Starting phenix.real_space_refine on Sat Feb 7 16:02:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r21_14244/02_2026/7r21_14244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r21_14244/02_2026/7r21_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/cci-nas-00/data/ceres_data/7r21_14244/02_2026/7r21_14244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r21_14244/02_2026/7r21_14244.map" model { file = "/net/cci-nas-00/data/ceres_data/7r21_14244/02_2026/7r21_14244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r21_14244/02_2026/7r21_14244.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } 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. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU: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: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 8.57, per 1000 atoms: 0.24 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 - 3.00 Amino acid : True - 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: 3.29 Conformation dependent library (CDL) restraints added in 1.5 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: 4.25 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: 6.58 Time building geometry restraints manager: 4.41 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: 0.00 - 2.99: 48511 2.99 - 5.97: 278 5.97 - 8.96: 15 8.96 - 11.95: 3 11.95 - 14.94: 3 Bond angle restraints: 48810 Sorted by residual: angle pdb=" N PRO Q 274 " pdb=" CD PRO Q 274 " pdb=" CG PRO Q 274 " ideal model delta sigma weight residual 103.20 88.26 14.94 1.50e+00 4.44e-01 9.91e+01 angle pdb=" N PRO P 80 " pdb=" CD PRO P 80 " pdb=" CG PRO P 80 " ideal model delta sigma weight residual 103.20 90.48 12.72 1.50e+00 4.44e-01 7.19e+01 angle pdb=" CA PRO P 80 " pdb=" N PRO P 80 " pdb=" CD PRO P 80 " ideal model delta sigma weight residual 112.00 101.60 10.40 1.40e+00 5.10e-01 5.52e+01 angle pdb=" CA PRO Q 274 " pdb=" CB PRO Q 274 " pdb=" CG PRO Q 274 " ideal model delta sigma weight residual 104.50 92.08 12.42 1.90e+00 2.77e-01 4.27e+01 angle pdb=" CA PRO L 274 " pdb=" N PRO L 274 " pdb=" CD PRO L 274 " ideal model delta sigma weight residual 112.00 104.30 7.70 1.40e+00 5.10e-01 3.02e+01 ... (remaining 48805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 21127 35.52 - 71.04: 501 71.04 - 106.55: 45 106.55 - 142.07: 1 142.07 - 177.59: 8 Dihedral angle restraints: 21682 sinusoidal: 9272 harmonic: 12410 Sorted by residual: dihedral pdb=" CB CYS G 63 " pdb=" SG CYS G 63 " pdb=" SG CYS G 108 " pdb=" CB CYS G 108 " ideal model delta sinusoidal sigma weight residual -86.00 -170.16 84.16 1 1.00e+01 1.00e-02 8.62e+01 dihedral pdb=" O4' C R 52 " pdb=" C1' C R 52 " pdb=" N1 C R 52 " pdb=" C2 C R 52 " ideal model delta sinusoidal sigma weight residual 200.00 38.75 161.25 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' C R 40 " pdb=" C1' C R 40 " pdb=" N1 C R 40 " pdb=" C2 C R 40 " ideal model delta sinusoidal sigma weight residual 200.00 39.88 160.12 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 21679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 4208 0.045 - 0.089: 1027 0.089 - 0.134: 347 0.134 - 0.178: 16 0.178 - 0.223: 4 Chirality restraints: 5602 Sorted by residual: chirality pdb=" CB ILE Q 224 " pdb=" CA ILE Q 224 " pdb=" CG1 ILE Q 224 " pdb=" CG2 ILE Q 224 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C3' G R 57 " pdb=" C4' G R 57 " pdb=" O3' G R 57 " pdb=" C2' G R 57 " both_signs ideal model delta sigma weight residual False -2.74 -2.54 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' G R 18 " pdb=" C4' G R 18 " pdb=" O3' G R 18 " pdb=" C2' G R 18 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.19 2.00e-01 2.50e+01 9.48e-01 ... (remaining 5599 not shown) Planarity restraints: 6062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA P 79 " -0.105 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO P 80 " 0.259 5.00e-02 4.00e+02 pdb=" CA PRO P 80 " -0.078 5.00e-02 4.00e+02 pdb=" CD PRO P 80 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE S 258 " -0.077 5.00e-02 4.00e+02 1.14e-01 2.06e+01 pdb=" N PRO S 259 " 0.196 5.00e-02 4.00e+02 pdb=" CA PRO S 259 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO S 259 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY L 273 " 0.075 5.00e-02 4.00e+02 1.09e-01 1.91e+01 pdb=" N PRO L 274 " -0.189 5.00e-02 4.00e+02 pdb=" CA PRO L 274 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO L 274 " 0.059 5.00e-02 4.00e+02 ... (remaining 6059 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 1044 2.70 - 3.25: 35710 3.25 - 3.80: 55929 3.80 - 4.35: 73713 4.35 - 4.90: 123241 Nonbonded interactions: 289637 Sorted by model distance: nonbonded pdb=" OD1 ASP H 26 " pdb=" OH TYR N 26 " model vdw 2.156 3.040 nonbonded pdb=" OD1 ASN M 12 " pdb=" OG1 THR M 191 " model vdw 2.161 3.040 nonbonded pdb=" O2' A R 1 " pdb=" OP2 U R 2 " model vdw 2.167 3.040 nonbonded pdb=" OG SER T 324 " pdb=" OE1 GLU T 327 " model vdw 2.181 3.040 nonbonded pdb=" NZ LYS P 69 " pdb=" OH TYR P 136 " model vdw 2.188 3.120 ... (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 Time spend for trying shortcut: 0.00 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: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 35.770 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.350 ------------------------------------------------------------------------------- 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 35799 Z= 0.129 Angle : 0.584 14.936 48824 Z= 0.308 Chirality : 0.043 0.223 5602 Planarity : 0.005 0.150 6062 Dihedral : 15.778 177.588 13705 