Starting phenix.real_space_refine on Mon Mar 18 08:53:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odn_16810/03_2024/8odn_16810.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odn_16810/03_2024/8odn_16810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odn_16810/03_2024/8odn_16810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odn_16810/03_2024/8odn_16810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odn_16810/03_2024/8odn_16810.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8odn_16810/03_2024/8odn_16810.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 143 5.16 5 C 26624 2.51 5 N 7826 2.21 5 O 7995 1.98 5 H 42445 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 85033 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "B" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "C" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "D" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "E" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "F" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "G" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "H" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "I" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "J" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "K" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "L" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "M" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "N" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "O" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "P" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "Q" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "R" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "S" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "T" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "V" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "W" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "X" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "Y" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "Z" Number of atoms: 3640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3640 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 12, 'TRANS': 231} Chain breaks: 2 Chain: "a" Number of atoms: 2901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2901 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Time building chain proxies: 27.94, per 1000 atoms: 0.33 Number of scatterers: 85033 At special positions: 0 Unit cell: (209, 209, 103.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 143 16.00 O 7995 8.00 N 7826 7.00 C 26624 6.00 H 42445 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS B 29 " - pdb=" SG CYS B 97 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 29 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS J 29 " - pdb=" SG CYS J 97 " distance=2.03 Simple disulfide: pdb=" SG CYS L 29 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 29 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS P 29 " - pdb=" SG CYS P 97 " distance=2.03 Simple disulfide: pdb=" SG CYS R 29 " - pdb=" SG CYS R 97 " distance=2.03 Simple disulfide: pdb=" SG CYS T 29 " - pdb=" SG CYS T 97 " distance=2.03 Simple disulfide: pdb=" SG CYS W 29 " - pdb=" SG CYS W 97 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 29 " - pdb=" SG CYS Y 97 " distance=2.03 Simple disulfide: pdb=" SG CYS a 29 " - pdb=" SG CYS a 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.50 Conformation dependent library (CDL) restraints added in 6.8 seconds 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10010 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 2 sheets defined 39.9% alpha, 17.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.90 Creating SS restraints... Processing helix chain 'A' and resid 338 through 342 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.599A pdb=" N ALA A 347 " --> pdb=" O ILE A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET B 41 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 63 Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 85 through 94 Processing helix chain 'B' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA B 102 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.643A pdb=" N LEU B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 168 through 182 removed outlier: 3.929A pdb=" N THR B 172 " --> pdb=" O LYS B 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 177 " --> pdb=" O ASN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 195 Processing helix chain 'B' and resid 197 through 211 removed outlier: 4.190A pdb=" N ALA B 203 " --> pdb=" O ARG B 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 342 Processing helix chain 'C' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA C 347 " --> pdb=" O ILE C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 51 removed outlier: 3.584A pdb=" N MET D 41 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 63 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 85 through 94 Processing helix chain 'D' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA D 102 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 Processing helix chain 'D' and resid 149 through 164 Processing helix chain 'D' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR D 172 " --> pdb=" O LYS D 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 197 through 211 removed outlier: 4.190A pdb=" N ALA D 203 " --> pdb=" O ARG D 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 342 Processing helix chain 'E' and resid 344 through 348 removed outlier: 3.599A pdb=" N ALA E 347 " --> pdb=" O ILE E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 51 removed outlier: 3.584A pdb=" N MET F 41 " --> pdb=" O GLN F 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET F 43 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 63 Processing helix chain 'F' and resid 67 through 82 Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA F 102 " --> pdb=" O LYS F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU F 121 " --> pdb=" O ALA F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 148 Processing helix chain 'F' and resid 149 through 164 Processing helix chain 'F' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 195 Processing helix chain 'F' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA F 203 " --> pdb=" O ARG F 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 342 Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.599A pdb=" N ALA G 347 " --> pdb=" O ILE G 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET H 43 " --> pdb=" O LEU H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 63 Processing helix chain 'H' and resid 67 through 82 Processing helix chain 'H' and resid 85 through 94 Processing helix chain 'H' and resid 98 through 114 removed outlier: 3.582A pdb=" N ALA H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU H 121 " --> pdb=" O ALA H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 148 Processing helix chain 'H' and resid 149 through 164 Processing helix chain 'H' and resid 168 through 182 removed outlier: 3.929A pdb=" N THR H 172 " --> pdb=" O LYS H 168 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU H 177 " --> pdb=" O ASN H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 195 Processing helix chain 'H' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA H 203 " --> pdb=" O ARG H 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'I' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA I 347 " --> pdb=" O ILE I 344 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET J 41 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET J 43 " --> pdb=" O LEU J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 63 Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 85 through 94 Processing helix chain 'J' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA J 102 " --> pdb=" O LYS J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 148 Processing helix chain 'J' and resid 149 through 164 Processing helix chain 'J' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR J 172 " --> pdb=" O LYS J 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 177 " --> pdb=" O ASN J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 195 Processing helix chain 'J' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA J 203 " --> pdb=" O ARG J 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 342 Processing helix chain 'K' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA K 347 " --> pdb=" O ILE K 344 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET L 41 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET L 43 " --> pdb=" O LEU L 39 " (cutoff:3.500A) Processing helix chain 'L' and resid 52 through 63 Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 85 through 94 Processing helix chain 'L' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA L 102 " --> pdb=" O LYS L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 148 Processing helix chain 'L' and resid 149 through 164 Processing helix chain 'L' and resid 168 through 182 removed outlier: 3.929A pdb=" N THR L 172 " --> pdb=" O LYS L 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU L 177 " --> pdb=" O ASN L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 195 Processing helix chain 'L' and resid 197 through 211 removed outlier: 4.190A pdb=" N ALA L 203 " --> pdb=" O ARG L 199 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 342 Processing helix chain 'M' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA M 347 " --> pdb=" O ILE M 344 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET N 41 " --> pdb=" O GLN N 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET N 43 " --> pdb=" O LEU N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 63 Processing helix chain 'N' and resid 67 through 82 Processing helix chain 