Starting phenix.real_space_refine on Sat Mar 23 00:01:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/03_2024/7r21_14244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/03_2024/7r21_14244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/03_2024/7r21_14244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/03_2024/7r21_14244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/03_2024/7r21_14244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/03_2024/7r21_14244.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 69 5.16 5 C 22119 2.51 5 N 5999 2.21 5 O 6732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 42": "OE1" <-> "OE2" Residue "D ASP 17": "OD1" <-> "OD2" Residue "D GLU 78": "OE1" <-> "OE2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 78": "OE1" <-> "OE2" Residue "F TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 82": "OE1" <-> "OE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 38": "OE1" <-> "OE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G GLU 78": "OE1" <-> "OE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G GLU 82": "OE1" <-> "OE2" Residue "H TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 17": "OD1" <-> "OD2" Residue "H TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 78": "OE1" <-> "OE2" Residue "I PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 264": "OE1" <-> "OE2" Residue "I TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 284": "OE1" <-> "OE2" Residue "K GLU 315": "OE1" <-> "OE2" Residue "L TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 318": "OE1" <-> "OE2" Residue "M ASP 65": "OD1" <-> "OD2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M ASP 312": "OD1" <-> "OD2" Residue "N ASP 107": "OD1" <-> "OD2" Residue "N ASP 285": "OD1" <-> "OD2" Residue "O ASP 65": "OD1" <-> "OD2" Residue "O GLU 288": "OE1" <-> "OE2" Residue "P PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 65": "OD1" <-> "OD2" Residue "Q GLU 272": "OE1" <-> "OE2" Residue "Q GLU 284": "OE1" <-> "OE2" Residue "S PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 201": "OD1" <-> "OD2" Residue "S PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 326": "OE1" <-> "OE2" Residue "T GLU 39": "OE1" <-> "OE2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 230": "OE1" <-> "OE2" Residue "T GLU 265": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 34980 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1320 Classifications: {'RNA': 62} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 24, 'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2350 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 18.80, per 1000 atoms: 0.54 Number of scatterers: 34980 At special positions: 0 Unit cell: (131.203, 136.67, 247.373, 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 69 16.00 P 61 15.00 O 6732 8.00 N 5999 7.00 C 22119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 108 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 108 " 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: 14.52 Conformation dependent library (CDL) restraints added in 6.7 seconds 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7956 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 57 sheets defined 37.2% alpha, 12.0% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 11.24 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.910A pdb=" N ILE A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.616A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.325A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.929A pdb=" N GLU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 4.024A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.706A pdb=" N VAL C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 33 removed outlier: 4.283A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.937A pdb=" N LEU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 removed outlier: 4.144A pdb=" N GLU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 4.028A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.754A pdb=" N LEU C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.250A pdb=" N PHE C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 103 " --> pdb=" O TRP C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.508A pdb=" N TYR D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.669A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.586A pdb=" N SER D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.616A pdb=" N ILE D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.938A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.878A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.816A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.866A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 removed outlier: 3.872A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.962A pdb=" N LYS E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 24 through 33 removed outlier: 4.016A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.959A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 removed outlier: 4.230A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.738A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.775A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'G' and resid 5 through 15 removed outlier: 3.529A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 15 " --> pdb=" O TYR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.683A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 4.102A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 60 removed outlier: 3.619A pdb=" N LEU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.536A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 removed outlier: 3.829A pdb=" N LEU H 15 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.145A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.728A pdb=" N LEU H 40 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 62 removed outlier: 4.216A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.891A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 100 removed outlier: 3.926A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.699A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.632A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 285 through 300 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.632A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.629A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 removed outlier: 3.565A pdb=" N ILE J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 121 Processing helix chain 'J' and resid 144 through 152 removed outlier: 3.587A pdb=" N GLU J 152 " --> pdb=" O ILE J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 205 removed outlier: 3.557A pdb=" N VAL J 205 " --> pdb=" O LEU J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 202 through 205' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 241 through 246 removed outlier: 3.512A pdb=" N MET J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 301 Processing helix chain 'J' and resid 324 through 334 Processing helix chain 'K' and resid 51 through 69 removed outlier: 4.175A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.697A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 removed outlier: 3.539A pdb=" N ILE K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 242 through 247 removed outlier: 3.523A pdb=" N SER K 247 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'L' and