m-30) REVERT: K 10 ASP cc_start: 0.8186 (m-30) cc_final: 0.6805 (t0) REVERT: K 57 TYR cc_start: 0.8506 (t80) cc_final: 0.7975 (t80) REVERT: L 29 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: M 10 ASP cc_start: 0.8140 (t0) cc_final: 0.7844 (t0) REVERT: M 65 VAL cc_start: 0.8573 (t) cc_final: 0.8229 (p) REVERT: N 17 ASP cc_start: 0.8259 (m-30) cc_final: 0.7785 (m-30) REVERT: N 24 GLN cc_start: 0.7677 (pm20) cc_final: 0.6972 (tp40) REVERT: N 31 LEU cc_start: 0.9004 (tp) cc_final: 0.8692 (mp) REVERT: N 34 LEU cc_start: 0.8921 (mt) cc_final: 0.8718 (mt) REVERT: N 59 ASN cc_start: 0.7872 (t0) cc_final: 0.7507 (t0) REVERT: N 66 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7768 (tmtt) REVERT: O 161 THR cc_start: 0.8563 (m) cc_final: 0.8325 (m) REVERT: O 169 ASP cc_start: 0.7742 (t0) cc_final: 0.7357 (m-30) REVERT: O 288 GLN cc_start: 0.7750 (mm110) cc_final: 0.7363 (pt0) REVERT: O 294 PHE cc_start: 0.7517 (OUTLIER) cc_final: 0.6230 (t80) REVERT: O 316 ASN cc_start: 0.8444 (m-40) cc_final: 0.7870 (m110) REVERT: P 47 TYR cc_start: 0.7390 (t80) cc_final: 0.6942 (t80) REVERT: P 48 GLN cc_start: 0.8060 (pp30) cc_final: 0.7627 (pp30) REVERT: P 54 TYR cc_start: 0.7828 (t80) cc_final: 0.7392 (t80) REVERT: P 66 LYS cc_start: 0.7750 (tptm) cc_final: 0.7121 (tptt) REVERT: P 72 ASP cc_start: 0.8302 (m-30) cc_final: 0.8098 (m-30) REVERT: Q 57 TYR cc_start: 0.6785 (t80) cc_final: 0.6527 (t80) REVERT: Q 58 ARG cc_start: 0.8524 (tpt170) cc_final: 0.8082 (mtt180) REVERT: Q 75 ILE cc_start: 0.7396 (tt) cc_final: 0.7088 (tp) REVERT: R 215 PHE cc_start: 0.8036 (t80) cc_final: 0.7770 (t80) REVERT: T 11 ASP cc_start: 0.7097 (m-30) cc_final: 0.6782 (m-30) REVERT: T 23 LEU cc_start: 0.8138 (mp) cc_final: 0.7656 (mt) REVERT: T 52 SER cc_start: 0.9037 (t) cc_final: 0.8647 (p) REVERT: U 15 LYS cc_start: 0.7546 (tptp) cc_final: 0.6930 (tmtt) REVERT: U 16 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7412 (t80) REVERT: U 43 LEU cc_start: 0.7549 (mt) cc_final: 0.7132 (mt) REVERT: V 150 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7712 (mp) REVERT: V 215 PHE cc_start: 0.7733 (t80) cc_final: 0.7390 (t80) REVERT: V 282 MET cc_start: 0.6835 (tpp) cc_final: 0.6501 (tpp) REVERT: V 298 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8537 (mm-30) REVERT: V 300 ASN cc_start: 0.8051 (OUTLIER) cc_final: 0.7798 (t0) REVERT: V 340 PHE cc_start: 0.7498 (m-80) cc_final: 0.7278 (m-10) REVERT: X 189 LEU cc_start: 0.8520 (tt) cc_final: 0.8304 (pp) REVERT: X 298 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7389 (tm-30) outliers start: 95 outliers final: 59 residues processed: 609 average time/residue: 0.2865 time to fit residues: 276.7466 Evaluate side-chains 566 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 495 time to evaluate : 2.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 141 ASN Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 76 ILE Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 66 LYS Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain V residue 301 MET Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 171 optimal weight: 1.9990 chunk 94 optimal weight: 0.0000 chunk 196 optimal weight: 4.9990 chunk 159 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 ASN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20052 Z= 0.165 Angle : 0.589 9.293 27243 Z= 0.298 Chirality : 0.039 0.191 3119 Planarity : 0.003 0.044 3524 Dihedral : 4.079 19.425 2693 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.45 % Allowed : 23.88 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.59 (0.17), residues: 2487 helix: 1.86 (0.12), residues: 1886 sheet: -1.79 (0.76), residues: 50 loop : -1.54 (0.26), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 177 PHE 0.013 0.001 PHE O 167 TYR 0.024 0.002 TYR H 54 ARG 0.006 0.000 ARG S 58 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 529 time to evaluate : 2.438 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: A 16 PHE cc_start: 0.8582 (OUTLIER) cc_final: 0.7955 (t80) REVERT: A 66 LYS cc_start: 0.8862 (tmmt) cc_final: 0.8285 (tptp) REVERT: A 72 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.8227 (t0) REVERT: A 78 ASN cc_start: 0.7341 (m110) cc_final: 0.7077 (m-40) REVERT: B 11 ASP cc_start: 0.8891 (m-30) cc_final: 0.8552 (m-30) REVERT: B 28 THR cc_start: 0.8419 (m) cc_final: 0.7965 (p) REVERT: C 33 LYS cc_start: 0.8677 (mmtm) cc_final: 0.8475 (mmtm) REVERT: C 34 LEU cc_start: 0.8229 (tp) cc_final: 0.7975 (tt) REVERT: C 53 GLU cc_start: 0.7825 (tt0) cc_final: 0.7451 (mt-10) REVERT: C 54 TYR cc_start: 0.8776 (t80) cc_final: 0.8456 (t80) REVERT: C 66 LYS cc_start: 0.8512 (tptp) cc_final: 0.7906 (tppt) REVERT: C 70 ASP cc_start: 0.7679 (m-30) cc_final: 0.7191 (m-30) REVERT: D 20 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8318 (p) REVERT: D 69 LYS cc_start: 0.8925 (tptt) cc_final: 0.8332 (tptt) REVERT: E 11 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.7950 (m-30) REVERT: E 23 LEU cc_start: 0.8715 (tt) cc_final: 0.7582 (tt) REVERT: E 26 GLN cc_start: 0.8374 (mt0) cc_final: 0.7457 (mp10) REVERT: E 53 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7730 (tm-30) REVERT: E 76 ILE cc_start: 0.8791 (pt) cc_final: 0.8466 (mm) REVERT: F 141 ASN cc_start: 0.7965 (t0) cc_final: 0.7527 (m-40) REVERT: F 214 LEU cc_start: 0.7952 (mt) cc_final: 0.7720 (mt) REVERT: F 215 PHE cc_start: 0.7383 (t80) cc_final: 0.7151 (t80) REVERT: F 318 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6476 (tt) REVERT: G 69 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8125 (tptm) REVERT: G 72 ASP cc_start: 0.8913 (OUTLIER) cc_final: 0.7940 (p0) REVERT: I 17 ASP cc_start: 0.7270 (m-30) cc_final: 0.5521 (t70) REVERT: J 59 ASN cc_start: 0.8255 (m-40) cc_final: 0.7367 (m-40) REVERT: J 66 LYS cc_start: 0.8368 (tptm) cc_final: 0.6732 (tppt) REVERT: J 69 LYS cc_start: 0.8878 (tmtt) cc_final: 0.8226 (tppt) REVERT: J 70 ASP cc_start: 0.7079 (m-30) cc_final: 0.6396 (m-30) REVERT: K 10 ASP cc_start: 0.8151 (m-30) cc_final: 0.6829 (t0) REVERT: K 57 TYR cc_start: 0.8435 (t80) cc_final: 0.7657 (t80) REVERT: M 8 TYR cc_start: 0.7762 (t80) cc_final: 0.6272 (m-80) REVERT: M 10 ASP cc_start: 0.8151 (t0) cc_final: 0.7834 (t0) REVERT: M 23 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8123 (mp) REVERT: M 65 VAL cc_start: 0.8569 (t) cc_final: 0.8201 (p) REVERT: N 17 ASP cc_start: 0.8271 (m-30) cc_final: 0.7783 (m-30) REVERT: N 24 GLN cc_start: 0.7470 (pm20) cc_final: 0.7211 (tp-100) REVERT: N 59 ASN cc_start: 0.7840 (t0) cc_final: 0.7437 (t0) REVERT: N 66 LYS cc_start: 0.8176 (tmtt) cc_final: 0.7873 (tmtt) REVERT: O 169 ASP cc_start: 0.7446 (t0) cc_final: 0.7116 (m-30) REVERT: O 288 GLN cc_start: 0.7750 (mm110) cc_final: 0.7398 (pt0) REVERT: O 294 PHE cc_start: 0.7115 (OUTLIER) cc_final: 0.5897 (t80) REVERT: O 316 ASN cc_start: 0.8459 (m-40) cc_final: 0.8110 (m110) REVERT: O 322 LEU cc_start: 0.8802 (tp) cc_final: 0.8531 (tp) REVERT: P 48 GLN cc_start: 0.8135 (pp30) cc_final: 0.7692 (pp30) REVERT: P 54 TYR cc_start: 0.7937 (t80) cc_final: 0.7494 (t80) REVERT: P 72 ASP cc_start: 0.8412 (m-30) cc_final: 0.8107 (m-30) REVERT: Q 58 ARG cc_start: 0.8316 (tpt170) cc_final: 0.8077 (mtt180) REVERT: Q 61 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6697 (mt0) REVERT: Q 75 ILE cc_start: 0.7412 (tt) cc_final: 0.7078 (tp) REVERT: R 215 PHE cc_start: 0.8156 (t80) cc_final: 0.7944 (t80) REVERT: S 68 PHE cc_start: 0.8291 (m-80) cc_final: 0.8052 (m-10) REVERT: S 79 PHE cc_start: 0.2238 (OUTLIER) cc_final: 0.1684 (t80) REVERT: T 11 ASP cc_start: 0.6962 (m-30) cc_final: 0.6642 (m-30) REVERT: T 23 LEU cc_start: 0.8085 (mp) cc_final: 0.7742 (mt) REVERT: T 29 GLU cc_start: 0.7971 (tp30) cc_final: 0.7684 (tm-30) REVERT: T 52 SER cc_start: 0.9122 (t) cc_final: 0.8616 (p) REVERT: U 15 LYS cc_start: 0.7548 (tptp) cc_final: 0.6916 (tmtt) REVERT: U 16 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7676 (t80) REVERT: V 150 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7647 (mp) REVERT: V 215 PHE cc_start: 0.7798 (t80) cc_final: 0.7401 (t80) REVERT: V 282 MET cc_start: 0.6884 (tpp) cc_final: 0.6586 (tpp) REVERT: V 300 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7563 (t0) REVERT: W 71 ILE cc_start: 0.9347 (pt) cc_final: 0.9043 (pt) REVERT: X 189 LEU cc_start: 0.8530 (tt) cc_final: 0.8284 (pp) REVERT: X 298 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7307 (tm-30) REVERT: X 299 GLU cc_start: 0.7836 (mm-30) cc_final: 0.6879 (mm-30) outliers start: 96 outliers final: 58 residues processed: 585 average time/residue: 0.2721 time to fit residues: 251.9512 Evaluate side-chains 559 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 488 time to evaluate : 4.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain M residue 23 LEU Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 79 PHE Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain Q residue 12 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain V residue 301 MET Chi-restraints excluded: chain V residue 339 SER Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 8.9990 chunk 207 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 135 optimal weight: 0.8980 chunk 56 optimal weight: 0.3980 chunk 230 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 120 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN C 78 ASN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 55 ASN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 ASN ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 59 ASN ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 26 GLN U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN W 63 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20052 Z= 0.182 Angle : 0.603 9.602 27243 Z= 0.308 Chirality : 0.040 0.196 3119 Planarity : 0.003 0.035 3524 Dihedral : 4.089 26.935 2693 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.73 % Allowed : 24.94 % Favored : 70.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.64 (0.17), residues: 2487 helix: 1.89 (0.12), residues: 1884 sheet: -1.75 (0.77), residues: 50 loop : -1.51 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP X 177 PHE 0.012 0.001 PHE O 167 TYR 0.026 0.002 TYR H 54 ARG 0.006 0.000 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 509 time to evaluate : 2.322 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: A 16 PHE cc_start: 0.8465 (OUTLIER) cc_final: 0.7653 (t80) REVERT: A 66 LYS cc_start: 0.8856 (tmmt) cc_final: 0.8315 (tptp) REVERT: A 72 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8249 (t0) REVERT: B 11 ASP cc_start: 0.8748 (m-30) cc_final: 0.8320 (m-30) REVERT: B 16 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: B 63 ASN cc_start: 0.8725 (m-40) cc_final: 0.8419 (m-40) REVERT: C 33 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8384 (mmtm) REVERT: C 34 LEU cc_start: 0.8494 (tp) cc_final: 0.7934 (tt) REVERT: C 53 GLU cc_start: 0.7918 (tt0) cc_final: 0.7544 (mt-10) REVERT: C 66 LYS cc_start: 0.8579 (tptp) cc_final: 0.7985 (tppt) REVERT: C 70 ASP cc_start: 0.7743 (m-30) cc_final: 0.7170 (m-30) REVERT: D 20 VAL cc_start: 0.8974 (OUTLIER) cc_final: 0.8215 (p) REVERT: D 69 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8391 (tptt) REVERT: E 11 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.7821 (m-30) REVERT: E 23 LEU cc_start: 0.8704 (tt) cc_final: 0.7695 (tt) REVERT: E 26 GLN cc_start: 0.8485 (mt0) cc_final: 0.7660 (mp10) REVERT: E 34 LEU cc_start: 0.8198 (tt) cc_final: 0.7808 (tp) REVERT: E 53 GLU cc_start: 0.8231 (tm-30) cc_final: 0.7626 (tm-30) REVERT: E 76 ILE cc_start: 0.8841 (pt) cc_final: 0.8546 (mm) REVERT: F 215 PHE cc_start: 0.7428 (t80) cc_final: 0.6962 (t80) REVERT: F 318 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6803 (tt) REVERT: G 69 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8276 (tptm) REVERT: I 17 ASP cc_start: 0.7649 (m-30) cc_final: 0.5927 (t70) REVERT: J 59 ASN cc_start: 0.8033 (m-40) cc_final: 0.7458 (m-40) REVERT: J 66 LYS cc_start: 0.8329 (tptm) cc_final: 0.6703 (tppt) REVERT: J 69 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8214 (tppt) REVERT: J 70 ASP cc_start: 0.7159 (m-30) cc_final: 0.6520 (m-30) REVERT: K 10 ASP cc_start: 0.7216 (m-30) cc_final: 0.6526 (t0) REVERT: K 17 ASP cc_start: 0.8274 (m-30) cc_final: 0.8045 (m-30) REVERT: K 57 TYR cc_start: 0.8514 (t80) cc_final: 0.8146 (t80) REVERT: L 29 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: M 8 TYR cc_start: 0.7784 (t80) cc_final: 0.6303 (m-80) REVERT: M 10 ASP cc_start: 0.7956 (t0) cc_final: 0.7682 (t0) REVERT: N 17 ASP cc_start: 0.8027 (m-30) cc_final: 0.7616 (m-30) REVERT: N 43 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7676 (tt) REVERT: N 59 ASN cc_start: 0.7890 (t0) cc_final: 0.7657 (t0) REVERT: N 66 LYS cc_start: 0.8136 (tmtt) cc_final: 0.7817 (tmtt) REVERT: O 169 ASP cc_start: 0.7590 (t0) cc_final: 0.7131 (m-30) REVERT: O 288 GLN cc_start: 0.7805 (mm110) cc_final: 0.7450 (pt0) REVERT: O 294 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.5917 (t80) REVERT: O 316 ASN cc_start: 0.8423 (m-40) cc_final: 0.8061 (m110) REVERT: O 322 LEU cc_start: 0.8715 (tp) cc_final: 0.8483 (tp) REVERT: P 47 TYR cc_start: 0.7074 (t80) cc_final: 0.6831 (t80) REVERT: P 54 TYR cc_start: 0.8070 (t80) cc_final: 0.7555 (t80) REVERT: P 72 ASP cc_start: 0.8416 (m-30) cc_final: 0.8180 (m-30) REVERT: Q 17 ASP cc_start: 0.7157 (t0) cc_final: 0.6912 (t0) REVERT: Q 37 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8231 (mmtm) REVERT: Q 58 ARG cc_start: 0.8478 (tpt170) cc_final: 0.8155 (mtt180) REVERT: Q 75 ILE cc_start: 0.7449 (tt) cc_final: 0.7119 (tp) REVERT: R 215 PHE cc_start: 0.8147 (t80) cc_final: 0.7694 (t80) REVERT: S 53 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7629 (tp30) REVERT: S 79 PHE cc_start: 0.2287 (OUTLIER) cc_final: 0.1729 (t80) REVERT: T 23 LEU cc_start: 0.8289 (mp) cc_final: 0.7965 (mt) REVERT: U 15 LYS cc_start: 0.7704 (tptp) cc_final: 0.7106 (tmtt) REVERT: U 16 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7923 (t80) REVERT: U 43 LEU cc_start: 0.7755 (mt) cc_final: 0.7262 (mt) REVERT: V 150 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7716 (mp) REVERT: V 215 PHE cc_start: 0.7876 (t80) cc_final: 0.7443 (t80) REVERT: V 300 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7699 (t0) REVERT: X 298 GLU cc_start: 0.7891 (tm-30) cc_final: 0.7536 (tm-30) outliers start: 102 outliers final: 68 residues processed: 570 average time/residue: 0.2739 time to fit residues: 246.5701 Evaluate side-chains 567 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 485 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 66 LYS Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain N residue 43 LEU Chi-restraints excluded: chain N residue 57 TYR Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 245 LEU Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 227 THR Chi-restraints excluded: chain S residue 64 THR Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 25 THR Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 300 ASN Chi-restraints excluded: chain V residue 301 MET Chi-restraints excluded: chain V residue 320 ASP Chi-restraints excluded: chain V residue 339 SER Chi-restraints excluded: chain W residue 11 ASP Chi-restraints excluded: chain W residue 28 THR Chi-restraints excluded: chain W residue 61 GLN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 177 TRP Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 193 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 229 optimal weight: 0.6980 chunk 143 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 61 GLN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 300 ASN ** W 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20052 Z= 0.251 Angle : 0.671 10.091 27243 Z= 0.348 Chirality : 0.043 0.233 3119 Planarity : 0.004 0.042 3524 Dihedral : 4.310 29.092 2693 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.42 % Allowed : 25.36 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.34 (0.17), residues: 2487 helix: 1.67 (0.12), residues: 1899 sheet: -1.78 (0.75), residues: 50 loop : -1.68 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP F 234 PHE 0.023 0.002 PHE K 79 TYR 0.031 0.002 TYR H 54 ARG 0.008 0.001 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 521 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8844 (tmmt) cc_final: 0.8434 (tptp) REVERT: A 72 ASP cc_start: 0.8557 (OUTLIER) cc_final: 0.8211 (t0) REVERT: B 16 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: B 63 ASN cc_start: 0.8877 (m-40) cc_final: 0.8529 (m-40) REVERT: C 10 ASP cc_start: 0.8101 (t0) cc_final: 0.7762 (t0) REVERT: C 33 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8815 (mmtm) REVERT: C 34 LEU cc_start: 0.8895 (tp) cc_final: 0.8629 (tt) REVERT: C 53 GLU cc_start: 0.8605 (tt0) cc_final: 0.8016 (mt-10) REVERT: C 66 LYS cc_start: 0.8816 (tptp) cc_final: 0.8266 (tppt) REVERT: C 70 ASP cc_start: 0.7895 (m-30) cc_final: 0.7245 (m-30) REVERT: C 78 ASN cc_start: 0.8529 (OUTLIER) cc_final: 0.7975 (t0) REVERT: D 31 LEU cc_start: 0.9464 (tp) cc_final: 0.9225 (tt) REVERT: D 69 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8566 (tptt) REVERT: D 75 ILE cc_start: 0.9105 (mm) cc_final: 0.8831 (tp) REVERT: E 11 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: E 23 LEU cc_start: 0.8848 (tt) cc_final: 0.8586 (tt) REVERT: E 26 GLN cc_start: 0.8660 (mt0) cc_final: 0.8008 (mt0) REVERT: E 53 GLU cc_start: 0.8388 (tm-30) cc_final: 0.7729 (tm-30) REVERT: E 76 ILE cc_start: 0.8853 (pt) cc_final: 0.8448 (mm) REVERT: F 198 LEU cc_start: 0.6042 (mm) cc_final: 0.5550 (mm) REVERT: F 215 PHE cc_start: 0.7716 (t80) cc_final: 0.7353 (t80) REVERT: F 252 TYR cc_start: 0.6867 (m-10) cc_final: 0.6566 (m-10) REVERT: F 318 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7424 (tt) REVERT: G 63 ASN cc_start: 0.8716 (t0) cc_final: 0.8238 (t0) REVERT: G 69 LYS cc_start: 0.8925 (tmtt) cc_final: 0.8481 (tptm) REVERT: I 17 ASP cc_start: 0.8550 (m-30) cc_final: 0.7890 (m-30) REVERT: J 34 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8692 (mm) REVERT: J 59 ASN cc_start: 0.8496 (m-40) cc_final: 0.7814 (m110) REVERT: J 66 LYS cc_start: 0.8667 (tptm) cc_final: 0.7026 (tppt) REVERT: J 69 LYS cc_start: 0.9211 (tmtt) cc_final: 0.8587 (tppt) REVERT: J 70 ASP cc_start: 0.7348 (m-30) cc_final: 0.6888 (m-30) REVERT: K 10 ASP cc_start: 0.8323 (m-30) cc_final: 0.7098 (t0) REVERT: K 57 TYR cc_start: 0.8741 (t80) cc_final: 0.8302 (t80) REVERT: L 25 THR cc_start: 0.9024 (m) cc_final: 0.8525 (p) REVERT: L 29 GLU cc_start: 0.8395 (pm20) cc_final: 0.8142 (pm20) REVERT: L 69 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8932 (ttmt) REVERT: L 77 GLN cc_start: 0.8937 (tt0) cc_final: 0.8512 (tm-30) REVERT: M 8 TYR cc_start: 0.7933 (t80) cc_final: 0.6429 (m-80) REVERT: M 10 ASP cc_start: 0.8528 (t0) cc_final: 0.8224 (t0) REVERT: M 51 LEU cc_start: 0.8854 (tt) cc_final: 0.8623 (tt) REVERT: M 76 ILE cc_start: 0.6569 (tt) cc_final: 0.6281 (tt) REVERT: N 17 ASP cc_start: 0.8213 (m-30) cc_final: 0.7975 (m-30) REVERT: N 24 GLN cc_start: 0.7800 (pm20) cc_final: 0.7557 (pp30) REVERT: N 66 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7668 (tmtt) REVERT: O 169 ASP cc_start: 0.7781 (t0) cc_final: 0.7563 (t70) REVERT: O 261 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9116 (mp) REVERT: O 294 PHE cc_start: 0.7441 (OUTLIER) cc_final: 0.6279 (t80) REVERT: O 316 ASN cc_start: 0.8642 (m-40) cc_final: 0.8338 (m110) REVERT: P 16 PHE cc_start: 0.8757 (OUTLIER) cc_final: 0.8184 (t80) REVERT: P 54 TYR cc_start: 0.8388 (t80) cc_final: 0.7840 (t80) REVERT: P 55 ASN cc_start: 0.8896 (OUTLIER) cc_final: 0.8291 (t0) REVERT: P 72 ASP cc_start: 0.8280 (m-30) cc_final: 0.8031 (m-30) REVERT: Q 17 ASP cc_start: 0.7575 (t0) cc_final: 0.7341 (t0) REVERT: Q 58 ARG cc_start: 0.8438 (tpt170) cc_final: 0.7810 (mtt180) REVERT: R 160 TYR cc_start: 0.5191 (t80) cc_final: 0.4963 (t80) REVERT: S 53 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7924 (tp30) REVERT: T 11 ASP cc_start: 0.7841 (m-30) cc_final: 0.7223 (m-30) REVERT: T 29 GLU cc_start: 0.8360 (tp30) cc_final: 0.8096 (tm-30) REVERT: U 10 ASP cc_start: 0.8366 (t0) cc_final: 0.8162 (t0) REVERT: U 15 LYS cc_start: 0.8009 (tptp) cc_final: 0.7421 (tmtt) REVERT: U 16 PHE cc_start: 0.8852 (OUTLIER) cc_final: 0.8047 (t80) REVERT: V 150 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7462 (mp) REVERT: V 282 MET cc_start: 0.6902 (tpp) cc_final: 0.6554 (tpp) REVERT: V 298 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8732 (tp30) REVERT: V 340 PHE cc_start: 0.7261 (m-10) cc_final: 0.6876 (m-80) REVERT: W 50 LYS cc_start: 0.8328 (mtpt) cc_final: 0.8100 (mtmt) REVERT: X 150 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7562 (mp) REVERT: X 230 GLU cc_start: 0.8084 (pt0) cc_final: 0.7852 (pt0) REVERT: X 282 MET cc_start: 0.7317 (tmm) cc_final: 0.7081 (tmm) outliers start: 117 outliers final: 67 residues processed: 593 average time/residue: 0.2749 time to fit residues: 256.0450 Evaluate side-chains 558 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 476 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 34 LEU Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 71 ILE Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain P residue 16 PHE Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 221 SER Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 291 GLN Chi-restraints excluded: chain V residue 301 MET Chi-restraints excluded: chain V residue 339 SER Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 137 MET Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.0980 chunk 91 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 156 optimal weight: 0.0050 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 180 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 61 GLN ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 59 ASN ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 22 ASN U 26 GLN ** U 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.7598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20052 Z= 0.183 Angle : 0.663 11.279 27243 Z= 0.336 Chirality : 0.041 0.234 3119 Planarity : 0.003 0.045 3524 Dihedral : 4.208 26.891 2693 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.27 % Allowed : 27.49 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.44 (0.17), residues: 2487 helix: 1.74 (0.12), residues: 1893 sheet: -1.83 (0.74), residues: 50 loop : -1.57 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 234 PHE 0.023 0.001 PHE X 215 TYR 0.033 0.002 TYR P 47 ARG 0.007 0.000 ARG I 58 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 516 time to evaluate : 2.