'N' and resid 85 through 94 Processing helix chain 'N' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA N 102 " --> pdb=" O LYS N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU N 121 " --> pdb=" O ALA N 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 133 through 148 Processing helix chain 'N' and resid 149 through 164 Processing helix chain 'N' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR N 172 " --> pdb=" O LYS N 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU N 177 " --> pdb=" O ASN N 173 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 195 Processing helix chain 'N' and resid 197 through 211 removed outlier: 4.190A pdb=" N ALA N 203 " --> pdb=" O ARG N 199 " (cutoff:3.500A) Processing helix chain 'O' and resid 338 through 342 Processing helix chain 'O' and resid 344 through 348 removed outlier: 3.599A pdb=" N ALA O 347 " --> pdb=" O ILE O 344 " (cutoff:3.500A) Processing helix chain 'P' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET P 41 " --> pdb=" O GLN P 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 63 Processing helix chain 'P' and resid 67 through 82 Processing helix chain 'P' and resid 85 through 94 Processing helix chain 'P' and resid 98 through 114 removed outlier: 3.582A pdb=" N ALA P 102 " --> pdb=" O LYS P 98 " (cutoff:3.500A) Processing helix chain 'P' and resid 115 through 130 removed outlier: 3.643A pdb=" N LEU P 121 " --> pdb=" O ALA P 117 " (cutoff:3.500A) Processing helix chain 'P' and resid 133 through 148 Processing helix chain 'P' and resid 149 through 164 Processing helix chain 'P' and resid 168 through 182 removed outlier: 3.929A pdb=" N THR P 172 " --> pdb=" O LYS P 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU P 177 " --> pdb=" O ASN P 173 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 195 Processing helix chain 'P' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA P 203 " --> pdb=" O ARG P 199 " (cutoff:3.500A) Processing helix chain 'Q' and resid 338 through 342 Processing helix chain 'Q' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA Q 347 " --> pdb=" O ILE Q 344 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET R 43 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 63 Processing helix chain 'R' and resid 67 through 82 Processing helix chain 'R' and resid 85 through 94 Processing helix chain 'R' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA R 102 " --> pdb=" O LYS R 98 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 148 Processing helix chain 'R' and resid 149 through 164 Processing helix chain 'R' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR R 172 " --> pdb=" O LYS R 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU R 177 " --> pdb=" O ASN R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 195 Processing helix chain 'R' and resid 197 through 211 removed outlier: 4.190A pdb=" N ALA R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A) Processing helix chain 'S' and resid 338 through 342 Processing helix chain 'S' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA S 347 " --> pdb=" O ILE S 344 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET T 41 " --> pdb=" O GLN T 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET T 43 " --> pdb=" O LEU T 39 " (cutoff:3.500A) Processing helix chain 'T' and resid 52 through 63 Processing helix chain 'T' and resid 67 through 82 Processing helix chain 'T' and resid 85 through 94 Processing helix chain 'T' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA T 102 " --> pdb=" O LYS T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU T 121 " --> pdb=" O ALA T 117 " (cutoff:3.500A) Processing helix chain 'T' and resid 133 through 148 Processing helix chain 'T' and resid 149 through 164 Processing helix chain 'T' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR T 172 " --> pdb=" O LYS T 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU T 177 " --> pdb=" O ASN T 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 195 Processing helix chain 'T' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA T 203 " --> pdb=" O ARG T 199 " (cutoff:3.500A) Processing helix chain 'V' and resid 338 through 342 Processing helix chain 'V' and resid 344 through 348 removed outlier: 3.599A pdb=" N ALA V 347 " --> pdb=" O ILE V 344 " (cutoff:3.500A) Processing helix chain 'W' and resid 37 through 51 removed outlier: 3.583A pdb=" N MET W 41 " --> pdb=" O GLN W 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET W 43 " --> pdb=" O LEU W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 67 through 82 Processing helix chain 'W' and resid 85 through 94 Processing helix chain 'W' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA W 102 " --> pdb=" O LYS W 98 " (cutoff:3.500A) Processing helix chain 'W' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU W 121 " --> pdb=" O ALA W 117 " (cutoff:3.500A) Processing helix chain 'W' and resid 133 through 148 Processing helix chain 'W' and resid 149 through 164 Processing helix chain 'W' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR W 172 " --> pdb=" O LYS W 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 183 through 195 Processing helix chain 'W' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA W 203 " --> pdb=" O ARG W 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 338 through 342 Processing helix chain 'X' and resid 344 through 348 removed outlier: 3.600A pdb=" N ALA X 347 " --> pdb=" O ILE X 344 " (cutoff:3.500A) Processing helix chain 'Y' and resid 37 through 51 removed outlier: 3.584A pdb=" N MET Y 41 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET Y 43 " --> pdb=" O LEU Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 52 through 63 Processing helix chain 'Y' and resid 67 through 82 Processing helix chain 'Y' and resid 85 through 94 Processing helix chain 'Y' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA Y 102 " --> pdb=" O LYS Y 98 " (cutoff:3.500A) Processing helix chain 'Y' and resid 115 through 130 removed outlier: 3.643A pdb=" N LEU Y 121 " --> pdb=" O ALA Y 117 " (cutoff:3.500A) Processing helix chain 'Y' and resid 133 through 148 Processing helix chain 'Y' and resid 149 through 164 Processing helix chain 'Y' and resid 168 through 182 removed outlier: 3.930A pdb=" N THR Y 172 " --> pdb=" O LYS Y 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU Y 177 " --> pdb=" O ASN Y 173 " (cutoff:3.500A) Processing helix chain 'Y' and resid 183 through 195 Processing helix chain 'Y' and resid 197 through 211 removed outlier: 4.190A pdb=" N ALA Y 203 " --> pdb=" O ARG Y 199 " (cutoff:3.500A) Processing helix chain 'Z' and resid 338 through 342 Processing helix chain 'Z' and resid 344 through 348 removed outlier: 3.599A pdb=" N ALA Z 347 " --> pdb=" O ILE Z 344 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 51 removed outlier: 3.584A pdb=" N MET a 41 " --> pdb=" O GLN a 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET a 43 " --> pdb=" O LEU a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 52 through 63 Processing helix chain 'a' and resid 67 through 82 Processing helix chain 'a' and resid 85 through 94 Processing helix chain 'a' and resid 98 through 114 removed outlier: 3.583A pdb=" N ALA a 102 " --> pdb=" O LYS a 98 " (cutoff:3.500A) Processing helix chain 'a' and resid 115 through 130 removed outlier: 3.644A pdb=" N LEU a 121 " --> pdb=" O ALA a 117 " (cutoff:3.500A) Processing helix chain 'a' and resid 133 through 148 Processing helix chain 'a' and resid 149 through 164 Processing helix chain 'a' and resid 168 through 182 removed outlier: 3.929A pdb=" N THR a 172 " --> pdb=" O LYS a 168 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU a 177 " --> pdb=" O ASN a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 183 through 195 Processing helix chain 'a' and resid 197 through 211 removed outlier: 4.189A pdb=" N ALA a 203 " --> pdb=" O ARG a 199 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 157 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 162 through 166 current: chain 'A' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 203 through 220 current: chain 'A' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 350 through 370 current: chain 'C' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 162 through 166 current: chain 'C' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 203 through 220 current: chain 'C' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 350 through 370 current: chain 'E' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 162 through 166 current: chain 'E' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 203 through 220 current: chain 'E' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 350 through 370 current: chain 'G' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 162 through 166 current: chain 'G' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 203 through 220 current: chain 'G' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 350 through 370 current: chain 'I' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 162 through 166 current: chain 'I' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 203 through 220 current: chain 'I' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 350 through 370 current: chain 'K' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 162 through 166 current: chain 'K' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 203 through 220 current: chain 'K' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 350 through 370 current: chain 'M' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 162 through 166 current: chain 'M' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 203 through 220 current: chain 'M' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 350 through 370 current: chain 'O' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 162 through 166 