resid 51 through 67 Processing helix chain 'L' and resid 77 through 83 removed outlier: 3.697A pdb=" N ARG L 82 " --> pdb=" O ARG L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.539A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 179 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.818A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 301 removed outlier: 3.687A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 299 " --> pdb=" O LYS L 295 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 300 " --> pdb=" O ASN L 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.632A pdb=" N MET L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.528A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.904A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.936A pdb=" N ILE M 111 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 Processing helix chain 'M' and resid 144 through 152 removed outlier: 3.823A pdb=" N GLU M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL M 151 " --> pdb=" O PHE M 147 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 removed outlier: 3.650A pdb=" N SER M 247 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 301 removed outlier: 3.661A pdb=" N LYS M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY M 301 " --> pdb=" O ALA M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.734A pdb=" N MET M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 69 removed outlier: 4.312A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.819A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 122 Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.680A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.667A pdb=" N ALA N 299 " --> pdb=" O LYS N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.906A pdb=" N LEU N 328 " --> pdb=" O SER N 324 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET N 335 " --> pdb=" O ASN N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 24 removed outlier: 3.529A pdb=" N THR O 24 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.532A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.559A pdb=" N LEU O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 82' Processing helix chain 'O' and resid 107 through 115 removed outlier: 3.653A pdb=" N ILE O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 122 Processing helix chain 'O' and resid 144 through 152 removed outlier: 3.761A pdb=" N GLU O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL O 151 " --> pdb=" O PHE O 147 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU O 152 " --> pdb=" O ILE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.674A pdb=" N LYS O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN O 296 " --> pdb=" O SER O 292 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA O 297 " --> pdb=" O ILE O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 3.834A pdb=" N LEU O 328 " --> pdb=" O SER O 324 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 46 removed outlier: 3.681A pdb=" N LEU P 38 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 51 removed outlier: 4.049A pdb=" N TYR P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 46 through 51' Processing helix chain 'P' and resid 54 through 69 removed outlier: 3.595A pdb=" N LYS P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.978A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 24 removed outlier: 3.799A pdb=" N GLY Q 23 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 69 removed outlier: 4.233A pdb=" N THR Q 69 " --> pdb=" O ASP Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.076A pdb=" N ARG Q 82 " --> pdb=" O GLU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 115 removed outlier: 3.970A pdb=" N ILE Q 111 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS Q 113 " --> pdb=" O ALA Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 122 removed outlier: 3.579A pdb=" N ASP Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 151 Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 227 through 241 Processing helix chain 'Q' and resid 285 through 301 Processing helix chain 'Q' and resid 325 through 335 removed outlier: 3.881A pdb=" N MET Q 335 " --> pdb=" O ASN Q 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 removed outlier: 3.714A pdb=" N GLY S 23 " --> pdb=" O GLY S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 69 removed outlier: 3.533A pdb=" N LEU S 55 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 82 removed outlier: 3.857A pdb=" N ARG S 82 " --> pdb=" O GLU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 115 removed outlier: 3.881A pdb=" N ILE S 111 " --> pdb=" O ASP S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 122 Processing helix chain 'S' and resid 144 through 152 removed outlier: 4.329A pdb=" N GLU S 150 " --> pdb=" O ASP S 146 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL S 151 " --> pdb=" O PHE S 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU S 152 " --> pdb=" O ILE S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 227 through 241 Processing helix chain 'S' and resid 285 through 301 removed outlier: 3.557A pdb=" N ASN S 296 " --> pdb=" O SER S 292 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 297 " --> pdb=" O ILE S 293 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY S 301 " --> pdb=" O ALA S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 335 removed outlier: 3.782A pdb=" N MET S 335 " --> pdb=" O ASN S 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 24 removed outlier: 3.776A pdb=" N GLY T 23 " --> pdb=" O GLY T 20 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR T 24 " --> pdb=" O GLY T 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 20 through 24' Processing helix chain 'T' and resid 51 through 69 removed outlier: 3.764A pdb=" N LEU T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 75 removed outlier: 4.113A pdb=" N VAL T 74 " --> pdb=" O PRO T 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN T 75 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.623A pdb=" N LEU T 81 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG T 82 " --> pdb=" O GLU T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.735A pdb=" N LYS T 113 " --> pdb=" O ALA T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 122 removed outlier: 3.535A pdb=" N ASP T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 152 removed outlier: 3.603A pdb=" N ILE T 148 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU T 152 " --> pdb=" O ILE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 203 through 205 No H-bonds generated for 'chain 'T' and resid 203 through 205' Processing helix chain 'T' and resid 227 through 241 Processing helix chain 'T' and resid 285 through 301 removed outlier: 3.774A pdb=" N ALA T 297 " --> pdb=" O ILE T 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY T 301 " --> pdb=" O ALA T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 335 removed outlier: 4.283A pdb=" N MET T 335 " --> pdb=" O ASN T 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 12 current: chain 'I' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 193 through 201 current: chain 'I' and resid 305 through 309 Processing sheet with id=AA2, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.606A pdb=" N GLU I 188 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET I 183 