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.7312 (t80) REVERT: A 66 LYS cc_start: 0.8657 (tmmt) cc_final: 0.8251 (tptp) REVERT: A 72 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.8301 (t0) REVERT: B 16 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: B 29 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7644 (mm-30) REVERT: B 63 ASN cc_start: 0.8908 (m-40) cc_final: 0.8610 (m-40) REVERT: B 80 ARG cc_start: 0.7919 (ptp90) cc_final: 0.7430 (ptp-170) REVERT: C 33 LYS cc_start: 0.9170 (mmtm) cc_final: 0.8718 (mmtm) REVERT: C 34 LEU cc_start: 0.8708 (tp) cc_final: 0.8322 (tt) REVERT: C 53 GLU cc_start: 0.8593 (tt0) cc_final: 0.8015 (mt-10) REVERT: C 54 TYR cc_start: 0.9107 (t80) cc_final: 0.8773 (t80) REVERT: C 57 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.8552 (t80) REVERT: C 66 LYS cc_start: 0.8793 (tptp) cc_final: 0.7968 (tppt) REVERT: C 70 ASP cc_start: 0.7854 (m-30) cc_final: 0.7201 (m-30) REVERT: C 78 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7780 (t0) REVERT: D 31 LEU cc_start: 0.9495 (tp) cc_final: 0.9278 (tp) REVERT: D 69 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8534 (tptt) REVERT: D 75 ILE cc_start: 0.9084 (mm) cc_final: 0.8794 (tp) REVERT: E 11 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.7435 (m-30) REVERT: E 23 LEU cc_start: 0.8740 (tt) cc_final: 0.8007 (tt) REVERT: E 26 GLN cc_start: 0.8515 (mt0) cc_final: 0.7762 (mt0) REVERT: E 49 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8814 (t) REVERT: E 53 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7721 (tm-30) REVERT: E 56 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8390 (tt) REVERT: F 198 LEU cc_start: 0.6041 (mm) cc_final: 0.5655 (mm) REVERT: F 215 PHE cc_start: 0.7698 (t80) cc_final: 0.7382 (t80) REVERT: F 237 GLU cc_start: 0.7605 (pp20) cc_final: 0.7132 (pp20) REVERT: F 252 TYR cc_start: 0.6769 (m-10) cc_final: 0.6468 (m-10) REVERT: F 318 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7463 (tt) REVERT: G 63 ASN cc_start: 0.8418 (t0) cc_final: 0.8090 (t0) REVERT: G 69 LYS cc_start: 0.8857 (tmtt) cc_final: 0.8400 (tptm) REVERT: H 21 ASP cc_start: 0.6367 (m-30) cc_final: 0.6049 (m-30) REVERT: H 63 ASN cc_start: 0.8690 (t0) cc_final: 0.8387 (t0) REVERT: I 17 ASP cc_start: 0.8278 (m-30) cc_final: 0.6393 (t0) REVERT: J 18 THR cc_start: 0.9440 (t) cc_final: 0.9082 (p) REVERT: J 59 ASN cc_start: 0.8440 (m-40) cc_final: 0.7743 (m110) REVERT: J 66 LYS cc_start: 0.8749 (tptm) cc_final: 0.7120 (tppt) REVERT: J 69 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8883 (tptp) REVERT: J 70 ASP cc_start: 0.7364 (m-30) cc_final: 0.6931 (m-30) REVERT: J 77 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7643 (tm-30) REVERT: K 10 ASP cc_start: 0.8400 (m-30) cc_final: 0.7231 (t0) REVERT: K 57 TYR cc_start: 0.8712 (t80) cc_final: 0.8352 (t80) REVERT: K 69 LYS cc_start: 0.9082 (tmtt) cc_final: 0.8795 (tptt) REVERT: L 25 THR cc_start: 0.9010 (m) cc_final: 0.8502 (p) REVERT: L 29 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8004 (pm20) REVERT: L 69 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8954 (ttmt) REVERT: L 77 GLN cc_start: 0.8896 (tt0) cc_final: 0.8558 (tm-30) REVERT: M 8 TYR cc_start: 0.7863 (t80) cc_final: 0.6451 (m-80) REVERT: M 10 ASP cc_start: 0.7883 (t0) cc_final: 0.7558 (t0) REVERT: M 51 LEU cc_start: 0.8806 (tt) cc_final: 0.8595 (tt) REVERT: M 76 ILE cc_start: 0.6704 (tt) cc_final: 0.6481 (tt) REVERT: N 17 ASP cc_start: 0.8264 (m-30) cc_final: 0.8046 (m-30) REVERT: N 66 LYS cc_start: 0.8061 (tmtt) cc_final: 0.7617 (tmtt) REVERT: O 294 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.6558 (t80) REVERT: O 316 ASN cc_start: 0.8524 (m-40) cc_final: 0.8144 (m110) REVERT: P 48 GLN cc_start: 0.8490 (pp30) cc_final: 0.8219 (pp30) REVERT: P 54 TYR cc_start: 0.8511 (t80) cc_final: 0.8092 (t80) REVERT: P 72 ASP cc_start: 0.8161 (m-30) cc_final: 0.7960 (m-30) REVERT: Q 29 GLU cc_start: 0.8228 (pt0) cc_final: 0.7704 (mt-10) REVERT: Q 58 ARG cc_start: 0.8460 (tpt170) cc_final: 0.7821 (mtt180) REVERT: R 160 TYR cc_start: 0.5277 (t80) cc_final: 0.4762 (t80) REVERT: S 53 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7852 (tp30) REVERT: T 11 ASP cc_start: 0.7837 (m-30) cc_final: 0.7219 (m-30) REVERT: U 10 ASP cc_start: 0.8317 (t0) cc_final: 0.8103 (t0) REVERT: U 15 LYS cc_start: 0.7990 (tptp) cc_final: 0.7397 (tmtt) REVERT: U 16 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8041 (t80) REVERT: V 150 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7510 (mp) REVERT: V 340 PHE cc_start: 0.7234 (m-10) cc_final: 0.6909 (m-80) REVERT: W 50 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8085 (mtmt) REVERT: X 150 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7498 (mp) REVERT: X 161 THR cc_start: 0.8536 (m) cc_final: 0.8231 (p) REVERT: X 230 GLU cc_start: 0.7949 (pt0) cc_final: 0.7702 (pt0) outliers start: 92 outliers final: 61 residues processed: 571 average time/residue: 0.2702 time to fit residues: 243.4494 Evaluate side-chains 564 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 487 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 236 SER Chi-restraints excluded: chain F residue 259 THR Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 55 ASN Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 61 GLN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 213 optimal weight: 0.7980 chunk 128 optimal weight: 0.2980 chunk 93 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 202 optimal weight: 0.5980 chunk 140 optimal weight: 10.