current: chain 'O' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 203 through 220 current: chain 'O' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 350 through 370 current: chain 'Q' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 162 through 166 current: chain 'Q' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 203 through 220 current: chain 'Q' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 350 through 370 current: chain 'S' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 162 through 166 current: chain 'S' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 203 through 220 current: chain 'S' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 350 through 370 current: chain 'V' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 162 through 166 current: chain 'V' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 203 through 220 current: chain 'V' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 350 through 370 current: chain 'X' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 162 through 166 current: chain 'X' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 203 through 220 current: chain 'X' and resid 350 through 370 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 350 through 370 current: chain 'Z' and resid 162 through 166 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 162 through 166 current: chain 'Z' and resid 203 through 220 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 203 through 220 current: chain 'Z' and resid 350 through 370 Processing sheet with id=AA2, first strand: chain 'A' and resid 232 through 235 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 232 through 235 current: chain 'A' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 257 through 259 current: chain 'A' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 232 through 235 current: chain 'C' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 257 through 259 current: chain 'C' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 232 through 235 current: chain 'E' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 257 through 259 current: chain 'E' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 232 through 235 current: chain 'G' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 257 through 259 current: chain 'G' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 232 through 235 current: chain 'I' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 257 through 259 current: chain 'I' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 232 through 235 current: chain 'K' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 257 through 259 current: chain 'K' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 232 through 235 current: chain 'M' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 257 through 259 current: chain 'M' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 232 through 235 current: chain 'O' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 257 through 259 current: chain 'O' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 232 through 235 current: chain 'Q' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 257 through 259 current: chain 'Q' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 232 through 235 current: chain 'S' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 257 through 259 current: chain 'S' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 232 through 235 current: chain 'V' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 257 through 259 current: chain 'V' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 232 through 235 current: chain 'X' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 257 through 259 current: chain 'X' and resid 274 through 287 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 232 through 235 current: chain 'Z' and resid 257 through 259 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 257 through 259 current: chain 'Z' and resid 274 through 287 1690 hydrogen bonds defined for protein. 4914 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: 31.06 Time building geometry restraints manager: 58.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 42432 1.03 - 1.23: 16 1.23 - 1.42: 17664 1.42 - 1.62: 25298 1.62 - 1.81: 260 Bond restraints: 85670 Sorted by residual: bond pdb=" CA GLY I 201 " pdb=" C GLY I 201 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.04e-02 9.25e+03 3.13e+00 bond pdb=" CA GLY A 201 " pdb=" C GLY A 201 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.99e+00 bond pdb=" CA GLY V 201 " pdb=" C GLY V 201 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.88e+00 bond pdb=" CA GLY Q 201 " pdb=" C GLY Q 201 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.85e+00 bond pdb=" CA GLY Z 201 " pdb=" C GLY Z 201 " ideal model delta sigma weight residual 1.530 1.513 0.018 1.04e-02 9.25e+03 2.85e+00 ... (remaining 85665 not shown) Histogram of bond angle deviations from ideal: 64.95 - 79.89: 26 79.89 - 94.82: 39 94.82 - 109.75: 63423 109.75 - 124.69: 87881 124.69 - 139.62: 3123 Bond angle restraints: 154492 Sorted by residual: angle pdb=" C SER O 415 " pdb=" N ASP O 416 " pdb=" H ASP O 416 " ideal model delta sigma weight residual 124.30 74.59 49.71 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C SER Q 415 " pdb=" N ASP Q 416 " pdb=" H ASP Q 416 " ideal model delta sigma weight residual 124.30 74.60 49.70 3.00e+00 1.11e-01 2.74e+02 angle pdb=" C SER C 415 " pdb=" N ASP C 416 " pdb=" H ASP C 416 " ideal model delta sigma weight residual 124.30 74.60 49.70 3.00e+00 1.11e-01 2.74e+02 angle pdb=" C SER X 415 " pdb=" N ASP X 416 " pdb=" H ASP X 416 " ideal model delta sigma weight residual 124.30 74.60 49.70 3.00e+00 1.11e-01 2.74e+02 angle pdb=" C SER G 415 " pdb=" N ASP G 416 " pdb=" H ASP G 416 " ideal model delta sigma weight residual 124.30 74.60 49.70 3.00e+00 1.11e-01 2.74e+02 ... (remaining 154487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 36300 17.75 - 35.50: 2180 35.50 - 53.24: 910 53.24 - 70.99: 468 70.99 - 88.74: 65 Dihedral angle restraints: 39923 sinusoidal: 22477 harmonic: 17446 Sorted by residual: dihedral pdb=" CA PHE O 319 " pdb=" C PHE O 319 " pdb=" N VAL O 320 " pdb=" CA VAL O 320 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PHE M 319 " pdb=" C PHE M 319 " pdb=" N VAL M 320 " pdb=" CA VAL M 320 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PHE X 319 " pdb=" C PHE X 319 " pdb=" N VAL X 320 " pdb=" CA VAL X 320 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 39920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.316: 6526 0.316 - 0.632: 0 0.632 - 0.949: 0 0.949 - 1.265: 0 1.265 - 1.581: 13 Chirality restraints: 6539 Sorted by residual: chirality pdb=" CG LEU F 39 " pdb=" CB LEU F 39 " pdb=" CD1 LEU F 39 " pdb=" CD2 LEU F 39 " both_signs ideal model delta sigma weight residual False -2.59 -1.01 -1.58 2.00e-01 2.50e+01 6.25e+01 chirality pdb=" CG LEU a 39 " pdb=" CB LEU a 39 " pdb=" CD1 LEU a 39 " pdb=" CD2 LEU a 39 " both_signs ideal model delta sigma weight residual False -2.59 -1.01 -1.58 2.00e-01 2.50e+01 6.25e+01 chirality pdb=" CG LEU R 39 " pdb=" CB LEU R 39 " pdb=" CD1 LEU R 39 " pdb=" CD2 LEU R 39 " both_signs ideal model delta sigma weight residual False -2.59 -1.01 -1.58 2.00e-01 2.50e+01 6.25e+01 ... (remaining 6536 not shown) Planarity restraints: 12922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU L 169 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO L 170 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO L 170 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 170 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 169 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO B 170 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 170 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 170 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU W 169 " 0.024 5.00e-02 4.00e+02 3.59e-02 2.07e+00 pdb=" N PRO W 170 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO W 170 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO W 170 " 0.020 5.00e-02 4.00e+02 ... (remaining 12919 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 3930 2.18 - 2.78: 172040 2.78 - 3.39: 236575 3.39 - 3.99: 304470 3.99 - 4.60: 477968 Nonbonded interactions: 1194983 Sorted by model distance: nonbonded pdb=" OE1 GLU E 142 " pdb="HH11 ARG E 305 " model vdw 1.570 1.850 nonbonded pdb=" OE1 GLU K 142 " pdb="HH11 ARG K 305 " model vdw 1.570 1.850 nonbonded pdb=" OE1 GLU I 142 " pdb="HH11 ARG I 305 " model vdw 1.570 1.850 nonbonded pdb=" OE1 GLU Z 142 " pdb="HH11 ARG Z 305 " model vdw 1.570 1.850 nonbonded pdb=" OE1 GLU S 142 " pdb="HH11 ARG S 305 " model vdw 1.570 1.850 ... (remaining 1194978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'a' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 1.020 Extract box with map and model: 12.590 Check model and map are aligned: 0.950 Set scattering table: 0.680 Process input model: 212.220 Find NCS groups from input model: 3.750 Set up NCS constraints: 0.620 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: 0.020 Load rotamer database and sin/cos tables:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 248.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 43225 Z= 0.197 Angle : 0.625 17.922 58292 Z= 0.320 Chirality : 0.080 1.581 6539 Planarity : 0.004 0.036 7722 Dihedral : 12.943 88.738 16276 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.58 % Allowed : 5.35 % Favored : 94.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.11), residues: 5473 helix: -0.23 (0.10), residues: 2080 sheet: -0.17 (0.13), residues: 1807 loop : -0.55 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 211 HIS 0.003 0.001 HIS D 54 PHE 0.009 0.001 PHE E 319 TYR 0.004 0.001 TYR C 217 ARG 0.004 0.000 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 899 time to evaluate : 7.