Starting phenix.real_space_refine on Sat Dec 16 12:06:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/12_2023/7r21_14244.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/12_2023/7r21_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_14244/12_2023/7r21_14244.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/12_2023/7r21_14244.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/12_2023/7r21_14244.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r21_14244/12_2023/7r21_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-1.21rc1-5172/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: 17.15, per 1000 atoms: 0.49 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: 13.91 Conformation dependent library (CDL) restraints added in 5.5 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: 9.80 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: 10.32 Time building geometry restraints manager: 14.90 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: 21094 35.52 - 71.04: 474 71.04 - 106.55: 45 106.55 - 142.07: 1 142.07 - 177.59: 8 Dihedral angle restraints: 21622 sinusoidal: 9212 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 21619 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: 1.970 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: 0.030 Extract box with map and model: 7.880 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 87.850 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.180 ------------------------------------------------------------------------------- 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 : 15.603 177.588 13645 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 : 4.014 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.5146 time to fit residues: 407.7721 Evaluate side-chains 432 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 432 time to evaluate : 3.863 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2843 ------------------------------------------------------------------------------- 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: 0.6980 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: 1.0982 ------------------------------------------------------------------------------- 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 K 75 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35792 Z= 0.209 Angle : 0.555 10.216 48810 Z= 0.285 Chirality : 0.044 0.208 5602 Planarity : 0.005 0.073 6062 Dihedral : 12.596 179.262 5610 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.39 % Favored : 92.54 % Rotamer: Outliers : 0.81 % Allowed : 8.87 % Favored : 90.31 % 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: 0.33 (0.15), residues: 1463 sheet: -0.52 (0.21), residues: 672 loop : -1.12 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 4 HIS 0.006 0.001 HIS J 280 PHE 0.017 0.002 PHE L 258 TYR 0.026 0.001 TYR P 231 ARG 0.004 0.000 ARG P 201 *********************** 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: 29 poor density : 478 time to evaluate : 4.253 Fit side-chains outliers start: 29 outliers final: 20 residues processed: 492 average time/residue: 0.5600 time to fit residues: 434.3581 Evaluate side-chains 453 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 433 time to evaluate : 4.145 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.3455 time to fit residues: 18.6865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 215 optimal weight: 5.9990 chunk 120 optimal weight: 0.0970 chunk 322 optimal weight: 8.9990 chunk 264 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 388 optimal weight: 0.1980 chunk 419 optimal weight: 0.0570 chunk 345 optimal weight: 0.6980 chunk 385 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 311 optimal weight: 9.9990 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 L 84 ASN L 219 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 35792 Z= 0.137 Angle : 0.514 11.051 48810 Z= 0.261 Chirality : 0.042 0.207 5602 Planarity : 0.004 0.063 6062 Dihedral : 12.566 178.301 5610 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.69 % Favored : 93.24 % Rotamer: Outliers : 0.62 % Allowed : 12.35 % Favored : 87.04 % 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: -0.65 (0.13), residues: 4275 helix: 0.64 (0.15), residues: 1409 sheet: -0.42 (0.21), residues: 672 loop : -1.13 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 4 HIS 0.005 0.001 HIS N 280 PHE 0.013 0.001 PHE K 258 TYR 0.014 0.001 TYR P 231 ARG 0.008 0.000 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 496 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 474 time to evaluate : 3.796 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 487 average time/residue: 0.5188 time to fit residues: 397.4434 Evaluate side-chains 445 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 435 time to evaluate : 3.734 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.3178 time to fit residues: 11.