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 ASN ** E 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN J 24 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.7901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20052 Z= 0.195 Angle : 0.668 10.556 27243 Z= 0.340 Chirality : 0.042 0.244 3119 Planarity : 0.003 0.047 3524 Dihedral : 4.215 26.789 2693 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 4.17 % Allowed : 28.00 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.43 (0.17), residues: 2487 helix: 1.73 (0.12), residues: 1899 sheet: -1.89 (0.73), residues: 50 loop : -1.61 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP X 177 PHE 0.029 0.001 PHE H 79 TYR 0.036 0.002 TYR P 47 ARG 0.002 0.000 ARG H 58 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 508 time to evaluate : 2.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7448 (t80) REVERT: A 66 LYS cc_start: 0.8646 (tmmt) cc_final: 0.8274 (tptp) REVERT: A 72 ASP cc_start: 0.8648 (OUTLIER) cc_final: 0.8420 (t0) REVERT: B 16 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7114 (m-80) REVERT: B 29 GLU cc_start: 0.8094 (mm-30) cc_final: 0.7694 (mt-10) REVERT: B 63 ASN cc_start: 0.8935 (m-40) cc_final: 0.8586 (m-40) REVERT: B 80 ARG cc_start: 0.8070 (ptp90) cc_final: 0.7550 (ptp-170) REVERT: C 9 LEU cc_start: 0.8717 (mt) cc_final: 0.8326 (mp) REVERT: C 33 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8686 (mmtm) REVERT: C 34 LEU cc_start: 0.9107 (tp) cc_final: 0.8899 (tt) REVERT: C 53 GLU cc_start: 0.8577 (tt0) cc_final: 0.8036 (mt-10) REVERT: C 54 TYR cc_start: 0.9082 (t80) cc_final: 0.8747 (t80) REVERT: C 57 TYR cc_start: 0.8829 (OUTLIER) cc_final: 0.8529 (t80) REVERT: C 66 LYS cc_start: 0.8841 (tptp) cc_final: 0.7978 (tppt) REVERT: C 70 ASP cc_start: 0.7942 (m-30) cc_final: 0.7296 (m-30) REVERT: D 31 LEU cc_start: 0.9452 (tp) cc_final: 0.9211 (tt) REVERT: D 69 LYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8387 (tptt) REVERT: D 71 ILE cc_start: 0.9423 (mm) cc_final: 0.9060 (mt) REVERT: D 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.7967 (p0) REVERT: D 77 GLN cc_start: 0.8523 (pp30) cc_final: 0.7978 (pp30) REVERT: E 11 ASP cc_start: 0.8642 (OUTLIER) cc_final: 0.7493 (m-30) REVERT: E 26 GLN cc_start: 0.8587 (mt0) cc_final: 0.8258 (mt0) REVERT: E 34 LEU cc_start: 0.8562 (tt) cc_final: 0.8053 (tp) REVERT: E 49 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8755 (t) REVERT: E 53 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7757 (tm-30) REVERT: E 56 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8442 (tt) REVERT: F 237 GLU cc_start: 0.7711 (pp20) cc_final: 0.7153 (pp20) REVERT: F 252 TYR cc_start: 0.6811 (m-10) cc_final: 0.6473 (m-10) REVERT: F 318 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7569 (tt) REVERT: G 63 ASN cc_start: 0.8436 (t0) cc_final: 0.8025 (t0) REVERT: G 69 LYS cc_start: 0.8931 (tmtt) cc_final: 0.8475 (tptm) REVERT: H 21 ASP cc_start: 0.6731 (m-30) cc_final: 0.6394 (m-30) REVERT: I 17 ASP cc_start: 0.8324 (m-30) cc_final: 0.7811 (m-30) REVERT: J 18 THR cc_start: 0.9477 (t) cc_final: 0.9136 (p) REVERT: J 59 ASN cc_start: 0.8475 (m-40) cc_final: 0.7793 (m110) REVERT: J 66 LYS cc_start: 0.8725 (tptm) cc_final: 0.7406 (tppt) REVERT: J 69 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8921 (tptp) REVERT: J 70 ASP cc_start: 0.7432 (m-30) cc_final: 0.6829 (m-30) REVERT: J 77 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7647 (tm-30) REVERT: K 10 ASP cc_start: 0.8347 (m-30) cc_final: 0.7351 (t0) REVERT: K 57 TYR cc_start: 0.8739 (t80) cc_final: 0.8332 (t80) REVERT: K 69 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8797 (tptt) REVERT: K 79 PHE cc_start: 0.8457 (m-10) cc_final: 0.7809 (m-80) REVERT: L 16 PHE cc_start: 0.6891 (OUTLIER) cc_final: 0.6494 (m-10) REVERT: L 25 THR cc_start: 0.9028 (m) cc_final: 0.8740 (p) REVERT: L 69 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8970 (ttmt) REVERT: L 77 GLN cc_start: 0.8775 (tt0) cc_final: 0.8456 (tm-30) REVERT: M 8 TYR cc_start: 0.7875 (t80) cc_final: 0.6504 (m-80) REVERT: M 10 ASP cc_start: 0.8300 (t0) cc_final: 0.7974 (t0) REVERT: M 76 ILE cc_start: 0.6738 (tt) cc_final: 0.6503 (tt) REVERT: N 17 ASP cc_start: 0.8364 (m-30) cc_final: 0.8064 (m-30) REVERT: N 66 LYS cc_start: 0.8015 (tmtt) cc_final: 0.7547 (tmtt) REVERT: O 261 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.9044 (mp) REVERT: O 294 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.6670 (t80) REVERT: P 54 TYR cc_start: 0.8574 (t80) cc_final: 0.8036 (t80) REVERT: P 55 ASN cc_start: 0.8849 (t0) cc_final: 0.8485 (t0) REVERT: Q 58 ARG cc_start: 0.8574 (tpt170) cc_final: 0.7732 (mtt180) REVERT: R 160 TYR cc_start: 0.5044 (t80) cc_final: 0.4772 (t80) REVERT: R 174 MET cc_start: 0.7086 (tmm) cc_final: 0.6554 (ttt) REVERT: S 53 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7777 (tp30) REVERT: T 11 ASP cc_start: 0.7906 (m-30) cc_final: 0.7272 (m-30) REVERT: U 10 ASP cc_start: 0.8334 (t0) cc_final: 0.8092 (t0) REVERT: U 15 LYS cc_start: 0.8013 (tptp) cc_final: 0.7423 (tmtt) REVERT: U 16 PHE cc_start: 0.8805 (OUTLIER) cc_final: 0.8050 (t80) REVERT: U 23 LEU cc_start: 0.9423 (tt) cc_final: 0.9129 (tt) REVERT: V 150 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7537 (mp) REVERT: V 340 PHE cc_start: 0.7299 (m-10) cc_final: 0.6931 (m-80) REVERT: W 50 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8147 (mtmt) REVERT: X 150 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7546 (mp) REVERT: X 161 THR cc_start: 0.8719 (m) cc_final: 0.8347 (p) REVERT: X 177 TRP cc_start: 0.7942 (p90) cc_final: 0.7646 (p90) REVERT: X 298 GLU cc_start: 0.8005 (tp30) cc_final: 0.7766 (tp30) REVERT: X 314 ASN cc_start: 0.8735 (m110) cc_final: 0.8081 (p0) outliers start: 90 outliers final: 65 residues processed: 561 average time/residue: 0.2780 time to fit residues: 246.4164 Evaluate side-chains 565 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 484 time to evaluate : 2.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 49 SER Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 16 PHE Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain L residue 69 LYS Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 303 THR Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 16 PHE Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain V residue 237 GLU Chi-restraints excluded: chain V residue 264 MET Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 61 GLN Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.0020 chunk 137 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 199 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.8152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20052 Z= 0.201 Angle : 0.678 10.997 27243 Z= 0.346 Chirality : 0.042 0.281 3119 Planarity : 0.003 0.047 3524 Dihedral : 4.219 26.372 2693 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.08 % Allowed : 28.51 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 1.44 (0.17), residues: 2487 helix: 1.72 (0.12), residues: 1904 sheet: -1.88 (0.73), residues: 50 loop : -1.56 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP F 234 PHE 0.020 0.001 PHE X 215 TYR 0.032 0.002 TYR P 47 ARG 0.004 0.000 ARG I 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4974 Ramachandran restraints generated. 2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 502 time to evaluate : 2.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 PHE cc_start: 0.8482 (OUTLIER) cc_final: 0.7443 (t80) REVERT: A 66 LYS cc_start: 0.8645 (tmmt) cc_final: 0.8313 (tptp) REVERT: A 72 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8421 (t0) REVERT: B 16 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7318 (m-80) REVERT: B 29 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7778 (mt-10) REVERT: B 63 ASN cc_start: 0.8966 (m-40) cc_final: 0.8644 (m-40) REVERT: B 80 ARG cc_start: 0.7714 (ptp90) cc_final: 0.7471 (ptp-110) REVERT: C 9 LEU cc_start: 0.8720 (mt) cc_final: 0.8322 (mp) REVERT: C 33 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8440 (mmtm) REVERT: C 53 GLU cc_start: 0.8561 (tt0) cc_final: 0.7999 (mt-10) REVERT: C 54 TYR cc_start: 0.9077 (t80) cc_final: 0.8725 (t80) REVERT: C 57 TYR cc_start: 0.8804 (OUTLIER) cc_final: 0.8478 (t80) REVERT: C 66 LYS cc_start: 0.8886 (tptp) cc_final: 0.8005 (tppt) REVERT: C 70 ASP cc_start: 0.7935 (m-30) cc_final: 0.7318 (m-30) REVERT: D 31 LEU cc_start: 0.9418 (tp) cc_final: 0.9189 (tt) REVERT: D 69 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8373 (tptt) REVERT: D 71 ILE cc_start: 0.9462 (mm) cc_final: 0.9205 (mt) REVERT: D 75 ILE cc_start: 0.9148 (mm) cc_final: 0.8845 (tp) REVERT: D 77 GLN cc_start: 0.8515 (pp30) cc_final: 0.7991 (pp30) REVERT: E 11 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.7563 (m-30) REVERT: E 26 GLN cc_start: 0.8415 (mt0) cc_final: 0.8090 (mt0) REVERT: E 34 LEU cc_start: 0.8560 (tt) cc_final: 0.8029 (tp) REVERT: E 53 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7704 (tm-30) REVERT: F 237 GLU cc_start: 0.7754 (pp20) cc_final: 0.7253 (pp20) REVERT: F 252 TYR cc_start: 0.6790 (m-10) cc_final: 0.6449 (m-10) REVERT: F 318 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7555 (tt) REVERT: G 63 ASN cc_start: 0.8466 (t0) cc_final: 0.8045 (t0) REVERT: G 69 LYS cc_start: 0.8939 (tmtt) cc_final: 0.8484 (tptm) REVERT: H 21 ASP cc_start: 0.6690 (m-30) cc_final: 0.6343 (m-30) REVERT: I 17 ASP cc_start: 0.8317 (m-30) cc_final: 0.7800 (m-30) REVERT: J 18 THR cc_start: 0.9506 (t) cc_final: 0.9183 (p) REVERT: J 59 ASN cc_start: 0.8464 (m-40) cc_final: 0.7817 (m110) REVERT: J 66 LYS cc_start: 0.8618 (tptm) cc_final: 0.7289 (tppt) REVERT: J 70 ASP cc_start: 0.7396 (m-30) cc_final: 0.6882 (m-30) REVERT: J 77 GLN cc_start: 0.8167 (tm-30) cc_final: 0.7851 (tm-30) REVERT: K 10 ASP cc_start: 0.8445 (m-30) cc_final: 0.7515 (t0) REVERT: K 57 TYR cc_start: 0.8715 (t80) cc_final: 0.8364 (t80) REVERT: L 16 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6672 (m-10) REVERT: L 17 ASP cc_start: 0.8043 (m-30) cc_final: 0.7736 (m-30) REVERT: L 25 THR cc_start: 0.9039 (m) cc_final: 0.8777 (p) REVERT: L 77 GLN cc_start: 0.8771 (tt0) cc_final: 0.8469 (tm-30) REVERT: M 8 TYR cc_start: 0.7901 (t80) cc_final: 0.6512 (m-80) REVERT: M 10 ASP cc_start: 0.8304 (t0) cc_final: 0.7964 (t0) REVERT: M 76 ILE cc_start: 0.6750 (tt) cc_final: 0.6509 (tt) REVERT: N 17 ASP cc_start: 0.8303 (m-30) cc_final: 0.8019 (m-30) REVERT: N 66 LYS cc_start: 0.8018 (tmtt) cc_final: 0.7596 (tmtt) REVERT: O 261 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.9022 (mp) REVERT: O 294 PHE cc_start: 0.7696 (OUTLIER) cc_final: 0.6532 (t80) REVERT: P 54 TYR cc_start: 0.8752 (t80) cc_final: 