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AA4, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'I' and resid 123 through 125 removed outlier: 7.052A pdb=" N PHE I 123 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG I 131 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 3 through 14 current: chain 'J' and resid 184 through 200 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 200 current: chain 'J' and resid 305 through 309 removed outlier: 7.206A pdb=" N VAL J 306 " --> pdb=" O THR J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AA8, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'J' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 304 through 309 removed outlier: 9.118A pdb=" N THR K 320 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB3, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'K' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 184 through 201 current: chain 'L' and resid 305 through 309 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AB7, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AB8, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AB9, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 190 through 196 current: chain 'M' and resid 306 through 309 Processing sheet with id=AC1, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC2, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AC3, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AC4, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AC5, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AC6, first strand: chain 'N' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 14 current: chain 'N' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 190 through 196 current: chain 'N' and resid 306 through 309 Processing sheet with id=AC7, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AC9, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'N' and resid 123 through 124 Processing sheet with id=AD2, first strand: chain 'N' and resid 213 through 215 Processing sheet with id=AD3, first strand: chain 'O' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 2 through 14 current: chain 'O' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 190 through 196 current: chain 'O' and resid 306 through 309 Processing sheet with id=AD4, first strand: chain 'O' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'O' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AD7, first strand: chain 'O' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'O' and resid 213 through 215 Processing sheet with id=AD9, first strand: chain 'P' and resid 77 through 79 removed outlier: 3.517A pdb=" N LEU P 120 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG P 9 " --> pdb=" O PRO P 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 12 through 13 Processing sheet with id=AE2, first strand: chain 'P' and resid 168 through 169 removed outlier: 3.932A pdb=" N ALA P 168 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL P 240 " --> pdb=" O ALA P 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 197 through 199 Processing sheet with id=AE4, first strand: chain 'P' and resid 243 through 246 Processing sheet with id=AE5, first strand: chain 'Q' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 2 through 14 current: chain 'Q' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 190 through 196 current: chain 'Q' and resid 306 through 309 removed outlier: 6.864A pdb=" N VAL Q 306 " --> pdb=" O THR Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'Q' and resid 26 through 27 Processing sheet with id=AE7, first strand: chain 'Q' and resid 31 through 36 Processing sheet with id=AE8, first strand: chain 'Q' and resid 94 through 96 Processing sheet with id=AE9, first strand: chain 'Q' and resid 123 through 124 Processing sheet with id=AF1, first strand: chain 'Q' and resid 213 through 215 Processing sheet with id=AF2, first strand: chain 'S' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 2 through 10 current: chain 'S' and resid 193 through 196 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 193 through 196 current: chain 'S' and resid 306 through 309 Processing sheet with id=AF3, first strand: chain 'S' and resid 26 through 27 Processing sheet with id=AF4, first strand: chain 'S' and resid 31 through 36 Processing sheet with id=AF5, first strand: chain 'S' and resid 94 through 96 Processing sheet with id=AF6, first strand: chain 'S' and resid 123 through 124 Processing sheet with id=AF7, first strand: chain 'S' and resid 213 through 215 Processing sheet with id=AF8, first strand: chain 'T' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 2 through 12 current: chain 'T' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 192 through 196 current: chain 'T' and resid 306 through 309 removed outlier: 7.079A pdb=" N VAL T 306 " --> pdb=" O THR T 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'T' and resid 31 through 36 Processing sheet with id=AG1, first strand: chain 'T' and resid 94 through 96 Processing sheet with id=AG2, first strand: chain 'T' and resid 123 through 124 Processing sheet with id=AG3, first strand: chain 'T' and resid 213 through 215 1036 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 11.58 Time building geometry restraints manager: 15.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10037 1.33 - 1.46: 6146 1.46 - 1.58: 19359 1.58 - 1.70: 127 1.70 - 1.82: 123 Bond restraints: 35792 Sorted by residual: bond pdb=" CG PRO P 80 " pdb=" CD PRO P 80 " ideal model delta sigma weight residual 1.503 1.296 0.207 3.40e-02 8.65e+02 3.69e+01 bond pdb=" CG PRO Q 274 " pdb=" CD PRO Q 274 " ideal model delta sigma weight residual 1.503 1.297 0.206 3.40e-02 8.65e+02 3.69e+01 bond pdb=" CB PRO P 80 " pdb=" CG PRO P 80 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.36e+00 bond pdb=" N PRO Q 274 " pdb=" CD PRO Q 274 " ideal model delta sigma weight residual 1.473 1.508 -0.035 1.40e-02 5.10e+03 6.23e+00 bond pdb=" CB PRO L 274 " pdb=" CG PRO L 274 " ideal model delta sigma weight residual 1.492 1.607 -0.115 5.00e-02 4.00e+02 5.25e+00 ... (remaining 35787 not shown) Histogram of bond angle deviations from ideal: 88.26 - 97.45: 6 97.45 - 106.63: 1305 106.63 - 115.81: 22609 115.81 - 124.99: 24188 124.99 - 134.17: 702 Bond angle restraints: 48810 Sorted by residual: angle pdb=" N PRO Q 274 " pdb=" CD PRO Q 274 " pdb=" CG PRO Q 274 " ideal model delta sigma weight residual 103.20 88.26 14.94 1.50e+00 4.44e-01 9.91e+01 angle pdb=" N PRO P 80 " pdb=" CD PRO P 80 " pdb=" CG PRO P 80 " ideal model delta sigma weight residual 103.20 90.48 12.72 1.50e+00 4.44e-01 7.19e+01 angle pdb=" CA PRO P 80 " pdb=" N PRO P 80 " pdb=" CD PRO P 80 " ideal model delta sigma weight residual 112.00 101.60 10.40 1.40e+00 5.10e-01 5.52e+01 angle pdb=" CA PRO Q 274 " pdb=" CB PRO Q 274 " pdb=" CG PRO Q 274 " ideal model delta sigma weight residual 104.50 92.08 12.42 1.90e+00 2.77e-01 4.27e+01 angle pdb=" CA PRO L 274 " pdb=" N PRO L 274 " pdb=" CD PRO L 274 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.02e+01 ... (remaining 48805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 21127 35.52 - 71.04: 501 71.04 - 106.55: 45 106.55 - 142.07: 1 142.07 - 177.59: 8 Dihedral angle restraints: 21682 sinusoidal: 9272 harmonic: 12410 Sorted by residual: dihedral pdb=" CB CYS G 63 " pdb=" SG CYS G 63 " pdb=" SG CYS G 108 " pdb=" CB CYS G 108 " ideal model delta sinusoidal sigma weight residual -86.00 -170.16 84.16 