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.000 ARG G 67 TYR 0.030 0.001 TYR G 45 PHE 0.013 0.001 PHE P 12 TRP 0.027 0.002 TRP C 4 HIS 0.004 0.001 HIS J 280 Details of bonding type rmsd covalent geometry : bond 0.00327 (35792) covalent geometry : angle 0.58406 (48810) SS BOND : bond 0.00289 ( 7) SS BOND : angle 0.79006 ( 14) hydrogen bonds : bond 0.14885 ( 1036) hydrogen bonds : angle 5.94515 ( 2967) *********************** 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 to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 1.383 Fit side-chains REVERT: A 57 LYS cc_start: 0.7718 (tttt) cc_final: 0.7459 (tppt) REVERT: A 72 GLU cc_start: 0.6983 (pm20) cc_final: 0.6738 (pm20) REVERT: E 80 LYS cc_start: 0.8349 (mmmm) cc_final: 0.8131 (mmmm) REVERT: K 112 ILE cc_start: 0.9014 (pt) cc_final: 0.8794 (pt) REVERT: L 93 THR cc_start: 0.7766 (m) cc_final: 0.7508 (m) REVERT: M 27 ILE cc_start: 0.8528 (pt) cc_final: 0.8224 (pt) REVERT: O 274 PRO cc_start: 0.8350 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: O 288 GLU cc_start: 0.7320 (tp30) cc_final: 0.6982 (tp30) REVERT: S 237 SER cc_start: 0.8013 (p) cc_final: 0.7775 (p) REVERT: T 130 ARG cc_start: 0.4954 (mmp80) cc_final: 0.4232 (mmp80) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.2422 time to fit residues: 192.3362 Evaluate side-chains 434 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 GLN J 182 GLN L 162 HIS N 296 ASN O 296 ASN Q 12 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 296 ASN T 17 ASN T 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.168971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.127527 restraints weight = 46585.229| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.11 r_work: 0.3297 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35799 Z= 0.131 Angle : 0.570 10.232 48824 Z= 0.294 Chirality : 0.044 0.230 5602 Planarity : 0.005 0.074 6062 Dihedral : 13.096 178.963 5670 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.06 % Favored : 92.87 % Rotamer: Outliers : 0.64 % Allowed : 8.62 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.13), residues: 4275 helix: 0.63 (0.15), residues: 1366 sheet: -0.49 (0.21), residues: 670 loop : -1.16 (0.13), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 201 TYR 0.024 0.001 TYR P 231 PHE 0.015 0.001 PHE L 258 TRP 0.020 0.002 TRP C 4 HIS 0.005 0.001 HIS N 57 Details of bonding type rmsd covalent geometry : bond 0.00299 (35792) covalent geometry : angle 0.57021 (48810) SS BOND : bond 0.00162 ( 7) SS BOND : angle 0.95061 ( 14) hydrogen bonds : bond 0.03973 ( 1036) hydrogen bonds : angle 4.64665 ( 2967) *********************** 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 514 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 491 time to evaluate : 1.557 Fit side-chains REVERT: A 57 LYS cc_start: 0.7536 (tttt) cc_final: 0.7296 (tppt) REVERT: A 72 GLU cc_start: 0.7154 (pm20) cc_final: 0.6742 (pm20) REVERT: E 80 LYS cc_start: 0.8292 (mmmm) cc_final: 0.8047 (mmmm) REVERT: F 22 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7134 (tm-30) REVERT: F 88 LYS cc_start: 0.8263 (tptp) cc_final: 0.7942 (tppt) REVERT: G 4 TRP cc_start: 0.6496 (t60) cc_final: 0.6153 (t60) REVERT: G 67 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.8082 (ttm110) REVERT: H 67 ARG cc_start: 0.7348 (tmt170) cc_final: 0.7140 (tmt170) REVERT: H 80 LYS cc_start: 0.7775 (tptm) cc_final: 0.7454 (tppt) REVERT: I 83 TYR cc_start: 0.7309 (m-10) cc_final: 0.6783 (m-10) REVERT: K 112 ILE cc_start: 0.9211 (pt) cc_final: 0.8984 (pt) REVERT: M 27 ILE cc_start: 0.8797 (pt) cc_final: 0.8574 (pt) REVERT: M 312 ASP cc_start: 0.7601 (p0) cc_final: 0.7167 (p0) REVERT: O 151 VAL cc_start: 0.7419 (m) cc_final: 0.7014 (m) REVERT: O 288 GLU cc_start: 0.8261 (tp30) cc_final: 0.7958 (tp30) REVERT: Q 219 GLN cc_start: 0.7226 (mm-40) cc_final: 0.7010 (mm-40) REVERT: S 68 LYS cc_start: 0.8722 (mmmt) cc_final: 0.8067 (pttp) REVERT: S 107 ASP cc_start: 0.7085 (t0) cc_final: 0.6659 (t0) REVERT: S 237 SER cc_start: 0.8333 (p) cc_final: 0.8100 (p) REVERT: S 309 TYR cc_start: 0.8134 (t80) cc_final: 0.7915 (t80) REVERT: T 11 LEU cc_start: 0.6773 (mt) cc_final: 0.6475 (tt) REVERT: T 70 THR cc_start: 0.8269 (t) cc_final: 0.7829 (p) REVERT: T 130 ARG cc_start: 0.5664 (mmp80) cc_final: 0.5456 (mmp80) REVERT: T 131 ARG cc_start: 0.7965 (ptm-80) cc_final: 0.6791 (ptp90) REVERT: T 245 MET cc_start: 0.7076 (mmp) cc_final: 0.6503 (mmp) outliers start: 23 outliers final: 15 residues processed: 505 average time/residue: 0.2527 time to fit residues: 200.3935 Evaluate side-chains 456 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 441 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 284 GLU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain T residue 139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 243 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 313 optimal weight: 0.7980 chunk 218 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 252 optimal weight: 0.0010 chunk 123 optimal weight: 3.9990 chunk 204 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 278 optimal weight: 5.