0.8172 (t80) REVERT: P 55 ASN cc_start: 0.8865 (t0) cc_final: 0.8475 (t0) REVERT: P 66 LYS cc_start: 0.8769 (tptt) cc_final: 0.8373 (tptt) REVERT: Q 22 ASN cc_start: 0.8628 (p0) cc_final: 0.8367 (p0) REVERT: Q 58 ARG cc_start: 0.8508 (tpt170) cc_final: 0.7732 (mtt180) REVERT: R 160 TYR cc_start: 0.5179 (t80) cc_final: 0.4725 (t80) REVERT: R 174 MET cc_start: 0.7303 (tmm) cc_final: 0.6750 (ttt) REVERT: S 53 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7784 (tp30) REVERT: T 11 ASP cc_start: 0.7927 (m-30) cc_final: 0.7318 (m-30) REVERT: T 31 LEU cc_start: 0.8547 (tp) cc_final: 0.8131 (tp) REVERT: U 10 ASP cc_start: 0.8345 (t0) cc_final: 0.8089 (t0) REVERT: U 15 LYS cc_start: 0.8023 (tptp) cc_final: 0.7417 (tmtt) REVERT: U 16 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8081 (t80) REVERT: U 47 TYR cc_start: 0.7690 (t80) cc_final: 0.7388 (t80) REVERT: V 150 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7510 (mp) REVERT: V 340 PHE cc_start: 0.7319 (m-10) cc_final: 0.6950 (m-80) REVERT: W 29 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8105 (tp30) REVERT: W 50 LYS cc_start: 0.8604 (mtpt) cc_final: 0.8230 (mtmt) REVERT: X 150 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7521 (mp) REVERT: X 161 THR cc_start: 0.8370 (m) cc_final: 0.8075 (p) REVERT: X 177 TRP cc_start: 0.7917 (p90) cc_final: 0.7683 (p90) REVERT: X 230 GLU cc_start: 0.7872 (pt0) cc_final: 0.7530 (pt0) outliers start: 88 outliers final: 62 residues processed: 553 average time/residue: 0.2746 time to fit residues: 239.2428 Evaluate side-chains 551 residues out of total 2167 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 476 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 16 PHE Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 57 TYR Chi-restraints excluded: chain C residue 78 ASN Chi-restraints excluded: chain C residue 79 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 16 PHE Chi-restraints excluded: chain E residue 56 LEU Chi-restraints excluded: chain F residue 240 LEU Chi-restraints excluded: chain F residue 301 MET Chi-restraints excluded: chain F residue 318 LEU Chi-restraints excluded: chain F residue 323 VAL Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain H residue 18 THR Chi-restraints excluded: chain H residue 25 THR Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 53 GLU Chi-restraints excluded: chain I residue 79 PHE Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 16 PHE Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 43 LEU Chi-restraints excluded: chain L residue 8 TYR Chi-restraints excluded: chain L residue 16 PHE Chi-restraints excluded: chain L residue 29 GLU Chi-restraints excluded: chain L residue 57 TYR Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 57 TYR Chi-restraints excluded: chain N residue 16 PHE Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain O residue 157 VAL Chi-restraints excluded: chain O residue 185 ASN Chi-restraints excluded: chain O residue 213 VAL Chi-restraints excluded: chain O residue 258 LEU Chi-restraints excluded: chain O residue 261 LEU Chi-restraints excluded: chain O residue 294 PHE Chi-restraints excluded: chain O residue 303 THR Chi-restraints excluded: chain O residue 312 TYR Chi-restraints excluded: chain O residue 323 VAL Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 SER Chi-restraints excluded: chain R residue 155 ASN Chi-restraints excluded: chain R residue 211 ASN Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain S residue 16 PHE Chi-restraints excluded: chain S residue 79 PHE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain U residue 16 PHE Chi-restraints excluded: chain U residue 21 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 57 TYR Chi-restraints excluded: chain U residue 79 PHE Chi-restraints excluded: chain U residue 80 ARG Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 157 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 79 PHE Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 157 VAL Chi-restraints excluded: chain X residue 268 ILE Chi-restraints excluded: chain X residue 322 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 189 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 166 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 24 GLN ** F 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN ** J 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN U 63 ASN ** V 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 297 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.087064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075975 restraints weight = 65070.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077893 restraints weight = 35741.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.079197 restraints weight = 22731.025| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.8458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 20052 Z= 0.206 Angle : 0.691 12.756 27243 Z= 0.351 Chirality : 0.042 0.263 3119 Planarity : 0.003 0.048 3524 Dihedral : 4.225 26.537 2693 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.71 % Allowed : 28.65 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.17), residues: 2487 helix: 1.69 (0.12), residues: 1904 sheet: -1.83 (0.74), residues: 50 loop : -1.56 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 177 PHE 0.029 0.001 PHE F 215 TYR 0.033 0.002 TYR P 47 ARG 0.004 0.000 ARG I 58 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4692.11 seconds wall clock time: 86 minutes 3.17 seconds (5163.17 seconds total)