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8585 (mtm) cc_final: 0.8278 (mtm) REVERT: B 33 LEU cc_start: 0.5213 (OUTLIER) cc_final: 0.4507 (pt) REVERT: C 285 GLU cc_start: 0.8342 (pt0) cc_final: 0.8126 (pt0) REVERT: D 33 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4620 (pt) REVERT: E 287 ASP cc_start: 0.7273 (t0) cc_final: 0.6981 (t0) REVERT: F 33 LEU cc_start: 0.4798 (OUTLIER) cc_final: 0.4495 (pt) REVERT: F 40 GLN cc_start: 0.6288 (tp40) cc_final: 0.6009 (tm-30) REVERT: H 33 LEU cc_start: 0.5062 (OUTLIER) cc_final: 0.4011 (pt) REVERT: J 33 LEU cc_start: 0.5243 (OUTLIER) cc_final: 0.4680 (pt) REVERT: L 33 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4909 (pt) REVERT: N 33 LEU cc_start: 0.5143 (OUTLIER) cc_final: 0.4890 (pt) REVERT: P 33 LEU cc_start: 0.5288 (OUTLIER) cc_final: 0.4951 (pt) REVERT: R 33 LEU cc_start: 0.5174 (OUTLIER) cc_final: 0.4737 (pt) REVERT: T 33 LEU cc_start: 0.4790 (OUTLIER) cc_final: 0.4294 (pt) REVERT: W 63 MET cc_start: 0.4079 (mtm) cc_final: 0.3576 (mpp) REVERT: Y 33 LEU cc_start: 0.5272 (OUTLIER) cc_final: 0.4517 (pt) REVERT: Y 47 MET cc_start: 0.2991 (mtm) cc_final: 0.2631 (mtm) REVERT: a 33 LEU cc_start: 0.4869 (OUTLIER) cc_final: 0.3956 (pt) outliers start: 26 outliers final: 1 residues processed: 916 average time/residue: 3.4717 time to fit residues: 3786.5229 Evaluate side-chains 619 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 606 time to evaluate : 5.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain F residue 33 LEU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain J residue 33 LEU Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain T residue 33 LEU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain a residue 33 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 461 optimal weight: 4.9990 chunk 413 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 10.0000 chunk 221 optimal weight: 1.9990 chunk 427 optimal weight: 0.7980 chunk 165 optimal weight: 9.9990 chunk 260 optimal weight: 1.9990 chunk 318 optimal weight: 0.9990 chunk 495 optimal weight: 9.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN B 40 GLN B 91 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN F 32 GLN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 133 GLN H 32 GLN ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN J 40 GLN ** J 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN K 161 ASN L 32 GLN L 42 ASN ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 133 GLN M 161 ASN ** N 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 133 GLN P 40 GLN ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 133 GLN ** R 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 133 GLN S 161 ASN T 32 GLN ** T 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 133 GLN V 161 ASN ** W 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 133 GLN Y 59 ASN ** Y 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 133 GLN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 43225 Z= 0.246 Angle : 0.668 18.024 58292 Z= 0.340 Chirality : 0.088 1.842 6539 Planarity : 0.005 0.076 7722 Dihedral : 4.978 44.176 6123 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.11 % Allowed : 10.71 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.12), residues: 5473 helix: 0.48 (0.11), residues: 2106 sheet: -0.34 (0.13), residues: 1742 loop : -0.48 (0.17), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP M 338 HIS 0.006 0.001 HIS H 103 PHE 0.012 0.002 PHE A 155 TYR 0.009 0.001 TYR Z 256 ARG 0.012 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 606 time to evaluate : 5.208 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8620 (mtm) cc_final: 0.8353 (mtm) REVERT: B 189 ARG cc_start: 0.2340 (OUTLIER) cc_final: 0.1956 (tmt170) REVERT: D 41 MET cc_start: 0.5220 (tmm) cc_final: 0.4929 (tmm) REVERT: D 189 ARG cc_start: 0.2511 (OUTLIER) cc_final: 0.2154 (tmt170) REVERT: F 46 ASP cc_start: 0.5887 (OUTLIER) cc_final: 0.5603 (m-30) REVERT: F 53 LEU cc_start: 0.4585 (mm) cc_final: 0.4361 (mt) REVERT: F 189 ARG cc_start: 0.2444 (OUTLIER) cc_final: 0.2231 (tmt170) REVERT: H 53 LEU cc_start: 0.4700 (mm) cc_final: 0.4480 (mp) REVERT: H 189 ARG cc_start: 0.2485 (OUTLIER) cc_final: 0.2023 (tmt170) REVERT: I 139 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7791 (ttt180) REVERT: I 303 ARG cc_start: 0.7846 (ttm-80) cc_final: 0.7405 (ttp-170) REVERT: I 355 ASP cc_start: 0.7305 (t0) cc_final: 0.7063 (t0) REVERT: J 91 GLN cc_start: 0.3812 (tm130) cc_final: 0.3399 (tp40) REVERT: K 139 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7923 (ttt90) REVERT: L 49 ARG cc_start: 0.6310 (ttm-80) cc_final: 0.5944 (mtm180) REVERT: L 189 ARG cc_start: 0.2345 (OUTLIER) cc_final: 0.1862 (ttt180) REVERT: N 47 MET cc_start: 0.2919 (mtm) cc_final: 0.2346 (mpp) REVERT: N 49 ARG cc_start: 0.6617 (ttm-80) cc_final: 0.6051 (mtm180) REVERT: O 303 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7535 (ttp-170) REVERT: P 42 ASN cc_start: 0.5383 (m-40) cc_final: 0.5021 (t0) REVERT: P 46 ASP cc_start: 0.5299 (OUTLIER) cc_final: 0.5004 (m-30) REVERT: P 53 LEU cc_start: 0.4583 (mm) cc_final: 0.4325 (mt) REVERT: R 43 MET cc_start: 0.4952 (ptt) cc_final: 0.4725 (ttm) REVERT: R 63 MET cc_start: 0.4521 (OUTLIER) cc_final: 0.3944 (mpm) REVERT: T 189 ARG cc_start: 0.2665 (OUTLIER) cc_final: 0.2215 (ttt180) REVERT: V 355 ASP cc_start: 0.7436 (t0) cc_final: 0.7139 (t0) REVERT: W 46 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5995 (m-30) REVERT: W 63 MET cc_start: 0.4211 (mtm) cc_final: 0.3687 (mpt) REVERT: W 189 ARG cc_start: 0.2080 (OUTLIER) cc_final: 0.1839 (tmt170) REVERT: Y 32 GLN cc_start: 0.5275 (OUTLIER) cc_final: 0.4823 (tp40) REVERT: Y 46 ASP cc_start: 0.5354 (OUTLIER) cc_final: 0.5127 (m-30) REVERT: Y 91 GLN cc_start: 0.4460 (tm130) cc_final: 0.4144 (tp-100) REVERT: Y 189 ARG cc_start: 0.2388 (OUTLIER) cc_final: 0.2179 (tmt170) REVERT: a 46 ASP cc_start: 0.5705 (OUTLIER) cc_final: 0.5421 (m-30) outliers start: 94 outliers final: 24 residues processed: 660 average time/residue: 3.3333 time to fit residues: 2685.4690 Evaluate side-chains 592 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 551 time to evaluate : 5.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 189 ARG Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain H residue 189 ARG Chi-restraints excluded: chain I residue 139 ARG Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 189 ARG Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 233 SER Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain T residue 189 ARG Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 360 GLU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 189 ARG Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 46 ASP Chi-restraints excluded: chain Y residue 189 ARG Chi-restraints excluded: chain Z residue 233 SER Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain a residue 46 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 275 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 412 optimal weight: 20.0000 chunk 337 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 496 optimal weight: 1.9990 chunk 536 optimal weight: 30.0000 chunk 442 optimal weight: 0.0770 chunk 492 optimal weight: 10.0000 chunk 169 optimal weight: 1.9990 chunk 398 optimal weight: 0.8980 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 59 ASN B 91 GLN B 173 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** H 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 40 GLN ** J 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 91 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 173 ASN ** Y 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 ASN a 40 GLN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43225 Z= 0.216 Angle : 0.660 17.951 58292 Z= 0.332 Chirality : 0.086 1.762 6539 Planarity : 0.005 0.060 7722 Dihedral : 4.899 22.883 6097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.73 % Allowed : 11.85 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.12), residues: 5473 helix: 1.00 (0.11), residues: 2093 sheet: -0.53 (0.12), residues: 1820 loop : -0.49 (0.17), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 163 HIS 0.005 0.001 HIS H 103 PHE 0.011 0.001 PHE G 319 TYR 0.025 0.001 TYR a 90 ARG 0.011 0.000 ARG L 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 569 time to evaluate : 5.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 270 MET cc_start: 0.8625 (mtm) cc_final: 0.8381 (mtm) REVERT: C 357 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7536 (p0) REVERT: D 63 MET cc_start: 0.5216 (ptp) cc_final: 0.5013 (ptp) REVERT: E 303 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7271 (ttm-80) REVERT: F 32 GLN cc_start: 0.4808 (OUTLIER) cc_final: 0.4594 (tm-30) REVERT: F 46 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5688 (m-30) REVERT: F 189 ARG cc_start: 0.2501 (OUTLIER) cc_final: 0.2296 (tmt170) REVERT: H 132 THR cc_start: 0.5420 (OUTLIER) cc_final: 0.5215 (p) REVERT: I 303 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7349 (ttp-170) REVERT: I 319 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7178 (m-80) REVERT: I 355 ASP cc_start: 0.7293 (t0) cc_final: 0.7085 (t0) REVERT: J 41 MET cc_start: 0.5101 (tmm) cc_final: 0.4638 (tmm) REVERT: J 91 GLN cc_start: 0.3893 (tm130) cc_final: 0.3511 (tp40) REVERT: L 32 GLN cc_start: 0.4345 (OUTLIER) cc_final: 0.3913 (tp40) REVERT: L 49 ARG cc_start: 0.6050 (ttm-80) cc_final: 0.5804 (mtm180) REVERT: N 49 ARG cc_start: 0.6614 (ttm-80) cc_final: 0.6093 (mtm180) REVERT: N 53 LEU cc_start: 0.4576 (mm) cc_final: 0.4374 (mt) REVERT: O 303 ARG cc_start: 0.7763 (ttm-80) cc_final: 0.7520 (ttp-170) REVERT: O 319 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: P 41 MET cc_start: 0.5106 (tmm) cc_final: 0.4811 (tmm) REVERT: P 42 ASN cc_start: 0.5673 (m-40) cc_final: 0.5358 (t0) REVERT: R 43 MET cc_start: 0.4735 (ptt) cc_final: 0.4456 (ttp) REVERT: R 63 MET cc_start: 0.4380 (OUTLIER) cc_final: 0.3668 (mpm) REVERT: R 83 ASP cc_start: 0.4720 (m-30) cc_final: 0.4467 (m-30) REVERT: R 189 ARG cc_start: 0.1956 (OUTLIER) cc_final: 0.1719 (tmt170) REVERT: S 319 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.7954 (m-80) REVERT: V 355 ASP cc_start: 0.7470 (t0) cc_final: 0.7236 (t0) REVERT: W 40 GLN cc_start: 0.6608 (mt0) cc_final: 0.6370 (mp10) REVERT: W 63 MET cc_start: 0.4230 (mtm) cc_final: 0.3557 (mpp) REVERT: X 273 ARG cc_start: 0.7820 (mmp80) cc_final: 0.7587 (mmt180) REVERT: X 355 ASP cc_start: 0.7446 (t0) cc_final: 0.7158 (t0) REVERT: Y 32 GLN cc_start: 0.4886 (OUTLIER) cc_final: 0.4534 (tp40) REVERT: Y 91 GLN cc_start: 0.4478 (tm130) cc_final: 0.4088 (tp-100) REVERT: a 41 MET cc_start: 0.5277 (tmm) cc_final: 0.5034 (tmm) outliers start: 77 outliers final: 36 residues processed: 613 average time/residue: 3.0886 time to fit residues: 2289.4301 Evaluate side-chains 579 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 531 time to evaluate : 6.