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" O4' C R 52 " pdb=" C1' C R 52 " pdb=" N1 C R 52 " pdb=" C2 C R 52 " ideal model delta sinusoidal sigma weight residual 200.00 38.75 161.25 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' C R 40 " pdb=" C1' C R 40 " pdb=" N1 C R 40 " pdb=" C2 C R 40 " ideal model delta sinusoidal sigma weight residual 200.00 39.88 160.12 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 21679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4208 0.045 - 0.089: 1027 0.089 - 0.134: 347 0.134 - 0.178: 16 0.178 - 0.223: 4 Chirality restraints: 5602 Sorted by residual: chirality pdb=" CB ILE Q 224 " pdb=" CA ILE Q 224 " pdb=" CG1 ILE Q 224 " pdb=" CG2 ILE Q 224 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' G R 57 " pdb=" C4' G R 57 " pdb=" O3' G R 57 " pdb=" C2' G R 57 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' G R 18 " pdb=" C4' G R 18 " pdb=" O3' G R 18 " pdb=" C2' G R 18 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 5599 not shown) Planarity restraints: 6062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 79 " -0.105 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO P 80 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO P 80 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO P 80 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE S 258 " -0.077 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO S 259 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO S 259 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 259 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 273 " 0.075 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO L 274 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO L 274 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 274 " 0.059 5.00e-02 4.00e+02 ... (remaining 6059 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1044 2.70 - 3.25: 35710 3.25 - 3.80: 55929 3.80 - 4.35: 73713 4.35 - 4.90: 123241 Nonbonded interactions: 289637 Sorted by model distance: nonbonded pdb=" OD1 ASP H 26 " pdb=" OH TYR N 26 " model vdw 2.156 2.440 nonbonded pdb=" OD1 ASN M 12 " pdb=" OG1 THR M 191 " model vdw 2.161 2.440 nonbonded pdb=" O2' A R 1 " pdb=" OP2 U R 2 " model vdw 2.167 2.440 nonbonded pdb=" OG SER T 324 " pdb=" OE1 GLU T 327 " model vdw 2.181 2.440 nonbonded pdb=" NZ LYS P 69 " pdb=" OH TYR P 136 " model vdw 2.188 2.520 ... (remaining 289632 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 'D' selection = (chain 'E' and resid 3 through 109) selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 144 or (resid 145 and (name N or na \ me CA or name C or name O or name CB )) or resid 146 through 157 or resid 190 th \ rough 335)) selection = (chain 'J' and (resid 1 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 through 157 or resid 190 through 335)) selection = (chain 'K' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'L' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'M' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'N' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'O' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'Q' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'S' and (resid 1 through 157 or resid 190 through 335)) selection = (chain 'T' and resid 1 through 335) } 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: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.120 Check model and map are aligned: 0.540 Set scattering table: 0.310 Process input model: 99.330 Find NCS groups from input model: 2.830 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 0.207 35792 Z= 0.213 Angle : 0.584 14.936 48810 Z= 0.308 Chirality : 0.043 0.223 5602 Planarity : 0.005 0.150 6062 Dihedral : 15.778 177.588 13705 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4275 helix: 0.43 (0.15), residues: 1354 sheet: -0.52 (0.21), residues: 683 loop : -1.13 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 4 HIS 0.004 0.001 HIS J 280 PHE 0.013 0.001 PHE P 12 TYR 0.030 0.001 TYR G 45 ARG 0.013 0.000 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 500 time to evaluate : 4.038 Fit side-chains REVERT: A 57 LYS cc_start: 0.7718 (tttt) cc_final: 0.7459 (tppt) REVERT: A 72 GLU cc_start: 0.6983 (pm20) cc_final: 0.6738 (pm20) REVERT: E 80 LYS cc_start: 0.8348 (mmmm) cc_final: 0.8130 (mmmm) REVERT: K 112 ILE cc_start: 0.9014 (pt) cc_final: 0.8794 (pt) REVERT: L 93 THR cc_start: 0.7766 (m) cc_final: 0.7508 (m) REVERT: M 27 ILE cc_start: 0.8528 (pt) cc_final: 0.8224 (pt) REVERT: O 274 PRO cc_start: 0.8350 (Cg_exo) cc_final: 0.8078 (Cg_endo) REVERT: O 288 GLU cc_start: 0.7319 (tp30) cc_final: 0.6982 (tp30) REVERT: S 237 SER cc_start: 0.8013 (p) cc_final: 0.7775 (p) REVERT: T 130 ARG cc_start: 0.4954 (mmp80) cc_final: 0.4232 (mmp80) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.5176 time to fit residues: 410.1880 Evaluate side-chains 434 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 434 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 179 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 218 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 334 optimal weight: 0.7980 chunk 129 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 387 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 182 GLN L 162 HIS O 296 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN T 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 35792 Z= 0.289 Angle : 0.602 10.301 48810 Z= 0.309 Chirality : 0.046 0.214 5602 Planarity : 0.005 0.077 6062 Dihedral : 13.205 179.439 5670 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.84 % Favored : 92.09 % Rotamer: Outliers : 0.92 % Allowed : 9.74 % Favored : 89.33 % 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: -0.98 (0.13), residues: 4275 helix: 0.12 (0.14), residues: 1476 sheet: -0.61 (0.20), residues: 672 loop : -1.17 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 4 HIS 0.008 0.002 HIS J 280 PHE 0.024 0.002 PHE I 258 TYR 0.028 0.002 TYR P 231 ARG 0.005 0.000 ARG I 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 474 time to evaluate : 3.739 Fit side-chains REVERT: A 57 LYS cc_start: 0.7898 (tttt) cc_final: 0.7661 (tppt) REVERT: A 72 GLU cc_start: 0.7352 (pm20) cc_final: 0.6990 (pm20) REVERT: E 80 LYS cc_start: 0.8450 (mmmm) cc_final: 0.8233 (mmmm) REVERT: F 22 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7316 (tm-30) REVERT: F 88 LYS cc_start: 0.8104 (tptp) cc_final: 0.7806 (tppt) REVERT: H 59 GLU cc_start: 0.7235 (mp0) cc_final: 0.6853 (mp0) REVERT: K 1 MET cc_start: 0.8308 (tmm) cc_final: 0.8020 (ttp) REVERT: K 112 ILE cc_start: 0.9062 (pt) cc_final: 0.8806 (pt) REVERT: L 65 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: M 27 ILE cc_start: 0.8751 (pt) cc_final: 0.8531 (pt) REVERT: N 285 ASP cc_start: 0.8436 (p0) cc_final: 0.8231 (p0) REVERT: O 288 GLU cc_start: 0.7267 (tp30) cc_final: 0.6976 (tp30) REVERT: S 1 MET cc_start: 0.7455 (tpp) cc_final: 0.7217 (tpt) REVERT: S 68 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8141 (pttp) REVERT: S 107 ASP cc_start: 0.6956 (t0) cc_final: 0.6595 (t0) REVERT: S 237 SER cc_start: 0.8129 (p) cc_final: 0.7890 (p) REVERT: S 309 TYR cc_start: 0.8107 (t80) cc_final: 0.7699 (t80) REVERT: T 131 ARG cc_start: 0.7810 (ptm-80) cc_final: 0.6962 (ptm-80) REVERT: T 242 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6917 (tt) REVERT: T 245 MET cc_start: 0.6788 (mmp) cc_final: 0.6428 (mmp) outliers start: 33 outliers final: 21 residues processed: 488 average time/residue: 0.5147 time to fit residues: 393.4487 Evaluate side-chains 451 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 428 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 4.9990 chunk 120 optimal weight: 0.0170 chunk 322 optimal weight: 4.9990 chunk 264 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 388 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 chunk 345 optimal weight: 0.8980 chunk 385 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 311 optimal weight: 30.0000 overall best weight: 2.