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 7 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN T 290 ASN T 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.165020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123667 restraints weight = 46646.188| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.12 r_work: 0.3213 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 35799 Z= 0.150 Angle : 0.577 9.639 48824 Z= 0.297 Chirality : 0.045 0.241 5602 Planarity : 0.005 0.072 6062 Dihedral : 13.166 179.706 5670 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.37 % Favored : 92.56 % Rotamer: Outliers : 1.37 % Allowed : 12.35 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.13), residues: 4275 helix: 0.42 (0.15), residues: 1414 sheet: -0.64 (0.21), residues: 658 loop : -1.07 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 49 TYR 0.015 0.001 TYR P 231 PHE 0.022 0.002 PHE I 258 TRP 0.021 0.002 TRP C 4 HIS 0.011 0.002 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00353 (35792) covalent geometry : angle 0.57694 (48810) SS BOND : bond 0.00131 ( 7) SS BOND : angle 0.92922 ( 14) hydrogen bonds : bond 0.03745 ( 1036) hydrogen bonds : angle 4.50422 ( 2967) *********************** 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 513 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 464 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7486 (tttt) cc_final: 0.7236 (tppt) REVERT: A 72 GLU cc_start: 0.7408 (pm20) cc_final: 0.7173 (pm20) REVERT: E 80 LYS cc_start: 0.8266 (mmmm) cc_final: 0.7953 (mmmm) REVERT: F 78 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7126 (mt-10) REVERT: F 88 LYS cc_start: 0.8304 (tptp) cc_final: 0.7988 (tppt) REVERT: G 4 TRP cc_start: 0.6529 (t60) cc_final: 0.6154 (t60) REVERT: G 67 ARG cc_start: 0.8277 (mtp-110) cc_final: 0.7987 (ttm110) REVERT: H 67 ARG cc_start: 0.7305 (tmt170) cc_final: 0.7089 (tmt170) REVERT: H 72 GLU cc_start: 0.7376 (pm20) cc_final: 0.7062 (pm20) REVERT: H 80 LYS cc_start: 0.7761 (tptm) cc_final: 0.7423 (tppt) REVERT: I 83 TYR cc_start: 0.7498 (m-10) cc_final: 0.7029 (m-10) REVERT: I 131 ARG cc_start: 0.7220 (ptm-80) cc_final: 0.6960 (ptt90) REVERT: I 308 THR cc_start: 0.7766 (p) cc_final: 0.7535 (p) REVERT: J 258 PHE cc_start: 0.8832 (t80) cc_final: 0.8578 (t80) REVERT: J 294 ILE cc_start: 0.9292 (mt) cc_final: 0.9087 (mt) REVERT: K 112 ILE cc_start: 0.9265 (pt) cc_final: 0.8995 (pt) REVERT: K 114 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7924 (pm20) REVERT: L 54 MET cc_start: 0.8994 (tpp) cc_final: 0.8688 (tpp) REVERT: L 219 GLN cc_start: 0.7239 (mm110) cc_final: 0.6663 (mm110) REVERT: O 274 PRO cc_start: 0.8750 (Cg_exo) cc_final: 0.8411 (Cg_endo) REVERT: O 288 GLU cc_start: 0.8199 (tp30) cc_final: 0.7882 (tp30) REVERT: P 50 TYR cc_start: 0.2759 (m-80) cc_final: 0.1441 (m-80) REVERT: P 136 TYR cc_start: 0.3807 (m-10) cc_final: 0.3570 (m-10) REVERT: S 68 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8066 (pttp) REVERT: S 107 ASP cc_start: 0.7186 (t0) cc_final: 0.6777 (t0) REVERT: S 240 LYS cc_start: 0.8516 (mtpt) cc_final: 0.8228 (mtmt) REVERT: S 309 TYR cc_start: 0.8112 (t80) cc_final: 0.7633 (t80) REVERT: T 131 ARG cc_start: 0.8047 (ptm-80) cc_final: 0.6831 (ptp90) REVERT: T 242 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.7086 (tt) REVERT: T 245 MET cc_start: 0.7199 (mmp) cc_final: 0.6763 (mmp) outliers start: 49 outliers final: 31 residues processed: 494 average time/residue: 0.2310 time to fit residues: 179.9449 Evaluate side-chains 467 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 434 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 182 optimal weight: 1.9990 chunk 404 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 272 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 406 optimal weight: 7.9990 chunk 33 optimal weight: 0.0000 chunk 50 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 59 HIS ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.166590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125140 restraints weight = 46393.651| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.12 r_work: 0.3232 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35799 Z= 0.114 Angle : 0.539 9.386 48824 Z= 0.278 Chirality : 0.044 0.227 5602 Planarity : 0.004 0.069 6062 Dihedral : 13.116 177.910 5670 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.71 % Favored : 93.22 % Rotamer: Outliers : 1.32 % Allowed : 14.08 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.13), residues: 4275 helix: 0.72 (0.15), residues: 1367 sheet: -0.53 (0.20), residues: 672 loop : -1.13 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 130 TYR 0.015 0.001 TYR T 309 PHE 0.015 0.001 PHE K 258 TRP 0.022 0.002 TRP C 4 HIS 0.006 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00256 (35792) covalent geometry : angle 0.53917 (48810) SS BOND : bond 0.00122 ( 7) SS BOND : angle 0.78001 ( 14) hydrogen bonds : bond 0.03161 ( 1036) hydrogen bonds : angle 4.31243 ( 2967) *********************** 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 518 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 471 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7525 (tttt) cc_final: 0.7270 (tppt) REVERT: D 78 GLU cc_start: 0.6433 (mp0) cc_final: 0.6166 (mp0) REVERT: E 35 ARG cc_start: 0.8018 (tpp80) cc_final: 0.7753 (tpp80) REVERT: E 80 LYS cc_start: 0.8278 (mmmm) cc_final: 0.7964 (mmmm) REVERT: F 73 ASP cc_start: 0.7388 (p0) cc_final: 0.6944 (p0) REVERT: F 88 LYS cc_start: 0.8281 (tptp) cc_final: 0.8014 (tppt) REVERT: G 4 TRP cc_start: 0.6438 (t60) cc_final: 0.6106 (t60) REVERT: G 38 GLU cc_start: 0.7836 (mp0) cc_final: 0.7609 (mp0) REVERT: G 67 ARG cc_start: 0.8213 (mtp-110) cc_final: 0.7932 (ttm110) REVERT: H 37 GLN cc_start: 0.7789 (tp40) cc_final: 0.7573 (tp40) REVERT: H 67 ARG cc_start: 0.7293 (tmt170) cc_final: 0.7030 (tmt170) REVERT: H 72 GLU cc_start: 0.7280 (pm20) cc_final: 0.6943 (pm20) REVERT: I 83 TYR cc_start: 0.7331 (m-10) cc_final: 0.6815 (m-10) REVERT: I 131 ARG cc_start: 0.7125 (ptm-80) cc_final: 0.6833 (ptt90) REVERT: I 298 ARG cc_start: 0.7170 (ttm-80) cc_final: 0.6724 (mtt180) REVERT: J 37 ARG cc_start: 0.6230 (mmm-85) cc_final: 0.5924 (mmm-85) REVERT: J 236 GLU cc_start: 0.8266 (mp0) cc_final: 0.7864 (mp0) REVERT: J 258 PHE cc_start: 0.8767 (t80) cc_final: 0.8558 (t80) REVERT: K 112 ILE cc_start: 0.9233 (pt) cc_final: 0.8969 (pt) REVERT: L 54 MET cc_start: 0.8870 (tpp) cc_final: 0.8629 (tpp) REVERT: M 312 ASP cc_start: 0.7659 (p0) cc_final: 0.7211 (p0) REVERT: O 151 VAL cc_start: 0.7421 (m) cc_final: 0.7029 (m) REVERT: O 157 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.8139 (mp) REVERT: O 219 GLN cc_start: 0.7777 (mm110) cc_final: 0.7515 (mm110) REVERT: O 288 GLU cc_start: 0.8153 (tp30) cc_final: 0.7845 (tp30) REVERT: P 50 TYR cc_start: 0.2901 (m-80) cc_final: 0.1551 (m-80) REVERT: P 110 ARG cc_start: 0.7481 (tmm-80) cc_final: 0.7162 (tmm-80) REVERT: P 176 TYR cc_start: 0.3993 (OUTLIER) cc_final: 0.2530 (m-10) REVERT: S 68 LYS cc_start: 0.8801 (mmmt) cc_final: 0.8087 (pttp) REVERT: S 107 ASP cc_start: 0.7150 (t0) cc_final: 0.6777 (t0) REVERT: S 240 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8216 (mtmt) REVERT: S 309 TYR cc_start: 0.8115 (t80) cc_final: 0.7623 (t80) REVERT: T 131 ARG cc_start: 0.7986 (ptm-80) cc_final: 0.6772 (ptp90) REVERT: T 242 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7042 (tt) REVERT: T 245 MET cc_start: 0.7130 (mmp) cc_final: 0.6620 (mmm) outliers start: 47 outliers final: 32 residues processed: 497 average time/residue: 0.2393 time to fit residues: 187.3789 Evaluate side-chains 476 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 441 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 258 optimal weight: 0.6980 chunk 306 optimal weight: 20.0000 chunk 189 optimal weight: 2.9990 chunk 313 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 406 optimal weight: 20.0000 chunk 56 optimal weight: 0.2980 chunk 261 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 251 optimal weight: 2.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 219 GLN O 53 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.165840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.125206 restraints weight = 46685.111| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.07 r_work: 0.3242 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 35799 Z= 0.105 Angle : 0.529 10.164 48824 Z= 0.271 Chirality : 0.043 0.224 5602 Planarity : 0.004 0.067 6062 Dihedral : 13.065 177.951 5670 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 1.74 % Allowed : 15.76 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4275 helix: 0.80 (0.15), residues: 1367 sheet: -0.47 (0.20), residues: 672 loop : -1.10 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 130 TYR 0.028 0.001 TYR P 231 PHE 0.014 0.001 PHE K 258 TRP 0.024 0.001 TRP C 4 HIS 0.005 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00234 (35792) covalent geometry : angle 0.52899 (48810) SS BOND : bond 0.00217 ( 7) SS BOND : angle 0.84101 ( 14) hydrogen bonds : bond 0.02977 ( 1036) hydrogen bonds : angle 4.21697 ( 2967) *********************** 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 519 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 457 time to evaluate : 1.549 Fit side-chains REVERT: A 57 LYS cc_start: 0.7462 (tttt) cc_final: 0.7205 (tppt) REVERT: A 72 GLU cc_start: 0.7042 (pm20) cc_final: 0.6739 (pm20) REVERT: D 78 GLU cc_start: 0.6497 (mp0) cc_final: 0.6168 (mp0) REVERT: E 35 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7928 (tpp80) REVERT: E 80 LYS cc_start: 0.8275 (mmmm) cc_final: 0.7927 (mmmm) REVERT: F 22 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7266 (tm-30) REVERT: F 73 ASP cc_start: 0.7291 (p0) cc_final: 0.6798 (p0) REVERT: F 88 LYS cc_start: 0.8271 (tptp) cc_final: 0.7978 (tppt) REVERT: G 4 TRP cc_start: 0.6316 (t60) cc_final: 0.5992 (t60) REVERT: G 67 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7887 (ttm110) REVERT: H 37 GLN cc_start: 0.7793 (tp40) cc_final: 0.7553 (tp40) REVERT: H 67 ARG cc_start: 0.7381 (tmt170) cc_final: 0.7029 (tmt170) REVERT: H 72 GLU cc_start: 0.7393 (pm20) cc_final: 0.7033 (pm20) REVERT: I 83 TYR cc_start: 0.7263 (m-10) cc_final: 0.6715 (m-10) REVERT: I 131 ARG cc_start: 0.7116 (ptm-80) cc_final: 0.6856 (ptt90) REVERT: I 298 ARG cc_start: 0.7139 (ttm-80) cc_final: 0.6715 (mtt180) REVERT: I 305 GLU cc_start: 0.8275 (mm-30) cc_final: 0.8068 (mm-30) REVERT: J 1 MET cc_start: 0.8593 (tpp) cc_final: 0.8261 (tpt) REVERT: K 112 ILE cc_start: 0.9252 (pt) cc_final: 0.8982 (pt) REVERT: K 114 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: M 86 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7970 (p) REVERT: M 219 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8104 (mm-40) REVERT: N 306 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.8882 (t) REVERT: O 151 VAL cc_start: 0.7238 (m) cc_final: 0.6842 (m) REVERT: O 157 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8120 (mp) REVERT: O 288 GLU cc_start: 0.8125 (tp30) cc_final: 0.7802 (tp30) REVERT: P 50 TYR cc_start: 0.2734 (m-80) cc_final: 0.1415 (m-80) REVERT: P 136 TYR cc_start: 0.3641 (m-10) cc_final: 0.3203 (m-10) REVERT: P 141 MET cc_start: 0.7012 (OUTLIER) cc_final: 0.6776 (mtm) REVERT: P 176 TYR cc_start: 0.3647 (m-80) cc_final: 0.2512 (m-10) REVERT: S 68 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8061 (pttp) REVERT: S 107 ASP cc_start: 0.7173 (t0) cc_final: 0.6778 (t0) REVERT: S 236 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: S 240 LYS cc_start: 0.8431 (mtpt) cc_final: 0.8183 (mtmt) REVERT: S 261 PHE cc_start: 0.8461 (t80) cc_final: 