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 147 ARG Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain L residue 32 GLN Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 189 ARG Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain T residue 63 MET Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 319 PHE Chi-restraints excluded: chain V residue 360 GLU Chi-restraints excluded: chain W residue 53 LEU Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 326 SER Chi-restraints excluded: chain Z residue 357 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 490 optimal weight: 9.9990 chunk 373 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 237 optimal weight: 10.0000 chunk 333 optimal weight: 10.0000 chunk 498 optimal weight: 30.0000 chunk 527 optimal weight: 0.7980 chunk 260 optimal weight: 1.9990 chunk 472 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 59 ASN B 91 GLN D 40 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 173 ASN ** W 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 43225 Z= 0.268 Angle : 0.661 18.039 58292 Z= 0.335 Chirality : 0.087 1.775 6539 Planarity : 0.005 0.065 7722 Dihedral : 4.870 21.092 6097 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.20 % Allowed : 11.99 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.12), residues: 5473 helix: 1.29 (0.11), residues: 2106 sheet: -0.73 (0.12), residues: 1807 loop : -0.76 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 163 HIS 0.007 0.001 HIS T 103 PHE 0.013 0.002 PHE G 319 TYR 0.025 0.002 TYR a 90 ARG 0.009 0.000 ARG N 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 536 time to evaluate : 5.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 270 MET cc_start: 0.8667 (mtm) cc_final: 0.8428 (mtm) REVERT: C 357 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7413 (p0) REVERT: D 41 MET cc_start: 0.4729 (tmm) cc_final: 0.4478 (tmm) REVERT: E 303 ARG cc_start: 0.7790 (ttm-80) cc_final: 0.7287 (ttm-80) REVERT: E 355 ASP cc_start: 0.7227 (t0) cc_final: 0.6900 (t0) REVERT: F 32 GLN cc_start: 0.4841 (OUTLIER) cc_final: 0.4236 (pp30) REVERT: F 46 ASP cc_start: 0.5972 (OUTLIER) cc_final: 0.5693 (m-30) REVERT: F 53 LEU cc_start: 0.4482 (mm) cc_final: 0.4277 (mt) REVERT: F 173 ASN cc_start: 0.1121 (m-40) cc_final: 0.0800 (m-40) REVERT: F 189 ARG cc_start: 0.2545 (OUTLIER) cc_final: 0.2338 (tmt170) REVERT: G 319 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8137 (m-80) REVERT: H 132 THR cc_start: 0.5387 (OUTLIER) cc_final: 0.5172 (t) REVERT: I 303 ARG cc_start: 0.7782 (ttm-80) cc_final: 0.7324 (ttp-170) REVERT: I 319 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: J 91 GLN cc_start: 0.3832 (tm130) cc_final: 0.3464 (tp40) REVERT: K 139 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7860 (ttt90) REVERT: L 32 GLN cc_start: 0.4135 (OUTLIER) cc_final: 0.3788 (tm-30) REVERT: L 49 ARG cc_start: 0.6087 (ttm-80) cc_final: 0.5788 (mtm180) REVERT: L 91 GLN cc_start: 0.4022 (tm-30) cc_final: 0.3706 (tp-100) REVERT: N 49 ARG cc_start: 0.6574 (ttm-80) cc_final: 0.6020 (mtm180) REVERT: N 74 ARG cc_start: 0.5340 (ttp-170) cc_final: 0.5098 (ttp-170) REVERT: O 319 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: P 42 ASN cc_start: 0.5534 (m-40) cc_final: 0.5260 (t0) REVERT: P 53 LEU cc_start: 0.4910 (mm) cc_final: 0.4667 (mt) REVERT: R 63 MET cc_start: 0.4277 (OUTLIER) cc_final: 0.3553 (mpm) REVERT: R 83 ASP cc_start: 0.4772 (m-30) cc_final: 0.4487 (m-30) REVERT: R 189 ARG cc_start: 0.2130 (OUTLIER) cc_final: 0.1911 (tmt170) REVERT: S 170 SER cc_start: 0.7307 (t) cc_final: 0.7086 (p) REVERT: S 319 PHE cc_start: 0.9003 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: X 170 SER cc_start: 0.7572 (t) cc_final: 0.6732 (p) REVERT: X 355 ASP cc_start: 0.7399 (t0) cc_final: 0.7185 (t0) REVERT: Y 32 GLN cc_start: 0.4610 (OUTLIER) cc_final: 0.4246 (tp40) REVERT: Y 91 GLN cc_start: 0.4616 (tm130) cc_final: 0.4234 (tp-100) REVERT: a 48 ILE cc_start: 0.3883 (mm) cc_final: 0.3448 (mt) REVERT: a 53 LEU cc_start: 0.5126 (OUTLIER) cc_final: 0.4699 (mm) REVERT: a 189 ARG cc_start: 0.2152 (OUTLIER) cc_final: 0.1732 (tmt170) outliers start: 98 outliers final: 49 residues processed: 592 average time/residue: 2.9363 time to fit residues: 2119.9952 Evaluate side-chains 577 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 512 time to evaluate : 5.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain K residue 360 GLU Chi-restraints excluded: chain L residue 32 GLN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 97 CYS Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 97 CYS Chi-restraints excluded: chain R residue 189 ARG Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain T residue 43 MET Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 CYS Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 360 GLU Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 97 CYS Chi-restraints excluded: chain a residue 189 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 439 optimal weight: 2.9990 chunk 299 optimal weight: 4.9990 chunk 7 optimal weight: 0.3980 chunk 392 optimal weight: 2.9990 chunk 217 optimal weight: 4.9990 chunk 450 optimal weight: 5.9990 chunk 364 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 chunk 473 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 91 GLN D 40 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** J 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 161 ASN O 293 GLN P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 293 GLN ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 ASN ** Y 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 43225 Z= 0.300 Angle : 0.675 18.114 58292 Z= 0.343 Chirality : 0.087 1.774 6539 Planarity : 0.005 0.054 7722 Dihedral : 4.949 22.908 6097 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 12.12 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.12), residues: 5473 helix: 1.62 (0.11), residues: 2093 sheet: -1.06 (0.12), residues: 1833 loop : -0.92 (0.15), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 163 HIS 0.007 0.001 HIS D 103 PHE 0.015 0.002 PHE G 319 TYR 0.033 0.002 TYR a 90 ARG 0.010 0.001 ARG V 303 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 517 time to evaluate : 5.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8673 (mtm) cc_final: 0.8360 (mtm) REVERT: D 41 MET cc_start: 0.5037 (tmm) cc_final: 0.4740 (tmm) REVERT: E 303 ARG cc_start: 0.7770 (ttm-80) cc_final: 0.7272 (ttp80) REVERT: E 357 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7778 (p0) REVERT: F 32 GLN cc_start: 0.4974 (OUTLIER) cc_final: 0.4373 (pp30) REVERT: F 46 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5695 (m-30) REVERT: F 173 ASN cc_start: 0.1234 (m-40) cc_final: 0.0925 (m-40) REVERT: F 189 ARG cc_start: 0.2429 (OUTLIER) cc_final: 0.2218 (tmt170) REVERT: G 173 ASP cc_start: 0.6021 (OUTLIER) cc_final: 0.5775 (m-30) REVERT: G 319 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.8227 (m-80) REVERT: H 74 ARG cc_start: 0.4918 (ttp-170) cc_final: 0.4552 (ttm-80) REVERT: H 132 THR cc_start: 0.5606 (OUTLIER) cc_final: 0.5394 (t) REVERT: I 303 ARG cc_start: 0.7745 (ttm-80) cc_final: 0.7288 (ttp-170) REVERT: I 313 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8363 (mp) REVERT: I 319 PHE cc_start: 0.9108 (OUTLIER) cc_final: 0.7064 (m-80) REVERT: J 41 MET cc_start: 0.5005 (tmm) cc_final: 0.4596 (tmm) REVERT: J 91 GLN cc_start: 0.3877 (tm130) cc_final: 0.3542 (tp40) REVERT: K 139 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7882 (ttt90) REVERT: K 319 PHE cc_start: 0.9131 (OUTLIER) cc_final: 0.8891 (m-80) REVERT: L 32 GLN cc_start: 0.4148 (OUTLIER) cc_final: 0.3883 (tp40) REVERT: L 49 ARG cc_start: 0.6060 (ttm-80) cc_final: 0.5625 (mtm180) REVERT: L 74 ARG cc_start: 0.4659 (ttp80) cc_final: 0.4458 (ttp80) REVERT: L 91 GLN cc_start: 0.4044 (tm-30) cc_final: 0.3704 (tp-100) REVERT: M 355 ASP cc_start: 0.7467 (t0) cc_final: 0.7193 (t0) REVERT: N 49 ARG cc_start: 0.6366 (ttm-80) cc_final: 0.5889 (mtm180) REVERT: N 74 ARG cc_start: 0.5288 (ttp-170) cc_final: 0.5049 (ttp-170) REVERT: O 303 ARG cc_start: 0.7821 (ttm-80) cc_final: 0.7538 (ttp-170) REVERT: O 313 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8313 (mp) REVERT: O 319 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7415 (m-80) REVERT: P 41 MET cc_start: 0.5401 (tmm) cc_final: 0.5101 (tmm) REVERT: P 42 ASN cc_start: 0.5487 (m-40) cc_final: 0.5023 (t0) REVERT: P 53 LEU cc_start: 0.5054 (mm) cc_final: 0.4785 (mt) REVERT: Q 313 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8393 (mp) REVERT: R 32 GLN cc_start: 0.4297 (OUTLIER) cc_final: 0.3745 (tp40) REVERT: R 63 MET cc_start: 0.4273 (OUTLIER) cc_final: 0.3500 (mpm) REVERT: R 189 ARG cc_start: 0.2095 (OUTLIER) cc_final: 0.1894 (tmt170) REVERT: S 170 SER cc_start: 0.7324 (t) cc_final: 0.7118 (p) REVERT: S 319 PHE cc_start: 0.9021 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: T 46 ASP cc_start: 0.5690 (OUTLIER) cc_final: 0.5488 (m-30) REVERT: T 53 LEU cc_start: 0.5157 (OUTLIER) cc_final: 0.4753 (mm) REVERT: W 53 LEU cc_start: 0.5285 (mp) cc_final: 0.4839 (mm) REVERT: X 170 SER cc_start: 0.7567 (t) cc_final: 0.6731 (p) REVERT: X 355 ASP cc_start: 0.7418 (t0) cc_final: 0.7204 (t0) REVERT: Y 32 GLN cc_start: 0.4406 (OUTLIER) cc_final: 0.3950 (tp40) REVERT: Y 91 GLN cc_start: 0.4357 (tm130) cc_final: 0.4047 (tp-100) REVERT: Z 173 ASP cc_start: 0.6231 (OUTLIER) cc_final: 0.5977 (m-30) REVERT: a 41 MET cc_start: 0.5443 (tmm) cc_final: 0.4950 (tmm) REVERT: a 48 ILE cc_start: 0.3973 (mm) cc_final: 0.3559 (mt) REVERT: a 53 LEU cc_start: 0.5160 (OUTLIER) cc_final: 0.4753 (mm) REVERT: a 189 ARG cc_start: 0.2112 (OUTLIER) cc_final: 0.1716 (tmt170) outliers start: 113 outliers final: 61 residues processed: 590 average time/residue: 2.9176 time to fit residues: 2105.6670 Evaluate side-chains 585 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 499 time to evaluate : 5.