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 ASN K 75 ASN O 40 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 35792 Z= 0.334 Angle : 0.618 9.985 48810 Z= 0.318 Chirality : 0.047 0.217 5602 Planarity : 0.005 0.080 6062 Dihedral : 13.290 179.416 5670 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.91 % Favored : 91.98 % Rotamer: Outliers : 2.02 % Allowed : 13.61 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.13), residues: 4275 helix: 0.35 (0.15), residues: 1369 sheet: -0.77 (0.20), residues: 656 loop : -1.27 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 4 HIS 0.016 0.002 HIS L 162 PHE 0.028 0.002 PHE I 258 TYR 0.019 0.002 TYR P 231 ARG 0.007 0.001 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 452 time to evaluate : 3.920 Fit side-chains REVERT: A 57 LYS cc_start: 0.7872 (tttt) cc_final: 0.7616 (tppt) REVERT: E 80 LYS cc_start: 0.8415 (mmmm) cc_final: 0.8178 (mmmm) REVERT: F 22 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7494 (tm-30) REVERT: F 42 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7474 (mt-10) REVERT: F 55 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7619 (mtmt) REVERT: F 88 LYS cc_start: 0.8146 (tptp) cc_final: 0.7850 (tppt) REVERT: H 70 SER cc_start: 0.7709 (t) cc_final: 0.7472 (t) REVERT: H 72 GLU cc_start: 0.6653 (pm20) cc_final: 0.6340 (pm20) REVERT: H 80 LYS cc_start: 0.8068 (tppt) cc_final: 0.7832 (tptm) REVERT: I 298 ARG cc_start: 0.7224 (ttm-80) cc_final: 0.6780 (mtt180) REVERT: J 245 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7819 (ttt) REVERT: K 1 MET cc_start: 0.8431 (tmm) cc_final: 0.7858 (ttp) REVERT: K 112 ILE cc_start: 0.9127 (pt) cc_final: 0.8897 (pt) REVERT: K 114 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: L 65 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7635 (m-30) REVERT: L 164 ARG cc_start: 0.7129 (mtt-85) cc_final: 0.6737 (ptp-110) REVERT: L 219 GLN cc_start: 0.6708 (mm110) cc_final: 0.6168 (mm110) REVERT: O 157 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7939 (mp) REVERT: O 288 GLU cc_start: 0.7272 (tp30) cc_final: 0.6966 (tp30) REVERT: P 110 ARG cc_start: 0.7176 (tmm-80) cc_final: 0.6969 (tmm-80) REVERT: P 176 TYR cc_start: 0.5145 (OUTLIER) cc_final: 0.3693 (m-10) REVERT: S 17 ASN cc_start: 0.7941 (OUTLIER) cc_final: 0.7147 (t160) REVERT: S 68 LYS cc_start: 0.8442 (mmmt) cc_final: 0.8165 (pttp) REVERT: S 237 SER cc_start: 0.8183 (p) cc_final: 0.7928 (p) REVERT: S 253 ASN cc_start: 0.7811 (t0) cc_final: 0.7490 (t0) REVERT: S 309 TYR cc_start: 0.8136 (t80) cc_final: 0.7750 (t80) REVERT: T 242 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6916 (tt) REVERT: T 245 MET cc_start: 0.6804 (mmp) cc_final: 0.6571 (mmp) outliers start: 72 outliers final: 45 residues processed: 493 average time/residue: 0.5349 time to fit residues: 416.4188 Evaluate side-chains 484 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 431 time to evaluate : 3.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 204 LEU Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 6.9990 chunk 292 optimal weight: 0.9980 chunk 201 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 chunk 260 optimal weight: 2.9990 chunk 389 optimal weight: 0.5980 chunk 412 optimal weight: 0.0370 chunk 203 optimal weight: 2.9990 chunk 369 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN M 59 HIS O 17 ASN O 253 ASN Q 17 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 35792 Z= 0.157 Angle : 0.534 9.309 48810 Z= 0.273 Chirality : 0.043 0.212 5602 Planarity : 0.004 0.072 6062 Dihedral : 13.179 178.548 5670 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.16 % Favored : 92.77 % Rotamer: Outliers : 1.96 % Allowed : 15.85 % Favored : 82.19 % 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: -0.86 (0.13), residues: 4275 helix: 0.42 (0.15), residues: 1418 sheet: -0.60 (0.20), residues: 672 loop : -1.20 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 4 HIS 0.005 0.001 HIS M 280 PHE 0.014 0.001 PHE J 258 TYR 0.014 0.001 TYR P 231 ARG 0.007 0.000 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 464 time to evaluate : 4.165 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7893 (tttt) cc_final: 0.7638 (tppt) REVERT: E 80 LYS cc_start: 0.8401 (mmmm) cc_final: 0.8121 (mmmm) REVERT: F 22 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7166 (tm-30) REVERT: F 73 ASP cc_start: 0.7172 (p0) cc_final: 0.6813 (p0) REVERT: F 88 LYS cc_start: 0.8092 (tptp) cc_final: 0.7850 (tppt) REVERT: G 83 GLN cc_start: 0.8108 (pt0) cc_final: 0.7890 (pt0) REVERT: H 80 LYS cc_start: 0.8026 (tppt) cc_final: 0.7816 (tptm) REVERT: I 230 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7368 (tt0) REVERT: I 298 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6755 (mtt180) REVERT: K 1 MET cc_start: 0.8412 (tmm) cc_final: 0.7811 (ttp) REVERT: K 112 ILE cc_start: 0.9055 (pt) cc_final: 0.8807 (pt) REVERT: K 114 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7363 (pm20) REVERT: L 65 ASP cc_start: 0.8120 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: N 285 ASP cc_start: 0.8404 (p0) cc_final: 0.8157 (p0) REVERT: O 219 GLN cc_start: 0.7162 (mm110) cc_final: 0.6955 (mm110) REVERT: O 288 GLU cc_start: 0.7316 (tp30) cc_final: 0.7058 (tp30) REVERT: P 50 TYR cc_start: 0.2850 (m-80) cc_final: 0.1503 (m-80) REVERT: S 1 MET cc_start: 0.7691 (tpp) cc_final: 0.7209 (tpt) REVERT: S 68 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8179 (pttp) REVERT: S 237 SER cc_start: 0.8177 (p) cc_final: 0.7920 (p) REVERT: S 253 ASN cc_start: 0.7793 (t0) cc_final: 0.7472 (t0) REVERT: S 261 PHE cc_start: 0.8167 (t80) cc_final: 0.7738 (t80) REVERT: S 309 TYR cc_start: 0.8122 (t80) cc_final: 0.7716 (t80) REVERT: T 242 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6864 (tt) REVERT: T 245 MET cc_start: 0.6888 (mmp) cc_final: 0.6552 (mmm) outliers start: 70 outliers final: 43 residues processed: 506 average time/residue: 0.5375 time to fit residues: 429.0187 Evaluate side-chains 479 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 432 time to evaluate : 4.