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 383 optimal weight: 0.9980 chunk 292 optimal weight: 0.3980 chunk 201 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 185 optimal weight: 0.9980 chunk 260 optimal weight: 0.9990 chunk 389 optimal weight: 9.9990 chunk 412 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 369 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 219 GLN L 84 ASN ** Q 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1151 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= 0.166 Angle : 0.515 9.264 48810 Z= 0.264 Chirality : 0.043 0.212 5602 Planarity : 0.004 0.062 6062 Dihedral : 12.563 178.417 5610 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.11 % Favored : 92.82 % Rotamer: Outliers : 1.15 % Allowed : 13.77 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.13), residues: 4275 helix: 0.65 (0.15), residues: 1413 sheet: -0.39 (0.21), residues: 672 loop : -1.09 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 4 HIS 0.007 0.001 HIS L 162 PHE 0.014 0.001 PHE L 258 TYR 0.026 0.001 TYR P 231 ARG 0.006 0.000 ARG E 49 *********************** 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 494 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 453 time to evaluate : 4.051 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 474 average time/residue: 0.5364 time to fit residues: 398.8020 Evaluate side-chains 447 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 423 time to evaluate : 3.811 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3604 time to fit residues: 20.7955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 343 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 307 optimal weight: 8.9990 chunk 170 optimal weight: 3.9990 chunk 352 optimal weight: 2.9990 chunk 285 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 chunk 370 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- 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 90 GLN J 219 GLN O 40 ASN O 296 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1424 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= 0.254 Angle : 0.569 9.591 48810 Z= 0.293 Chirality : 0.045 0.212 5602 Planarity : 0.005 0.070 6062 Dihedral : 12.627 178.294 5610 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.77 % Favored : 92.16 % Rotamer: Outliers : 1.18 % Allowed : 15.54 % Favored : 83.29 % 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: -0.75 (0.13), residues: 4275 helix: 0.37 (0.14), residues: 1466 sheet: -0.46 (0.21), residues: 672 loop : -1.09 (0.13), residues: 2137 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 0.024 0.002 PHE I 258 TYR 0.015 0.001 TYR P 231 ARG 0.008 0.000 ARG G 67 *********************** 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 475 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 433 time to evaluate : 3.979 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 19 residues processed: 460 average time/residue: 0.5424 time to fit residues: 391.4677 Evaluate side-chains 432 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 413 time to evaluate : 3.945 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3325 time to fit residues: 17.1569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 138 optimal weight: 2.9990 chunk 371 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 242 optimal weight: 0.6980 chunk 101 optimal weight: 0.0040 chunk 413 optimal weight: 10.0000 chunk 342 optimal weight: 0.0470 chunk 191 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 216 optimal weight: 0.1980 overall best weight: 0.3290 ------------------------------------------------------------------------------- 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 162 HIS K 75 ASN L 162 HIS M 17 ASN M 59 HIS 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35792 Z= 0.137 Angle : 0.517 9.193 48810 Z= 0.264 Chirality : 0.042 0.214 5602 Planarity : 0.004 0.065 6062 Dihedral : 12.596 177.524 5610 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.88 % Favored : 93.05 % Rotamer: Outliers : 0.70 % Allowed : 16.74 % Favored : 82.56 % 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: -0.55 (0.13), residues: 4275 helix: 0.72 (0.15), residues: 1413 sheet: -0.38 (0.21), residues: 672 loop : -1.07 (0.13), residues: 2190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 4 HIS 0.005 0.001 HIS N 280 PHE 0.014 0.001 PHE J 258 TYR 0.022 0.001 TYR J 309 ARG 0.009 0.000 ARG G 67 *********************** 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 471 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 446 time to evaluate : 3.635 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 463 average time/residue: 0.5377 time to fit residues: 389.0194 Evaluate side-chains 432 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 419 time to evaluate : 3.787 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3222 time to fit residues: 13.3205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 398 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 235 optimal weight: 3.9990 chunk 301 optimal weight: 0.6980 chunk 233 optimal weight: 0.6980 chunk 347 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 411 optimal weight: 0.1980 chunk 257 optimal weight: 1.9990 chunk 250 optimal weight: 0.0070 chunk 190 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 L 162 HIS M 17 ASN O 53 ASN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 35792 Z= 0.147 Angle : 0.519 10.208 48810 Z= 0.264 Chirality : 0.042 0.215 5602 Planarity : 0.004 0.063 6062 Dihedral : 12.560 177.545 5610 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer: Outliers : 0.39 % Allowed : 17.97 % Favored : 81.63 % 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: -0.49 (0.13), residues: 4275 helix: 0.77 (0.15), residues: 1392 sheet: -0.35 (0.21), residues: 672 loop : -1.02 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 4 HIS 0.004 0.001 HIS J 162 PHE 0.015 0.001 PHE J 258 TYR 0.020 0.001 TYR F 45 ARG 0.006 0.000 ARG E 49 *********************** 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 453 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 439 time to evaluate : 4.042 Fit side-chains outliers start: 14 outliers final: 8 residues processed: 447 average time/residue: 0.5470 time to fit residues: 385.4495 Evaluate side-chains 420 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 412 time to evaluate : 3.922 