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 189 ARG Chi-restraints excluded: chain G residue 173 ASP Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain G residue 357 ASP Chi-restraints excluded: chain G residue 360 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 355 ASP Chi-restraints excluded: chain K residue 357 ASP Chi-restraints excluded: chain K residue 358 ASP Chi-restraints excluded: chain L residue 32 GLN Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 96 THR Chi-restraints excluded: chain N residue 97 CYS Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 96 THR Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 173 ASP Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 355 ASP Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 CYS Chi-restraints excluded: chain R residue 189 ARG Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 173 ASP Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 53 LEU Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 319 PHE Chi-restraints excluded: chain W residue 40 GLN Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Z residue 173 ASP Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 326 SER Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 189 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 177 optimal weight: 1.9990 chunk 475 optimal weight: 1.9990 chunk 104 optimal weight: 0.1980 chunk 309 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 528 optimal weight: 20.0000 chunk 438 optimal weight: 0.3980 chunk 244 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 277 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN B 91 GLN ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN ** J 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN N 91 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 GLN ** T 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 40 GLN ** a 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 43225 Z= 0.175 Angle : 0.621 18.022 58292 Z= 0.311 Chirality : 0.086 1.759 6539 Planarity : 0.004 0.073 7722 Dihedral : 4.643 20.407 6097 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 13.18 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.12), residues: 5473 helix: 1.73 (0.11), residues: 2119 sheet: -0.98 (0.12), residues: 1807 loop : -0.68 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP O 163 HIS 0.003 0.001 HIS X 368 PHE 0.012 0.001 PHE G 319 TYR 0.019 0.002 TYR a 90 ARG 0.008 0.000 ARG K 303 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 517 time to evaluate : 5.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 270 MET cc_start: 0.8620 (mtm) cc_final: 0.8373 (mtm) REVERT: B 91 GLN cc_start: 0.4241 (mm-40) cc_final: 0.3393 (pp30) REVERT: D 41 MET cc_start: 0.5218 (tmm) cc_final: 0.4993 (tmm) REVERT: E 303 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7260 (ttp80) REVERT: F 32 GLN cc_start: 0.4909 (OUTLIER) cc_final: 0.4325 (pp30) REVERT: F 46 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5737 (m-30) REVERT: F 173 ASN cc_start: 0.1286 (m-40) cc_final: 0.0956 (m-40) REVERT: G 175 LYS cc_start: 0.8141 (mmtm) cc_final: 0.7875 (mmtt) REVERT: G 319 PHE cc_start: 0.9032 (OUTLIER) cc_final: 0.7879 (m-80) REVERT: H 74 ARG cc_start: 0.4889 (ttp-170) cc_final: 0.4390 (mtp85) REVERT: H 132 THR cc_start: 0.5516 (OUTLIER) cc_final: 0.5291 (t) REVERT: I 303 ARG cc_start: 0.7736 (ttm-80) cc_final: 0.7282 (ttp-170) REVERT: I 313 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8393 (mp) REVERT: I 319 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: I 355 ASP cc_start: 0.7424 (t0) cc_final: 0.7149 (t0) REVERT: K 139 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7752 (ttt90) REVERT: L 49 ARG cc_start: 0.6030 (ttm-80) cc_final: 0.5614 (mtm180) REVERT: L 91 GLN cc_start: 0.4237 (tm-30) cc_final: 0.3893 (tp-100) REVERT: N 49 ARG cc_start: 0.6346 (ttm-80) cc_final: 0.5910 (mtm180) REVERT: N 53 LEU cc_start: 0.5262 (mt) cc_final: 0.4945 (mm) REVERT: O 303 ARG cc_start: 0.7741 (ttm-80) cc_final: 0.7473 (ttp-170) REVERT: O 319 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: P 41 MET cc_start: 0.5317 (tmm) cc_final: 0.5091 (tmm) REVERT: P 42 ASN cc_start: 0.5533 (m-40) cc_final: 0.5159 (t0) REVERT: P 91 GLN cc_start: 0.4310 (tm130) cc_final: 0.3924 (tp-100) REVERT: Q 313 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8375 (mp) REVERT: R 63 MET cc_start: 0.4105 (OUTLIER) cc_final: 0.3393 (mpm) REVERT: S 170 SER cc_start: 0.7293 (t) cc_final: 0.7090 (p) REVERT: S 319 PHE cc_start: 0.9017 (OUTLIER) cc_final: 0.7796 (m-80) REVERT: W 53 LEU cc_start: 0.5244 (mp) cc_final: 0.4800 (mm) REVERT: X 170 SER cc_start: 0.7499 (t) cc_final: 0.6639 (p) REVERT: Y 32 GLN cc_start: 0.4210 (OUTLIER) cc_final: 0.3700 (tp40) REVERT: Y 91 GLN cc_start: 0.4377 (tm130) cc_final: 0.4040 (tp-100) REVERT: a 41 MET cc_start: 0.5302 (tmm) cc_final: 0.4809 (tmm) REVERT: a 48 ILE cc_start: 0.3897 (mm) cc_final: 0.3605 (mt) outliers start: 87 outliers final: 45 residues processed: 574 average time/residue: 2.9472 time to fit residues: 2069.4471 Evaluate side-chains 558 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 501 time to evaluate : 5.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 313 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 358 ASP Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 97 CYS Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 173 ASP Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 97 CYS Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain S residue 355 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 CYS Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 173 ASP Chi-restraints excluded: chain V residue 319 PHE Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Z residue 284 SER Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 97 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 509 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 385 optimal weight: 3.9990 chunk 298 optimal weight: 7.9990 chunk 444 optimal weight: 20.0000 chunk 294 optimal weight: 2.9990 chunk 526 optimal weight: 1.9990 chunk 329 optimal weight: 20.0000 chunk 320 optimal weight: 9.9990 chunk 242 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN B 40 GLN ** B 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 GLN D 40 GLN ** D 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 293 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN K 293 GLN ** L 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 293 GLN ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 59 ASN Z 293 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 43225 Z= 0.417 Angle : 0.731 18.170 58292 Z= 0.373 Chirality : 0.089 1.793 6539 Planarity : 0.005 0.059 7722 Dihedral : 5.111 24.326 6097 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.63 % Allowed : 12.93 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 5473 helix: 1.74 (0.11), residues: 2093 sheet: -1.47 (0.12), residues: 1859 loop : -1.09 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 163 HIS 0.006 0.001 HIS Z 368 PHE 0.019 0.002 PHE G 319 TYR 0.020 0.003 TYR W 90 ARG 0.010 0.001 ARG Z 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 499 time to evaluate : 5.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8693 (mtm) cc_final: 0.8448 (mtm) REVERT: B 91 GLN cc_start: 0.4684 (mm-40) cc_final: 0.3692 (pp30) REVERT: E 357 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7666 (p0) REVERT: F 32 GLN cc_start: 0.4922 (OUTLIER) cc_final: 0.4366 (pp30) REVERT: G 319 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8180 (m-80) REVERT: H 49 ARG cc_start: 0.5923 (OUTLIER) cc_final: 0.5409 (mtt-85) REVERT: H 53 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.4365 (mm) REVERT: H 63 MET cc_start: 0.4742 (OUTLIER) cc_final: 0.4421 (mpp) REVERT: H 74 ARG cc_start: 0.4901 (ttp-170) cc_final: 0.4546 (ttm-80) REVERT: I 303 ARG cc_start: 0.7723 (ttm-80) cc_final: 0.7490 (ttp-170) REVERT: J 41 MET cc_start: 0.4922 (tmm) cc_final: 0.4499 (tmm) REVERT: J 63 MET cc_start: 0.4891 (OUTLIER) cc_final: 0.4268 (mpm) REVERT: K 139 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (ttt90) REVERT: L 49 ARG cc_start: 0.5917 (ttm-80) cc_final: 0.5441 (mtm180) REVERT: N 43 MET cc_start: 0.4205 (OUTLIER) cc_final: 0.3754 (tmm) REVERT: N 49 ARG cc_start: 0.6390 (ttm-80) cc_final: 0.5948 (mtm180) REVERT: N 53 LEU cc_start: 0.5291 (mt) cc_final: 0.5029 (mm) REVERT: O 313 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8576 (mp) REVERT: P 41 MET cc_start: 0.5087 (tmm) cc_final: 0.4790 (tmm) REVERT: P 42 ASN cc_start: 0.5570 (m-40) cc_final: 0.5244 (t0) REVERT: Q 313 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8418 (mp) REVERT: R 32 GLN cc_start: 0.4198 (OUTLIER) cc_final: 0.3651 (tp40) REVERT: R 48 ILE cc_start: 0.3460 (mm) cc_final: 0.3060 (mt) REVERT: R 146 LYS cc_start: 0.3611 (OUTLIER) cc_final: 0.2951 (tppp) REVERT: S 170 SER cc_start: 0.7355 (t) cc_final: 0.7139 (p) REVERT: S 319 PHE cc_start: 0.9013 (OUTLIER) cc_final: 0.7827 (m-80) REVERT: T 63 MET cc_start: 0.4222 (mtm) cc_final: 0.3589 (mpt) REVERT: V 270 MET cc_start: 0.8793 (mtm) cc_final: 0.8541 (mtm) REVERT: W 53 LEU cc_start: 0.5390 (mp) cc_final: 0.4921 (mm) REVERT: X 170 SER cc_start: 0.7689 (t) cc_final: 0.6756 (p) REVERT: Y 32 GLN cc_start: 0.4237 (OUTLIER) cc_final: 0.3764 (tp40) REVERT: Y 91 GLN cc_start: 0.4326 (tm130) cc_final: 0.3992 (tp-100) REVERT: a 48 ILE cc_start: 0.3975 (mm) cc_final: 0.3683 (mt) REVERT: a 189 ARG cc_start: 0.2291 (OUTLIER) cc_final: 0.1902 (tmt170) outliers start: 117 outliers final: 64 residues processed: 577 average time/residue: 2.8247 time to fit residues: 2007.4178 Evaluate side-chains 566 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 486 time to evaluate : 5.