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 6.9990 chunk 234 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 307 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 352 optimal weight: 0.0870 chunk 285 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 0.5980 chunk 370 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 107 ASN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 GLN K 75 ASN L 310 ASN O 162 HIS O 253 ASN Q 17 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 35792 Z= 0.375 Angle : 0.649 9.919 48810 Z= 0.334 Chirality : 0.048 0.226 5602 Planarity : 0.005 0.082 6062 Dihedral : 13.326 178.478 5670 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.47 % Favored : 91.44 % Rotamer: Outliers : 3.64 % Allowed : 16.57 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.13), residues: 4275 helix: 0.35 (0.15), residues: 1365 sheet: -0.78 (0.21), residues: 654 loop : -1.27 (0.13), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 4 HIS 0.013 0.002 HIS L 162 PHE 0.034 0.002 PHE I 258 TYR 0.024 0.002 TYR P 231 ARG 0.009 0.001 ARG L 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 450 time to evaluate : 3.634 Fit side-chains REVERT: A 57 LYS cc_start: 0.7935 (tttt) cc_final: 0.7697 (tppt) REVERT: E 80 LYS cc_start: 0.8438 (mmmm) cc_final: 0.8131 (mmmm) REVERT: F 22 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7466 (tm-30) REVERT: F 55 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.7950 (mtmt) REVERT: G 67 ARG cc_start: 0.7921 (mtp-110) cc_final: 0.7689 (ttm110) REVERT: H 72 GLU cc_start: 0.6414 (pm20) cc_final: 0.6186 (pm20) REVERT: H 80 LYS cc_start: 0.8073 (tppt) cc_final: 0.7869 (tptm) REVERT: I 165 VAL cc_start: 0.6879 (OUTLIER) cc_final: 0.6609 (m) REVERT: I 230 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7300 (tt0) REVERT: I 298 ARG cc_start: 0.7245 (ttm-80) cc_final: 0.6821 (mtt180) REVERT: J 245 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7951 (ttt) REVERT: K 1 MET cc_start: 0.8443 (tmm) cc_final: 0.8024 (ttp) REVERT: K 112 ILE cc_start: 0.9126 (pt) cc_final: 0.8883 (pt) REVERT: K 114 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: L 65 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7636 (m-30) REVERT: M 239 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8678 (mm) REVERT: N 306 VAL cc_start: 0.9122 (OUTLIER) cc_final: 0.8706 (t) REVERT: N 326 GLU cc_start: 0.7741 (mp0) cc_final: 0.7540 (mp0) REVERT: O 157 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7959 (mp) REVERT: O 288 GLU cc_start: 0.7365 (tp30) cc_final: 0.7082 (tp30) REVERT: P 161 VAL cc_start: 0.4635 (OUTLIER) cc_final: 0.4392 (m) REVERT: P 176 TYR cc_start: 0.4612 (OUTLIER) cc_final: 0.3370 (m-10) REVERT: S 1 MET cc_start: 0.7268 (tpp) cc_final: 0.6876 (tpt) REVERT: S 17 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7138 (t160) REVERT: S 68 LYS cc_start: 0.8486 (mmmt) cc_final: 0.8200 (pttp) REVERT: S 253 ASN cc_start: 0.7890 (t0) cc_final: 0.7571 (t0) REVERT: S 309 TYR cc_start: 0.8255 (t80) cc_final: 0.7908 (t80) REVERT: T 131 ARG cc_start: 0.7876 (ptm-80) cc_final: 0.6999 (ptm-80) REVERT: T 242 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6814 (tt) REVERT: T 245 MET cc_start: 0.6987 (mmp) cc_final: 0.6638 (mmm) outliers start: 130 outliers final: 84 residues processed: 542 average time/residue: 0.4961 time to fit residues: 423.5792 Evaluate side-chains 508 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 411 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 306 VAL Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 311 VAL Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 61 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 311 VAL Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 204 LEU Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 1.9990 chunk 371 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 242 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 chunk 413 optimal weight: 2.9990 chunk 342 optimal weight: 40.0000 chunk 191 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN I 229 ASN K 17 ASN K 75 ASN L 99 ASN M 253 ASN O 17 ASN Q 17 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 35792 Z= 0.207 Angle : 0.568 9.497 48810 Z= 0.290 Chirality : 0.044 0.224 5602 Planarity : 0.005 0.077 6062 Dihedral : 13.252 178.475 5670 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.42 % Favored : 92.49 % Rotamer: Outliers : 2.94 % Allowed : 18.37 % Favored : 78.70 % 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: -0.95 (0.13), residues: 4275 helix: 0.37 (0.15), residues: 1413 sheet: -0.72 (0.21), residues: 654 loop : -1.25 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 4 HIS 0.008 0.002 HIS L 162 PHE 0.019 0.001 PHE I 258 TYR 0.019 0.001 TYR Q 309 ARG 0.007 0.000 ARG L 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 425 time to evaluate : 3.278 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7922 (tttt) cc_final: 0.7687 (tppt) REVERT: C 79 GLU cc_start: 0.5796 (OUTLIER) cc_final: 0.4419 (pm20) REVERT: E 68 ILE cc_start: 0.8834 (OUTLIER) cc_final: 0.8456 (mm) REVERT: E 80 LYS cc_start: 0.8449 (mmmm) cc_final: 0.8125 (mmmm) REVERT: F 22 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 42 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7485 (mt-10) REVERT: F 55 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7953 (mtmt) REVERT: G 67 ARG cc_start: 0.7904 (mtp-110) cc_final: 0.7693 (ttm110) REVERT: G 83 GLN cc_start: 0.8047 (pt0) cc_final: 0.7795 (pt0) REVERT: I 230 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7282 (tt0) REVERT: I 294 ILE cc_start: 0.7788 (pt) cc_final: 0.7546 (pt) REVERT: I 298 ARG cc_start: 0.7184 (ttm-80) cc_final: 0.6797 (mtt180) REVERT: J 1 MET cc_start: 0.8257 (tpt) cc_final: 0.7718 (tpt) REVERT: J 119 ASP cc_start: 0.8585 (OUTLIER) cc_final: 0.8283 (t0) REVERT: J 245 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7720 (ttt) REVERT: K 1 MET cc_start: 0.8361 (tmm) cc_final: 0.7871 (ttp) REVERT: K 112 ILE cc_start: 0.9075 (pt) cc_final: 0.8838 (pt) REVERT: K 114 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7368 (pm20) REVERT: L 65 ASP cc_start: 0.8168 (OUTLIER) cc_final: 0.7661 (m-30) REVERT: L 326 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6815 (mm-30) REVERT: M 86 THR cc_start: 0.8610 (OUTLIER) cc_final: 0.8309 (p) REVERT: M 239 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8792 (mm) REVERT: M 253 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8726 (t0) REVERT: N 306 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8743 (t) REVERT: O 157 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7917 (mp) REVERT: O 288 GLU cc_start: 0.7307 (tp30) cc_final: 0.7045 (tp30) REVERT: S 1 MET cc_start: 0.7223 (tpp) cc_final: 0.6811 (tpt) REVERT: S 253 ASN cc_start: 0.7844 (t0) cc_final: 0.7636 (t0) REVERT: S 254 LEU cc_start: 0.6242 (OUTLIER) cc_final: 0.5988 (mm) REVERT: T 131 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.6950 (ptp90) REVERT: T 242 LEU cc_start: 0.7192 (OUTLIER) cc_final: 0.6867 (tt) REVERT: T 245 MET cc_start: 0.6968 (mmp) cc_final: 0.6662 (mmm) outliers start: 105 outliers final: 70 residues processed: 496 average time/residue: 0.4834 time to fit residues: 378.6272 Evaluate side-chains 493 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 407 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 326 GLU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 253 ASN Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 257 SER Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 2.9990 chunk 46 optimal weight: 0.2980 chunk 235 optimal weight: 0.8980 chunk 301 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 347 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 411 optimal weight: 6.9990 chunk 257 optimal weight: 0.2980 chunk 250 optimal weight: 5.9990 chunk 190 optimal weight: 0.0010 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 ASN L 99 ASN O 17 ASN Q 17 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 35792 Z= 0.183 Angle : 0.551 9.316 48810 Z= 0.281 Chirality : 0.044 0.219 5602 Planarity : 0.004 0.076 6062 Dihedral : 13.181 178.199 5670 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.65 % Favored : 92.28 % Rotamer: Outliers : 3.16 % Allowed : 18.53 % Favored : 78.30 % 