0.8103 (t80) REVERT: S 309 TYR cc_start: 0.8097 (t80) cc_final: 0.7627 (t80) REVERT: T 131 ARG cc_start: 0.7999 (ptm-80) cc_final: 0.6786 (ptp90) REVERT: T 242 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.7034 (tt) REVERT: T 245 MET cc_start: 0.7154 (mmp) cc_final: 0.6631 (mmm) REVERT: T 265 GLU cc_start: 0.7263 (mp0) cc_final: 0.7015 (mp0) outliers start: 62 outliers final: 39 residues processed: 493 average time/residue: 0.2508 time to fit residues: 194.9557 Evaluate side-chains 474 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 428 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 417 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 253 optimal weight: 2.9990 chunk 367 optimal weight: 2.9990 chunk 6 optimal weight: 0.0010 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 355 optimal weight: 5.9990 chunk 316 optimal weight: 6.9990 chunk 404 optimal weight: 7.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 219 GLN Q 17 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.164494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123383 restraints weight = 46502.036| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.12 r_work: 0.3218 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35799 Z= 0.126 Angle : 0.550 9.691 48824 Z= 0.282 Chirality : 0.044 0.231 5602 Planarity : 0.004 0.068 6062 Dihedral : 13.080 178.623 5670 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.16 % Favored : 92.80 % Rotamer: Outliers : 2.07 % Allowed : 16.49 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4275 helix: 0.78 (0.15), residues: 1367 sheet: -0.48 (0.20), residues: 672 loop : -1.09 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 49 TYR 0.021 0.001 TYR G 45 PHE 0.016 0.001 PHE K 258 TRP 0.020 0.002 TRP C 4 HIS 0.008 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00293 (35792) covalent geometry : angle 0.55016 (48810) SS BOND : bond 0.00112 ( 7) SS BOND : angle 0.85200 ( 14) hydrogen bonds : bond 0.03114 ( 1036) hydrogen bonds : angle 4.22425 ( 2967) *********************** 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 529 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 455 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7491 (tttt) cc_final: 0.7230 (tppt) REVERT: D 78 GLU cc_start: 0.6524 (mp0) cc_final: 0.6127 (mp0) REVERT: E 35 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7842 (tpp80) REVERT: E 80 LYS cc_start: 0.8344 (mmmm) cc_final: 0.7980 (mmmm) REVERT: F 22 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7270 (tm-30) REVERT: F 73 ASP cc_start: 0.7297 (p0) cc_final: 0.6756 (p0) REVERT: F 88 LYS cc_start: 0.8276 (tptp) cc_final: 0.7976 (tppt) REVERT: G 4 TRP cc_start: 0.6364 (t60) cc_final: 0.6045 (t60) REVERT: G 67 ARG cc_start: 0.8193 (mtp-110) cc_final: 0.7936 (ttm110) REVERT: H 37 GLN cc_start: 0.7780 (tp40) cc_final: 0.7514 (tp40) REVERT: H 55 LYS cc_start: 0.8111 (mttp) cc_final: 0.7816 (mtmt) REVERT: H 67 ARG cc_start: 0.7362 (tmt170) cc_final: 0.6998 (tmt170) REVERT: H 72 GLU cc_start: 0.7402 (pm20) cc_final: 0.7030 (pm20) REVERT: I 72 TYR cc_start: 0.7724 (m-80) cc_final: 0.7505 (m-80) REVERT: I 83 TYR cc_start: 0.7457 (m-10) cc_final: 0.6921 (m-10) REVERT: I 131 ARG cc_start: 0.7258 (ptm-80) cc_final: 0.6997 (ptt90) REVERT: I 294 ILE cc_start: 0.7745 (pt) cc_final: 0.7510 (pt) REVERT: I 298 ARG cc_start: 0.7183 (ttm-80) cc_final: 0.6795 (mtt180) REVERT: I 305 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8124 (mm-30) REVERT: J 1 MET cc_start: 0.8674 (tpp) cc_final: 0.8248 (tpt) REVERT: J 236 GLU cc_start: 0.8260 (mp0) cc_final: 0.7940 (mp0) REVERT: K 112 ILE cc_start: 0.9269 (pt) cc_final: 0.9022 (pt) REVERT: K 114 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: M 239 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8906 (mm) REVERT: M 312 ASP cc_start: 0.7577 (p0) cc_final: 0.7046 (p0) REVERT: N 285 ASP cc_start: 0.9133 (p0) cc_final: 0.8819 (p0) REVERT: N 306 VAL cc_start: 0.9270 (OUTLIER) cc_final: 0.8817 (t) REVERT: O 151 VAL cc_start: 0.7437 (m) cc_final: 0.7030 (m) REVERT: O 157 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8120 (mp) REVERT: O 183 MET cc_start: 0.3869 (OUTLIER) cc_final: 0.2974 (ptp) REVERT: O 288 GLU cc_start: 0.8152 (tp30) cc_final: 0.7836 (tp30) REVERT: P 50 TYR cc_start: 0.2907 (m-80) cc_final: 0.1519 (m-80) REVERT: P 136 TYR cc_start: 0.3736 (m-10) cc_final: 0.3143 (m-10) REVERT: P 141 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6755 (mtm) REVERT: P 176 TYR cc_start: 0.3603 (m-80) cc_final: 0.2619 (m-10) REVERT: P 218 TYR cc_start: 0.4070 (t80) cc_final: 0.3749 (t80) REVERT: S 68 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8104 (pttp) REVERT: S 236 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: S 240 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8212 (mtmt) REVERT: S 261 PHE cc_start: 0.8483 (t80) cc_final: 0.8117 (t80) REVERT: S 309 TYR cc_start: 0.8157 (t80) cc_final: 0.7696 (t80) REVERT: T 10 ARG cc_start: 0.6806 (mtm180) cc_final: 0.6392 (mtp180) REVERT: T 131 ARG cc_start: 0.8088 (ptm-80) cc_final: 0.6887 (ptp90) REVERT: T 242 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6892 (tt) REVERT: T 245 MET cc_start: 0.7180 (mmp) cc_final: 0.6648 (mmm) outliers start: 74 outliers final: 51 residues processed: 502 average time/residue: 0.2481 time to fit residues: 196.1822 Evaluate side-chains 491 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 432 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 222 optimal weight: 0.5980 chunk 79 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 323 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 170 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 233 optimal weight: 3.9990 chunk 301 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN M 219 GLN Q 17 ASN ** S 253 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 = 0.3927 r_free = 0.3927 target = 0.163771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122459 restraints weight = 46621.895| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.13 r_work: 0.3186 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 35799 Z= 0.146 Angle : 0.566 9.633 48824 Z= 0.291 Chirality : 0.045 0.237 5602 Planarity : 0.004 0.071 6062 Dihedral : 13.130 178.701 5670 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.35 % Favored : 92.61 % Rotamer: Outliers : 2.44 % Allowed : 17.22 % Favored : 80.