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 32 GLN Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 173 ASP Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 173 ASP Chi-restraints excluded: chain E residue 175 LYS Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 357 ASP Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 173 ASP Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 173 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 173 ASP Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 97 CYS Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 173 ASP Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 173 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 40 GLN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 173 ASP Chi-restraints excluded: chain S residue 284 SER Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 CYS Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 173 ASP Chi-restraints excluded: chain V residue 357 ASP Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 96 THR Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Y residue 147 ARG Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 189 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 325 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 314 optimal weight: 4.9990 chunk 158 optimal weight: 20.0000 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 334 optimal weight: 8.9990 chunk 358 optimal weight: 0.5980 chunk 260 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 413 optimal weight: 20.0000 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 40 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN N 40 GLN N 91 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 GLN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 43225 Z= 0.224 Angle : 0.647 18.141 58292 Z= 0.325 Chirality : 0.087 1.792 6539 Planarity : 0.004 0.091 7722 Dihedral : 4.786 21.442 6097 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.05 % Allowed : 13.88 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 5473 helix: 1.84 (0.11), residues: 2106 sheet: -1.41 (0.12), residues: 1885 loop : -0.86 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP X 163 HIS 0.007 0.001 HIS W 103 PHE 0.014 0.001 PHE G 319 TYR 0.023 0.002 TYR W 90 ARG 0.014 0.000 ARG E 303 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 507 time to evaluate : 5.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 303 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7249 (ttm-80) REVERT: F 32 GLN cc_start: 0.4804 (OUTLIER) cc_final: 0.4281 (pp30) REVERT: G 175 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7720 (mmtt) REVERT: G 319 PHE cc_start: 0.9063 (OUTLIER) cc_final: 0.7942 (m-80) REVERT: H 74 ARG cc_start: 0.4892 (ttp-170) cc_final: 0.4375 (mtp85) REVERT: H 132 THR cc_start: 0.5536 (OUTLIER) cc_final: 0.5313 (t) REVERT: I 303 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7495 (ttp-170) REVERT: I 319 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: J 41 MET cc_start: 0.4933 (tmm) cc_final: 0.4696 (tmm) REVERT: K 139 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7812 (ttt90) REVERT: L 49 ARG cc_start: 0.5873 (ttm-80) cc_final: 0.5389 (mtm180) REVERT: N 43 MET cc_start: 0.4190 (tmm) cc_final: 0.3754 (tmm) REVERT: N 49 ARG cc_start: 0.6382 (ttm-80) cc_final: 0.5958 (mtm180) REVERT: N 53 LEU cc_start: 0.5273 (mt) cc_final: 0.5038 (mm) REVERT: O 313 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8283 (mp) REVERT: O 319 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: P 53 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.5006 (mm) REVERT: P 91 GLN cc_start: 0.4296 (tm130) cc_final: 0.3962 (tp-100) REVERT: Q 313 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8388 (mp) REVERT: R 32 GLN cc_start: 0.4061 (OUTLIER) cc_final: 0.3524 (tp40) REVERT: R 146 LYS cc_start: 0.3732 (ptmt) cc_final: 0.3089 (tppp) REVERT: S 319 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7760 (m-80) REVERT: T 63 MET cc_start: 0.4182 (mtm) cc_final: 0.3570 (mpt) REVERT: T 189 ARG cc_start: 0.2611 (OUTLIER) cc_final: 0.2365 (tmt170) REVERT: W 53 LEU cc_start: 0.5353 (mp) cc_final: 0.4910 (mm) REVERT: W 63 MET cc_start: 0.4249 (mtm) cc_final: 0.3445 (mpp) REVERT: X 170 SER cc_start: 0.7575 (t) cc_final: 0.6695 (p) REVERT: Y 32 GLN cc_start: 0.4144 (OUTLIER) cc_final: 0.3771 (tp40) REVERT: Y 91 GLN cc_start: 0.4504 (tm130) cc_final: 0.4157 (tp-100) REVERT: a 41 MET cc_start: 0.5465 (tmm) cc_final: 0.4943 (tmm) REVERT: a 48 ILE cc_start: 0.3902 (mm) cc_final: 0.3607 (mt) outliers start: 91 outliers final: 53 residues processed: 567 average time/residue: 2.8526 time to fit residues: 1986.6765 Evaluate side-chains 553 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 487 time to evaluate : 5.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain K residue 233 SER Chi-restraints excluded: chain K residue 360 GLU Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain M residue 173 ASP Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 97 CYS Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain P residue 53 LEU Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 173 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 355 ASP Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 284 SER Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain S residue 355 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 CYS Chi-restraints excluded: chain T residue 189 ARG Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 319 PHE Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Y residue 147 ARG Chi-restraints excluded: chain Z residue 284 SER Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 97 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 478 optimal weight: 2.9990 chunk 504 optimal weight: 1.9990 chunk 459 optimal weight: 9.9990 chunk 490 optimal weight: 9.9990 chunk 295 optimal weight: 0.8980 chunk 213 optimal weight: 0.1980 chunk 385 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 443 optimal weight: 0.8980 chunk 463 optimal weight: 1.9990 chunk 488 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 40 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 59 ASN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN N 40 GLN ** N 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 103 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 43225 Z= 0.190 Angle : 0.635 18.046 58292 Z= 0.317 Chirality : 0.087 1.782 6539 Planarity : 0.004 0.077 7722 Dihedral : 4.644 20.284 6097 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.87 % Allowed : 14.44 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.12), residues: 5473 helix: 1.97 (0.11), residues: 2106 sheet: -1.33 (0.12), residues: 1885 loop : -0.77 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 211 HIS 0.004 0.001 HIS W 103 PHE 0.013 0.001 PHE G 319 TYR 0.025 0.002 TYR W 90 ARG 0.010 0.000 ARG E 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 502 time to evaluate : 5.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8625 (mtm) cc_final: 0.8395 (mtm) REVERT: E 303 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7248 (ttm-80) REVERT: F 32 GLN cc_start: 0.4764 (OUTLIER) cc_final: 0.4245 (pp30) REVERT: G 319 PHE cc_start: 0.9031 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: H 63 MET cc_start: 0.4610 (OUTLIER) cc_final: 0.4218 (mpp) REVERT: H 74 ARG cc_start: 0.4953 (ttp-170) cc_final: 0.4424 (mtp85) REVERT: H 132 THR cc_start: 0.5471 (OUTLIER) cc_final: 0.5250 (t) REVERT: I 303 ARG cc_start: 0.7735 (ttm-80) cc_final: 0.7504 (ttp-170) REVERT: I 319 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: J 41 MET cc_start: 0.5057 (tmm) cc_final: 0.4817 (tmm) REVERT: K 139 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7803 (ttt90) REVERT: L 49 ARG cc_start: 0.5795 (ttm-80) cc_final: 0.5319 (mtm180) REVERT: N 43 MET cc_start: 0.4151 (OUTLIER) cc_final: 0.3735 (tmm) REVERT: N 49 ARG cc_start: 0.6346 (ttm-80) cc_final: 0.6132 (mtt90) REVERT: N 53 LEU cc_start: 0.5292 (mt) cc_final: 0.5062 (mm) REVERT: O 313 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8277 (mp) REVERT: O 319 PHE cc_start: 0.9007 (OUTLIER) cc_final: 0.7435 (m-80) REVERT: P 53 LEU cc_start: 0.5421 (mt) cc_final: 0.5153 (mm) REVERT: P 91 GLN cc_start: 0.4189 (tm130) cc_final: 0.3860 (tp-100) REVERT: Q 313 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8369 (mp) REVERT: R 32 GLN cc_start: 0.4255 (OUTLIER) cc_final: 0.3705 (tp40) REVERT: R 146 LYS cc_start: 0.3751 (ptmt) cc_final: 0.3111 (tppp) REVERT: S 319 PHE cc_start: 0.9019 (OUTLIER) cc_final: 0.7720 (m-80) REVERT: T 63 MET cc_start: 0.4187 (mtm) cc_final: 0.3568 (mpt) REVERT: T 189 ARG cc_start: 0.2625 (OUTLIER) cc_final: 0.2375 (tmt170) REVERT: W 42 ASN cc_start: 0.5100 (m-40) cc_final: 0.4597 (t0) REVERT: W 53 LEU cc_start: 0.5348 (mp) cc_final: 0.4908 (mm) REVERT: W 63 MET cc_start: 0.4243 (mtm) cc_final: 0.3434 (mpp) REVERT: X 170 SER cc_start: 0.7563 (t) cc_final: 0.6690 (p) REVERT: Y 32 GLN cc_start: 0.4188 (OUTLIER) cc_final: 0.3805 (tp40) REVERT: Y 91 GLN cc_start: 0.4480 (tm130) cc_final: 0.4137 (tp-100) REVERT: a 41 MET cc_start: 0.5521 (tmm) cc_final: 0.4984 (tmm) REVERT: a 48 ILE cc_start: 0.3942 (mm) cc_final: 0.3644 (mt) outliers start: 83 outliers final: 53 residues processed: 557 average time/residue: 2.9688 time to fit residues: 2050.8455 Evaluate side-chains 554 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 487 time to evaluate : 5.