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: -0.86 (0.13), residues: 4275 helix: 0.46 (0.15), residues: 1421 sheet: -0.66 (0.21), residues: 654 loop : -1.22 (0.13), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 4 HIS 0.007 0.001 HIS L 162 PHE 0.018 0.001 PHE J 258 TYR 0.027 0.001 TYR P 231 ARG 0.006 0.000 ARG L 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 417 time to evaluate : 4.294 Fit side-chains REVERT: C 79 GLU cc_start: 0.5737 (OUTLIER) cc_final: 0.5333 (pm20) REVERT: E 68 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8458 (mm) REVERT: E 80 LYS cc_start: 0.8362 (mmmm) cc_final: 0.8049 (mmmm) REVERT: F 22 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7339 (tm-30) REVERT: F 42 GLU cc_start: 0.7806 (mt-10) cc_final: 0.7473 (mt-10) REVERT: F 55 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7946 (mtmt) REVERT: I 230 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: I 298 ARG cc_start: 0.7145 (ttm-80) cc_final: 0.6813 (mtt180) REVERT: J 1 MET cc_start: 0.8251 (tpt) cc_final: 0.7695 (tpt) REVERT: K 1 MET cc_start: 0.8317 (tmm) cc_final: 0.7868 (ttp) REVERT: K 112 ILE cc_start: 0.9064 (pt) cc_final: 0.8823 (pt) REVERT: K 114 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: L 65 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: L 326 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6732 (mm-30) REVERT: M 86 THR cc_start: 0.8601 (OUTLIER) cc_final: 0.8293 (p) REVERT: M 239 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8799 (mm) REVERT: N 306 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8739 (t) REVERT: O 157 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7881 (mp) REVERT: O 288 GLU cc_start: 0.7225 (tp30) cc_final: 0.6958 (tp30) REVERT: S 1 MET cc_start: 0.7229 (tpp) cc_final: 0.6822 (tpt) REVERT: S 253 ASN cc_start: 0.8028 (t0) cc_final: 0.7787 (t0) REVERT: S 254 LEU cc_start: 0.6209 (OUTLIER) cc_final: 0.5956 (mm) REVERT: T 131 ARG cc_start: 0.7572 (ptm-80) cc_final: 0.6938 (ptp90) REVERT: T 242 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6856 (tt) REVERT: T 245 MET cc_start: 0.6952 (mmp) cc_final: 0.6620 (mmm) outliers start: 113 outliers final: 87 residues processed: 493 average time/residue: 0.5097 time to fit residues: 396.6983 Evaluate side-chains 495 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 395 time to evaluate : 3.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 326 GLU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 257 SER Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 261 optimal weight: 0.9990 chunk 280 optimal weight: 4.9990 chunk 203 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 323 optimal weight: 10.0000 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN N 90 GLN Q 17 ASN S 209 GLN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35792 Z= 0.277 Angle : 0.594 10.509 48810 Z= 0.303 Chirality : 0.045 0.234 5602 Planarity : 0.005 0.076 6062 Dihedral : 13.222 179.529 5670 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.91 % Favored : 92.02 % Rotamer: Outliers : 3.58 % Allowed : 18.70 % Favored : 77.72 % 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: -0.89 (0.13), residues: 4275 helix: 0.46 (0.15), residues: 1383 sheet: -0.71 (0.21), residues: 654 loop : -1.22 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 4 HIS 0.012 0.002 HIS L 162 PHE 0.025 0.002 PHE J 258 TYR 0.029 0.002 TYR F 45 ARG 0.013 0.000 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 410 time to evaluate : 4.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.4431 (pm20) REVERT: E 68 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8453 (mm) REVERT: E 80 LYS cc_start: 0.8420 (mmmm) cc_final: 0.8091 (mmmm) REVERT: F 22 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7378 (tm-30) REVERT: F 55 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7986 (mtmt) REVERT: I 230 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7340 (tt0) REVERT: I 298 ARG cc_start: 0.7194 (ttm-80) cc_final: 0.6831 (mtt180) REVERT: J 1 MET cc_start: 0.8481 (tpt) cc_final: 0.7915 (tpt) REVERT: J 119 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8244 (t0) REVERT: J 245 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7801 (ttt) REVERT: K 1 MET cc_start: 0.8319 (tmm) cc_final: 0.7913 (ttp) REVERT: K 112 ILE cc_start: 0.9089 (pt) cc_final: 0.8850 (pt) REVERT: K 114 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: L 65 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7668 (m-30) REVERT: M 239 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8658 (mm) REVERT: N 306 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8742 (t) REVERT: O 157 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7997 (mp) REVERT: O 288 GLU cc_start: 0.7217 (tp30) cc_final: 0.6939 (tp30) REVERT: S 1 MET cc_start: 0.7274 (tpp) cc_final: 0.6868 (tpt) REVERT: S 17 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7072 (t160) REVERT: S 253 ASN cc_start: 0.8057 (t0) cc_final: 0.7693 (t0) REVERT: S 254 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5992 (mm) REVERT: T 131 ARG cc_start: 0.7608 (ptm-80) cc_final: 0.6962 (ptp90) REVERT: T 242 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6859 (tt) REVERT: T 245 MET cc_start: 0.6984 (mmp) cc_final: 0.6643 (mmm) outliers start: 128 outliers final: 99 residues processed: 496 average time/residue: 0.4943 time to fit residues: 388.6573 Evaluate side-chains 517 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 404 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 247 SER Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 94 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 257 SER Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 204 LEU Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 267 VAL Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 9.9990 chunk 394 optimal weight: 1.9990 chunk 359 optimal weight: 6.9990 chunk 383 optimal weight: 0.7980 chunk 230 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 346 optimal weight: 0.7980 chunk 362 optimal weight: 5.9990 chunk 382 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN K 75 ASN L 99 ASN Q 17 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35792 Z= 0.201 Angle : 0.565 9.354 48810 Z= 0.288 Chirality : 0.044 0.250 5602 Planarity : 0.004 0.075 6062 Dihedral : 13.185 177.976 5670 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.42 % Favored : 92.51 % Rotamer: Outliers : 3.33 % Allowed : 19.32 % Favored : 77.35 % 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: -0.84 (0.13), residues: 4275 helix: 0.49 (0.15), residues: 1414 sheet: -0.66 (0.21), residues: 654 loop : -1.20 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 4 HIS 0.007 0.002 HIS L 162 PHE 0.020 0.001 PHE J 258 TYR 0.028 0.001 TYR F 45 ARG 0.008 0.000 ARG G 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 411 time to evaluate : 3.944 Fit side-chains revert: symmetry clash REVERT: C 79 GLU cc_start: 0.5787 (OUTLIER) cc_final: 0.5392 (pm20) REVERT: E 68 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8440 (mm) REVERT: E 80 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8018 (mmmm) REVERT: F 22 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7307 (tm-30) REVERT: F 55 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7964 (mtmt) REVERT: G 53 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8320 (mtmt) REVERT: I 230 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: I 298 ARG cc_start: 0.7109 (ttm-80) cc_final: 0.6768 (mtt180) REVERT: J 1 MET cc_start: 0.8501 (tpt) cc_final: 0.7990 (tpt) REVERT: J 119 ASP cc_start: 0.8574 (OUTLIER) cc_final: 0.8275 (t0) REVERT: J 245 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7653 (ttt) REVERT: K 1 MET cc_start: 0.8309 (tmm) cc_final: 0.7850 (ttp) REVERT: K 112 ILE cc_start: 0.9069 (pt) cc_final: 0.8828 (pt) REVERT: K 114 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: L 65 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7679 (m-30) REVERT: L 265 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7664 (pt0) REVERT: M 86 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8362 (p) REVERT: M 239 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8793 (mm) REVERT: O 157 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7903 (mp) REVERT: O 288 GLU cc_start: 0.7190 (tp30) cc_final: 0.6923 (tp30) REVERT: S 1 MET cc_start: 0.7232 (tpp) cc_final: 0.6817 (tpt) REVERT: S 17 ASN cc_start: 0.7822 (OUTLIER) cc_final: 0.6994 (t160) REVERT: S 253 ASN cc_start: 0.8025 (t0) cc_final: 0.7666 (t0) REVERT: S 254 LEU cc_start: 0.6120 (OUTLIER) cc_final: 0.5869 (mm) REVERT: T 131 ARG cc_start: 0.7604 (ptm-80) cc_final: 0.6995 (ptp90) REVERT: T 242 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6837 (tt) REVERT: T 245 MET cc_start: 0.6921 (mmp) cc_final: 0.6590 (mmm) outliers start: 119 outliers final: 95 residues processed: 495 average time/residue: 0.4989 time to fit residues: 389.8793 Evaluate side-chains 511 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 401 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 335 MET Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 257 SER Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 204 LEU Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 267 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 6.9990 chunk 405 optimal weight: 8.9990 chunk 247 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 281 optimal weight: 0.9990 chunk 425 optimal weight: 6.9990 chunk 391 optimal weight: 0.0770 chunk 338 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 207 optimal weight: 0.8980 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN Q 17 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35792 Z= 0.170 Angle : 0.560 9.292 48810 Z= 0.284 Chirality : 0.043 0.270 5602 Planarity : 0.004 0.074 6062 Dihedral : 13.148 177.478 5670 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.25 % Favored : 92.68 % Rotamer: Outliers : 3.02 % Allowed : 19.85 % Favored : 77.13 % 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: -0.73 (0.13), residues: 4275 helix: 0.58 (0.15), residues: 1397 sheet: -0.56 (0.21), residues: 670 loop : -1.14 (0.13), residues: 2208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 4 HIS 0.006 0.001 HIS L 162 PHE 0.018 0.001 PHE J 258 TYR 0.030 0.001 TYR F 45 ARG 0.016 0.000 ARG G 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 420 time to evaluate : 3.836 Fit side-chains revert: symmetry clash REVERT: C 79 GLU cc_start: 0.5636 (OUTLIER) cc_final: 0.5269 (pm20) REVERT: E 68 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8448 (mm) REVERT: E 80 LYS cc_start: 0.8390 (mmmm) cc_final: 0.8044 (mmmm) REVERT: F 22 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7412 (tm-30) REVERT: F 55 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7903 (mtmt) REVERT: F 73 ASP cc_start: 0.7162 (p0) cc_final: 0.6819 (p0) REVERT: G 53 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8274 (mtmt) REVERT: H 80 LYS cc_start: 0.8293 (tptm) cc_final: 0.7927 (tppt) REVERT: I 230 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: I 298 ARG cc_start: 0.7093 (ttm-80) cc_final: 0.6758 (mtt180) REVERT: I 300 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8507 (tt) REVERT: J 1 MET cc_start: 0.8467 (tpt) cc_final: 0.7930 (tpt) REVERT: J 119 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (t0) REVERT: K 1 MET cc_start: 0.8312 (tmm) cc_final: 0.7841 (ttp) REVERT: K 112 ILE cc_start: 0.9055 (pt) cc_final: 0.8813 (pt) REVERT: K 114 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: L 65 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: L 265 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7620 (pt0) REVERT: M 86 THR cc_start: 0.8617 (OUTLIER) cc_final: 0.8312 (p) REVERT: M 239 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8809 (mm) REVERT: O 157 ILE cc_start: 0.8168 (OUTLIER) cc_final: 0.7853 (mp) REVERT: O 288 GLU cc_start: 0.7180 (tp30) cc_final: 0.6908 (tp30) REVERT: P 50 TYR cc_start: 0.3094 (m-80) cc_final: 0.1644 (m-80) REVERT: S 1 MET cc_start: 0.7196 (tpp) cc_final: 0.6784 (tpt) REVERT: S 253 ASN cc_start: 0.7984 (t0) cc_final: 0.7608 (t0) REVERT: S 254 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5841 (mm) REVERT: T 131 ARG cc_start: 0.7604 (ptm-80) cc_final: 0.7011 (ptp90) REVERT: T 242 LEU cc_start: 0.7137 (OUTLIER) cc_final: 0.6774 (tt) REVERT: T 245 MET cc_start: 0.6906 (mmp) cc_final: 0.6565 (mmm) outliers start: 108 outliers final: 87 residues processed: 494 average time/residue: 0.5064 time to fit residues: 393.1237 Evaluate side-chains 508 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 407 time to evaluate : 3.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 70 SER Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 93 THR Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 119 ASP Chi-restraints excluded: chain J residue 144 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain K residue 316 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 25 ASN Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain L residue 335 MET Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 183 MET Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 308 THR Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 25 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 102 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 146 ASP Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 146 ASP Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 201 ASP Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 267 VAL Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 269 optimal weight: 4.9990 chunk 360 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 312 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 94 optimal weight: 0.0980 chunk 339 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 348 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 ASN L 17 ASN Q 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.122746 restraints weight = 46414.883| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.11 r_work: 0.3203 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35792 Z= 0.166 Angle : 0.548 9.098 48810 Z= 0.278 Chirality : 0.043 0.253 5602 Planarity : 0.004 0.072 6062 Dihedral : 13.111 177.352 5670 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.13 % Favored : 92.80 % Rotamer: Outliers : 3.02 % Allowed : 19.96 % Favored : 77.02 % 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: -0.66 (0.13), residues: 4275 helix: 0.66 (0.15), residues: 1392 sheet: -0.52 (0.21), residues: 670 loop : -1.11 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 4 HIS 0.005 0.001 HIS Q 280 PHE 0.018 0.001 PHE J 258 TYR 0.030 0.001 TYR F 45 ARG 0.011 0.000 ARG G 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8438.87 seconds wall clock time: 152 minutes 38.61 seconds (9158.61 seconds total)