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3871 time to fit residues: 10.8426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 254 optimal weight: 0.5980 chunk 164 optimal weight: 3.9990 chunk 245 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 280 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 323 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1599 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= 0.167 Angle : 0.531 9.261 48810 Z= 0.270 Chirality : 0.043 0.217 5602 Planarity : 0.004 0.064 6062 Dihedral : 12.560 177.789 5610 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.09 % Favored : 92.84 % Rotamer: Outliers : 0.48 % Allowed : 18.23 % Favored : 81.30 % 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: -0.50 (0.13), residues: 4275 helix: 0.79 (0.15), residues: 1393 sheet: -0.39 (0.21), residues: 672 loop : -1.02 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 4 HIS 0.005 0.001 HIS J 280 PHE 0.016 0.001 PHE J 258 TYR 0.026 0.001 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 439 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 422 time to evaluate : 3.727 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 431 average time/residue: 0.5311 time to fit residues: 359.1197 Evaluate side-chains 415 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 408 time to evaluate : 3.760 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3336 time to fit residues: 9.4192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 374 optimal weight: 10.0000 chunk 394 optimal weight: 0.8980 chunk 359 optimal weight: 6.9990 chunk 383 optimal weight: 0.6980 chunk 230 optimal weight: 0.8980 chunk 167 optimal weight: 0.1980 chunk 301 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 382 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 O 17 ASN O 296 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35792 Z= 0.160 Angle : 0.531 9.380 48810 Z= 0.269 Chirality : 0.043 0.217 5602 Planarity : 0.004 0.066 6062 Dihedral : 12.565 177.592 5610 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 0.22 % Allowed : 18.78 % Favored : 80.99 % 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: -0.47 (0.13), residues: 4275 helix: 0.83 (0.15), residues: 1393 sheet: -0.36 (0.21), residues: 672 loop : -1.02 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 4 HIS 0.004 0.001 HIS J 280 PHE 0.017 0.001 PHE J 258 TYR 0.028 0.001 TYR F 45 ARG 0.007 0.000 ARG T 130 *********************** 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 429 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 421 time to evaluate : 4.139 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 426 average time/residue: 0.5314 time to fit residues: 357.6305 Evaluate side-chains 406 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 403 time to evaluate : 3.724 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3176 time to fit residues: 6.8773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 251 optimal weight: 5.9990 chunk 405 optimal weight: 0.0670 chunk 247 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 281 optimal weight: 6.9990 chunk 425 optimal weight: 0.8980 chunk 391 optimal weight: 0.0770 chunk 338 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN K 75 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 17 ASN O 296 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 35792 Z= 0.152 Angle : 0.531 9.163 48810 Z= 0.270 Chirality : 0.042 0.216 5602 Planarity : 0.004 0.063 6062 Dihedral : 12.552 178.155 5610 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.90 % Favored : 93.03 % Rotamer: Outliers : 0.20 % Allowed : 18.98 % Favored : 80.82 % 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: -0.43 (0.13), residues: 4275 helix: 0.88 (0.15), residues: 1391 sheet: -0.35 (0.21), residues: 672 loop : -1.00 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP G 4 HIS 0.005 0.001 HIS N 280 PHE 0.014 0.001 PHE J 258 TYR 0.031 0.001 TYR F 45 ARG 0.015 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 419 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 412 time to evaluate : 4.186 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 417 average time/residue: 0.5402 time to fit residues: 354.5289 Evaluate side-chains 406 residues out of total 3591 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 403 time to evaluate : 3.816 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3167 time to fit residues: 7.1021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 50 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 339 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 348 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN J 219 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.167130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126363 restraints weight = 46426.850| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.13 r_work: 0.3245 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35792 Z= 0.167 Angle : 0.535 9.178 48810 Z= 0.271 Chirality : 0.043 0.212 5602 Planarity : 0.004 0.062 6062 Dihedral : 12.542 177.534 5610 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 0.25 % Allowed : 19.09 % Favored : 80.66 % 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: -0.45 (0.13), residues: 4275 helix: 0.86 (0.15), residues: 1391 sheet: -0.36 (0.21), residues: 672 loop : -1.01 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP G 4 HIS 0.005 0.001 HIS L 162 PHE 0.016 0.001 PHE J 258 TYR 0.035 0.001 TYR F 45 ARG 0.009 0.000 ARG G 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8283.31 seconds wall clock time: 151 minutes 5.95 seconds (9065.95 seconds total)