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 173 ASP Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain N residue 97 CYS Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain O residue 360 GLU Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 173 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 97 CYS Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 284 SER Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 CYS Chi-restraints excluded: chain T residue 189 ARG Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 319 PHE Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Y residue 147 ARG Chi-restraints excluded: chain Z residue 284 SER Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain Z residue 360 GLU Chi-restraints excluded: chain a residue 93 LEU Chi-restraints excluded: chain a residue 97 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 322 optimal weight: 9.9990 chunk 518 optimal weight: 4.9990 chunk 316 optimal weight: 0.7980 chunk 246 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 543 optimal weight: 8.9990 chunk 500 optimal weight: 30.0000 chunk 433 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 chunk 265 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 40 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 293 GLN ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 43225 Z= 0.411 Angle : 0.728 18.136 58292 Z= 0.371 Chirality : 0.090 1.830 6539 Planarity : 0.005 0.071 7722 Dihedral : 5.092 23.556 6097 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.89 % Allowed : 14.57 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 5473 helix: 1.79 (0.11), residues: 2119 sheet: -1.70 (0.12), residues: 1859 loop : -1.13 (0.15), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 163 HIS 0.007 0.001 HIS X 368 PHE 0.019 0.002 PHE G 319 TYR 0.024 0.003 TYR F 90 ARG 0.011 0.001 ARG E 303 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10946 Ramachandran restraints generated. 5473 Oldfield, 0 Emsley, 5473 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 488 time to evaluate : 5.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 MET cc_start: 0.8698 (mtm) cc_final: 0.8360 (mtm) REVERT: B 90 TYR cc_start: 0.4158 (m-80) cc_final: 0.3745 (m-80) REVERT: E 273 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7643 (mmt180) REVERT: E 303 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7367 (ttp-170) REVERT: F 32 GLN cc_start: 0.4898 (OUTLIER) cc_final: 0.4350 (pp30) REVERT: F 50 GLU cc_start: 0.5414 (mm-30) cc_final: 0.4514 (mt-10) REVERT: G 319 PHE cc_start: 0.9059 (OUTLIER) cc_final: 0.8172 (m-80) REVERT: H 49 ARG cc_start: 0.6091 (OUTLIER) cc_final: 0.5554 (mtt-85) REVERT: H 74 ARG cc_start: 0.4863 (ttp-170) cc_final: 0.4355 (mtp85) REVERT: I 303 ARG cc_start: 0.7718 (ttm-80) cc_final: 0.7484 (ttp-170) REVERT: I 355 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7265 (t70) REVERT: J 48 ILE cc_start: 0.3893 (mm) cc_final: 0.3651 (mt) REVERT: J 63 MET cc_start: 0.4296 (mtm) cc_final: 0.3635 (mpm) REVERT: K 139 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7880 (ttt90) REVERT: L 49 ARG cc_start: 0.5826 (ttm-80) cc_final: 0.5290 (mtm180) REVERT: M 355 ASP cc_start: 0.7411 (t0) cc_final: 0.7097 (t0) REVERT: N 43 MET cc_start: 0.4237 (OUTLIER) cc_final: 0.3811 (tmm) REVERT: N 49 ARG cc_start: 0.6418 (ttm-80) cc_final: 0.6191 (mtt90) REVERT: N 53 LEU cc_start: 0.5280 (mt) cc_final: 0.5060 (mm) REVERT: O 313 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8556 (mp) REVERT: P 42 ASN cc_start: 0.5427 (m-40) cc_final: 0.4933 (t0) REVERT: P 46 ASP cc_start: 0.5394 (OUTLIER) cc_final: 0.5094 (t70) REVERT: P 53 LEU cc_start: 0.5447 (mt) cc_final: 0.5170 (mm) REVERT: Q 313 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8413 (mp) REVERT: R 32 GLN cc_start: 0.4310 (OUTLIER) cc_final: 0.3701 (tp40) REVERT: R 48 ILE cc_start: 0.3574 (mm) cc_final: 0.3208 (mt) REVERT: R 146 LYS cc_start: 0.3753 (OUTLIER) cc_final: 0.3083 (tppp) REVERT: S 319 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: T 63 MET cc_start: 0.4174 (mtm) cc_final: 0.3574 (mpt) REVERT: T 189 ARG cc_start: 0.2596 (OUTLIER) cc_final: 0.2352 (tmt170) REVERT: W 42 ASN cc_start: 0.5121 (m-40) cc_final: 0.4581 (t0) REVERT: W 53 LEU cc_start: 0.5208 (mp) cc_final: 0.4758 (mm) REVERT: W 63 MET cc_start: 0.4267 (mtm) cc_final: 0.3443 (mpp) REVERT: X 170 SER cc_start: 0.7646 (t) cc_final: 0.6637 (p) REVERT: Y 32 GLN cc_start: 0.4355 (OUTLIER) cc_final: 0.3955 (tp40) REVERT: Y 91 GLN cc_start: 0.4527 (tm130) cc_final: 0.4169 (tp40) REVERT: a 41 MET cc_start: 0.5443 (tmm) cc_final: 0.4863 (tmm) REVERT: a 48 ILE cc_start: 0.4020 (mm) cc_final: 0.3720 (mt) outliers start: 84 outliers final: 53 residues processed: 548 average time/residue: 2.8403 time to fit residues: 1912.5906 Evaluate side-chains 544 residues out of total 4446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 477 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ARG Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 357 ASP Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 97 CYS Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 319 PHE Chi-restraints excluded: chain C residue 357 ASP Chi-restraints excluded: chain E residue 233 SER Chi-restraints excluded: chain F residue 32 GLN Chi-restraints excluded: chain G residue 319 PHE Chi-restraints excluded: chain H residue 49 ARG Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 132 THR Chi-restraints excluded: chain I residue 284 SER Chi-restraints excluded: chain I residue 355 ASP Chi-restraints excluded: chain K residue 139 ARG Chi-restraints excluded: chain L residue 97 CYS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 173 ASP Chi-restraints excluded: chain M residue 284 SER Chi-restraints excluded: chain M residue 313 LEU Chi-restraints excluded: chain M residue 319 PHE Chi-restraints excluded: chain M residue 357 ASP Chi-restraints excluded: chain N residue 43 MET Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 93 LEU Chi-restraints excluded: chain O residue 142 GLU Chi-restraints excluded: chain O residue 284 SER Chi-restraints excluded: chain O residue 313 LEU Chi-restraints excluded: chain O residue 319 PHE Chi-restraints excluded: chain O residue 357 ASP Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain Q residue 142 GLU Chi-restraints excluded: chain Q residue 173 ASP Chi-restraints excluded: chain Q residue 284 SER Chi-restraints excluded: chain Q residue 313 LEU Chi-restraints excluded: chain Q residue 319 PHE Chi-restraints excluded: chain Q residue 357 ASP Chi-restraints excluded: chain R residue 32 GLN Chi-restraints excluded: chain R residue 63 MET Chi-restraints excluded: chain R residue 96 THR Chi-restraints excluded: chain R residue 146 LYS Chi-restraints excluded: chain S residue 142 GLU Chi-restraints excluded: chain S residue 284 SER Chi-restraints excluded: chain S residue 319 PHE Chi-restraints excluded: chain S residue 357 ASP Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain T residue 96 THR Chi-restraints excluded: chain T residue 97 CYS Chi-restraints excluded: chain T residue 189 ARG Chi-restraints excluded: chain V residue 142 GLU Chi-restraints excluded: chain V residue 173 ASP Chi-restraints excluded: chain X residue 142 GLU Chi-restraints excluded: chain X residue 173 ASP Chi-restraints excluded: chain X residue 319 PHE Chi-restraints excluded: chain X residue 357 ASP Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 97 CYS Chi-restraints excluded: chain Y residue 147 ARG Chi-restraints excluded: chain Z residue 173 ASP Chi-restraints excluded: chain Z residue 319 PHE Chi-restraints excluded: chain Z residue 357 ASP Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 93 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 344 optimal weight: 0.9980 chunk 461 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 399 optimal weight: 0.9980 chunk 63 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 433 optimal weight: 0.9990 chunk 181 optimal weight: 0.6980 chunk 445 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 40 GLN D 40 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** J 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN ** N 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 40 GLN ** P 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.230380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.142833 restraints weight = 132792.373| |-----------------------------------------------------------------------------| r_work (start): 0.3890 rms_B_bonded: 2.27 r_work: 0.3704 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43225 Z= 0.187 Angle : 0.645 18.106 58292 Z= 0.322 Chirality : 0.087 1.800 6539 Planarity : 0.004 0.076 7722 Dihedral : 4.760 22.150 6097 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.53 % Allowed : 14.98 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 5473 helix: 1.94 (0.11), residues: 2119 sheet: -1.53 (0.12), residues: 1885 loop : -0.87 (0.16), residues: 1469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP J 211 HIS 0.004 0.001 HIS W 103 PHE 0.015 0.001 PHE Y 136 TYR 0.027 0.002 TYR W 90 ARG 0.010 0.000 ARG E 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32609.03 seconds wall clock time: 561 minutes 52.77 seconds (33712.77 seconds total)