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 4275 helix: 0.62 (0.15), residues: 1398 sheet: -0.56 (0.20), residues: 678 loop : -1.03 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 130 TYR 0.027 0.001 TYR P 231 PHE 0.023 0.002 PHE J 258 TRP 0.028 0.002 TRP C 4 HIS 0.010 0.002 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00343 (35792) covalent geometry : angle 0.56584 (48810) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.89345 ( 14) hydrogen bonds : bond 0.03280 ( 1036) hydrogen bonds : angle 4.25568 ( 2967) *********************** 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 528 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 441 time to evaluate : 1.326 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7429 (tttt) cc_final: 0.7175 (tppt) REVERT: A 72 GLU cc_start: 0.6652 (pm20) cc_final: 0.6396 (pm20) REVERT: C 79 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5099 (pm20) REVERT: D 78 GLU cc_start: 0.6412 (mp0) cc_final: 0.6058 (mp0) REVERT: E 35 ARG cc_start: 0.8321 (tpp80) cc_final: 0.8029 (tpp80) REVERT: E 80 LYS cc_start: 0.8367 (mmmm) cc_final: 0.7991 (mmmm) REVERT: F 73 ASP cc_start: 0.7380 (p0) cc_final: 0.6856 (p0) REVERT: F 88 LYS cc_start: 0.8270 (tptp) cc_final: 0.7977 (tppt) REVERT: G 4 TRP cc_start: 0.6542 (t60) cc_final: 0.6212 (t60) REVERT: G 67 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7942 (ttm110) REVERT: H 37 GLN cc_start: 0.7765 (tp40) cc_final: 0.7484 (tp40) REVERT: H 55 LYS cc_start: 0.8098 (mttp) cc_final: 0.7782 (mtmt) REVERT: H 67 ARG cc_start: 0.7357 (tmt170) cc_final: 0.6956 (tmt170) REVERT: I 83 TYR cc_start: 0.7427 (m-10) cc_final: 0.6912 (m-10) REVERT: I 131 ARG cc_start: 0.7344 (ptm-80) cc_final: 0.7071 (ptt90) REVERT: I 298 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6646 (mtt180) REVERT: I 305 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8051 (mm-30) REVERT: J 1 MET cc_start: 0.8650 (tpp) cc_final: 0.8279 (tpt) REVERT: J 83 TYR cc_start: 0.8754 (m-10) cc_final: 0.8516 (m-10) REVERT: J 221 ARG cc_start: 0.6934 (mmp80) cc_final: 0.6697 (mmp80) REVERT: J 236 GLU cc_start: 0.8259 (mp0) cc_final: 0.7814 (mp0) REVERT: K 112 ILE cc_start: 0.9313 (pt) cc_final: 0.9070 (pt) REVERT: K 114 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: M 239 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8893 (mm) REVERT: M 316 ASP cc_start: 0.7669 (p0) cc_final: 0.7464 (p0) REVERT: N 285 ASP cc_start: 0.9150 (p0) cc_final: 0.8799 (p0) REVERT: N 306 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.8864 (t) REVERT: O 157 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8185 (mp) REVERT: O 183 MET cc_start: 0.4003 (OUTLIER) cc_final: 0.2944 (ptp) REVERT: O 288 GLU cc_start: 0.8147 (tp30) cc_final: 0.7830 (tp30) REVERT: P 50 TYR cc_start: 0.2500 (m-80) cc_final: 0.1115 (m-80) REVERT: P 136 TYR cc_start: 0.3604 (m-10) cc_final: 0.3178 (m-10) REVERT: P 141 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6528 (mtm) REVERT: P 176 TYR cc_start: 0.3859 (m-80) cc_final: 0.2927 (m-10) REVERT: P 218 TYR cc_start: 0.4147 (t80) cc_final: 0.3814 (t80) REVERT: S 68 LYS cc_start: 0.8840 (mmmt) cc_final: 0.8072 (pttp) REVERT: S 240 LYS cc_start: 0.8468 (mtpt) cc_final: 0.8221 (mtmt) REVERT: S 261 PHE cc_start: 0.8535 (t80) cc_final: 0.8162 (t80) REVERT: S 309 TYR cc_start: 0.8148 (t80) cc_final: 0.7726 (t80) REVERT: T 130 ARG cc_start: 0.6189 (mmp80) cc_final: 0.5974 (mmp80) REVERT: T 131 ARG cc_start: 0.8093 (ptm-80) cc_final: 0.6855 (ptp90) REVERT: T 242 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6870 (tt) REVERT: T 245 MET cc_start: 0.7286 (mmp) cc_final: 0.6799 (mmm) outliers start: 87 outliers final: 64 residues processed: 497 average time/residue: 0.2346 time to fit residues: 185.1779 Evaluate side-chains 495 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 423 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 117 optimal weight: 1.9990 chunk 321 optimal weight: 9.9990 chunk 326 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 350 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 236 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 425 optimal weight: 0.9980 chunk 195 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 GLN M 219 GLN O 53 ASN Q 17 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.161542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120557 restraints weight = 46617.563| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.12 r_work: 0.3155 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 35799 Z= 0.181 Angle : 0.608 9.873 48824 Z= 0.312 Chirality : 0.046 0.244 5602 Planarity : 0.005 0.074 6062 Dihedral : 13.206 179.250 5670 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.72 % Favored : 92.23 % Rotamer: Outliers : 2.55 % Allowed : 17.69 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.13), residues: 4275 helix: 0.65 (0.15), residues: 1350 sheet: -0.78 (0.19), residues: 742 loop : -1.13 (0.13), residues: 2183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 256 TYR 0.023 0.002 TYR G 45 PHE 0.025 0.002 PHE I 258 TRP 0.027 0.002 TRP C 4 HIS 0.013 0.002 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00433 (35792) covalent geometry : angle 0.60830 (48810) SS BOND : bond 0.00135 ( 7) SS BOND : angle 1.00327 ( 14) hydrogen bonds : bond 0.03556 ( 1036) hydrogen bonds : angle 4.34861 ( 2967) *********************** 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 534 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 443 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7544 (tttt) cc_final: 0.7276 (tppt) REVERT: A 72 GLU cc_start: 0.6873 (pm20) cc_final: 0.6505 (pm20) REVERT: C 79 GLU cc_start: 0.5906 (OUTLIER) cc_final: 0.5309 (pm20) REVERT: D 78 GLU cc_start: 0.6170 (mp0) cc_final: 0.5728 (mp0) REVERT: E 35 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7974 (tpp80) REVERT: E 80 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8103 (mmmm) REVERT: F 73 ASP cc_start: 0.7661 (p0) cc_final: 0.6977 (p0) REVERT: F 88 LYS cc_start: 0.8171 (tptp) cc_final: 0.7877 (tppt) REVERT: G 53 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8786 (ttmt) REVERT: G 67 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7951 (ttm110) REVERT: H 67 ARG cc_start: 0.7335 (tmt170) cc_final: 0.7028 (tmt170) REVERT: H 72 GLU cc_start: 0.7171 (mp0) cc_final: 0.6741 (pm20) REVERT: I 83 TYR cc_start: 0.7593 (m-10) cc_final: 0.7180 (m-10) REVERT: I 131 ARG cc_start: 0.7506 (ptm-80) cc_final: 0.7220 (ptm-80) REVERT: I 294 ILE cc_start: 0.7799 (pt) cc_final: 0.7556 (pt) REVERT: I 298 ARG cc_start: 0.7265 (ttm-80) cc_final: 0.6783 (mtt180) REVERT: I 305 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8143 (mm-30) REVERT: I 308 THR cc_start: 0.7880 (p) cc_final: 0.7633 (p) REVERT: J 1 MET cc_start: 0.8683 (tpp) cc_final: 0.8301 (tpt) REVERT: K 112 ILE cc_start: 0.9265 (pt) cc_final: 0.9025 (pt) REVERT: K 114 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: M 239 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8891 (mm) REVERT: M 312 ASP cc_start: 0.7332 (p0) cc_final: 0.7020 (p0) REVERT: M 316 ASP cc_start: 0.7821 (p0) cc_final: 0.7532 (p0) REVERT: N 285 ASP cc_start: 0.9129 (p0) cc_final: 0.8882 (p0) REVERT: N 306 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.8832 (t) REVERT: O 157 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8144 (mp) REVERT: O 183 MET cc_start: 0.4209 (OUTLIER) cc_final: 0.3067 (ptp) REVERT: O 288 GLU cc_start: 0.8164 (tp30) cc_final: 0.7872 (tp30) REVERT: P 50 TYR cc_start: 0.2646 (m-80) cc_final: 0.1186 (m-80) REVERT: P 136 TYR cc_start: 0.3680 (m-10) cc_final: 0.3198 (m-10) REVERT: P 176 TYR cc_start: 0.4433 (OUTLIER) cc_final: 0.3525 (m-10) REVERT: P 218 TYR cc_start: 0.3936 (t80) cc_final: 0.3590 (t80) REVERT: S 83 TYR cc_start: 0.8359 (m-10) cc_final: 0.8133 (m-10) REVERT: S 240 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8256 (mtmt) REVERT: S 309 TYR cc_start: 0.8290 (t80) cc_final: 0.7858 (t80) REVERT: T 131 ARG cc_start: 0.8174 (ptm-80) cc_final: 0.6997 (ptp90) REVERT: T 242 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.6901 (tt) REVERT: T 245 MET cc_start: 0.7323 (mmp) cc_final: 0.6843 (mmm) outliers start: 91 outliers final: 66 residues processed: 506 average time/residue: 0.2458 time to fit residues: 196.7579 Evaluate side-chains 500 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 426 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 204 LEU Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 180 optimal weight: 2.9990 chunk 415 optimal weight: 4.9990 chunk 368 optimal weight: 4.9990 chunk 252 optimal weight: 9.9990 chunk 414 optimal weight: 7.9990 chunk 192 optimal weight: 0.9980 chunk 421 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 386 optimal weight: 0.2980 chunk 126 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN M 219 GLN O 17 ASN Q 17 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.160775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120156 restraints weight = 46360.195| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.12 r_work: 0.3157 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 35799 Z= 0.172 Angle : 0.610 9.757 48824 Z= 0.312 Chirality : 0.046 0.244 5602 Planarity : 0.005 0.075 6062 Dihedral : 13.220 179.219 5670 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.42 % Favored : 92.54 % Rotamer: Outliers : 2.72 % Allowed : 18.00 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4275 helix: 0.56 (0.15), residues: 1350 sheet: -0.80 (0.19), residues: 760 loop : -1.19 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 164 TYR 0.024 0.001 TYR G 45 PHE 0.023 0.002 PHE I 258 TRP 0.030 0.002 TRP G 4 HIS 0.012 0.002 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00409 (35792) covalent geometry : angle 0.60970 (48810) SS BOND : bond 0.00140 ( 7) SS BOND : angle 0.99727 ( 14) hydrogen bonds : bond 0.03509 ( 1036) hydrogen bonds : angle 4.36083 ( 2967) *********************** 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 536 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 439 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7496 (tttt) cc_final: 0.7235 (tppt) REVERT: A 72 GLU cc_start: 0.7228 (pm20) cc_final: 0.6934 (pm20) REVERT: A 106 ASN cc_start: 0.5093 (t0) cc_final: 0.4776 (p0) REVERT: C 79 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5472 (pm20) REVERT: D 78 GLU cc_start: 0.6312 (mp0) cc_final: 0.5891 (mp0) REVERT: E 35 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7987 (tpp80) REVERT: E 78 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6639 (mm-30) REVERT: E 80 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7951 (mmmm) REVERT: F 55 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7964 (mtmt) REVERT: F 73 ASP cc_start: 0.7664 (p0) cc_final: 0.6999 (p0) REVERT: G 53 LYS cc_start: 0.8985 (ttmt) cc_final: 0.8661 (mtmt) REVERT: G 67 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7969 (ttm110) REVERT: H 67 ARG cc_start: 0.7319 (tmt170) cc_final: 0.6979 (tmt170) REVERT: I 83 TYR cc_start: 0.7539 (m-10) cc_final: 0.7107 (m-10) REVERT: I 131 ARG cc_start: 0.7596 (ptm-80) cc_final: 0.7250 (ptm-80) REVERT: I 294 ILE cc_start: 0.7786 (pt) cc_final: 0.7530 (pt) REVERT: I 298 ARG cc_start: 0.7286 (ttm-80) cc_final: 0.6809 (mtt180) REVERT: I 300 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8527 (tt) REVERT: I 305 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8105 (mm-30) REVERT: I 308 THR cc_start: 0.7989 (p) cc_final: 0.7763 (p) REVERT: J 1 MET cc_start: 0.8681 (tpp) cc_final: 0.8334 (tpt) REVERT: K 112 ILE cc_start: 0.9283 (pt) cc_final: 0.9033 (pt) REVERT: K 114 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: K 246 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8743 (mm) REVERT: M 239 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8886 (mm) REVERT: M 312 ASP cc_start: 0.7287 (p0) cc_final: 0.6996 (p0) REVERT: N 306 VAL cc_start: 0.9307 (OUTLIER) cc_final: 0.8862 (t) REVERT: O 157 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8173 (mp) REVERT: O 183 MET cc_start: 0.4173 (OUTLIER) cc_final: 0.3044 (ptp) REVERT: O 288 GLU cc_start: 0.8170 (tp30) cc_final: 0.7867 (tp30) REVERT: P 50 TYR cc_start: 0.2736 (m-80) cc_final: 0.1252 (m-80) REVERT: P 136 TYR cc_start: 0.3709 (m-10) cc_final: 0.3215 (m-10) REVERT: P 176 TYR cc_start: 0.4404 (OUTLIER) cc_final: 0.3526 (m-10) REVERT: P 222 GLU cc_start: 0.5707 (pt0) cc_final: 0.4996 (pt0) REVERT: S 240 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8220 (mtmt) REVERT: S 309 TYR cc_start: 0.8254 (t80) cc_final: 0.7824 (t80) REVERT: T 131 ARG cc_start: 0.7904 (ptm-80) cc_final: 0.6970 (ptp90) REVERT: T 242 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7057 (tt) REVERT: T 245 MET cc_start: 0.7290 (mmp) cc_final: 0.6823 (mmm) outliers start: 97 outliers final: 69 residues processed: 505 average time/residue: 0.2441 time to fit residues: 195.9501 Evaluate side-chains 512 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 432 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 204 LEU Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 216 optimal weight: 1.9990 chunk 376 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 426 optimal weight: 6.9990 chunk 209 optimal weight: 0.7980 chunk 341 optimal weight: 4.9990 chunk 221 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 chunk 159 optimal weight: 6.9990 chunk 372 optimal weight: 0.9980 chunk 218 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 19 GLN M 219 GLN O 17 ASN Q 17 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.162229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.121049 restraints weight = 46373.218| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.11 r_work: 0.3193 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 35799 Z= 0.121 Angle : 0.576 9.490 48824 Z= 0.294 Chirality : 0.044 0.286 5602 Planarity : 0.004 0.073 6062 Dihedral : 13.158 178.745 5670 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 2.24 % Allowed : 18.67 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.13), residues: 4275 helix: 0.70 (0.15), residues: 1350 sheet: -0.71 (0.19), residues: 759 loop : -1.15 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 164 TYR 0.025 0.001 TYR G 45 PHE 0.016 0.001 PHE J 258 TRP 0.025 0.002 TRP C 4 HIS 0.006 0.001 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00277 (35792) covalent geometry : angle 0.57629 (48810) SS BOND : bond 0.00129 ( 7) SS BOND : angle 0.88910 ( 14) hydrogen bonds : bond 0.03077 ( 1036) hydrogen bonds : angle 4.26311 ( 2967) ********************** 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 517 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 437 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7440 (tttt) cc_final: 0.7194 (tppt) REVERT: A 72 GLU cc_start: 0.7045 (pm20) cc_final: 0.6787 (pm20) REVERT: A 106 ASN cc_start: 0.5191 (t0) cc_final: 0.4816 (p0) REVERT: C 79 GLU cc_start: 0.5789 (OUTLIER) cc_final: 0.5240 (pm20) REVERT: D 78 GLU cc_start: 0.6260 (mp0) cc_final: 0.5840 (mp0) REVERT: E 35 ARG cc_start: 0.8221 (tpp80) cc_final: 0.7972 (tpp80) REVERT: E 80 LYS cc_start: 0.8282 (mmmm) cc_final: 0.7874 (mmmm) REVERT: E 82 GLU cc_start: 0.6110 (tp30) cc_final: 0.5794 (pt0) REVERT: F 55 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7973 (mttt) REVERT: F 73 ASP cc_start: 0.7358 (p0) cc_final: 0.6853 (p0) REVERT: G 53 LYS cc_start: 0.8968 (ttmt) cc_final: 0.8645 (mtmt) REVERT: G 67 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7944 (ttm110) REVERT: H 55 LYS cc_start: 0.8109 (mttp) cc_final: 0.7798 (mtmt) REVERT: H 67 ARG cc_start: 0.7380 (tmt170) cc_final: 0.6806 (tpt170) REVERT: I 83 TYR cc_start: 0.7304 (m-10) cc_final: 0.6788 (m-10) REVERT: I 131 ARG cc_start: 0.7414 (ptm-80) cc_final: 0.7108 (ptm-80) REVERT: I 294 ILE cc_start: 0.7720 (pt) cc_final: 0.7469 (pt) REVERT: I 298 ARG cc_start: 0.7200 (ttm-80) cc_final: 0.6726 (mtt180) REVERT: I 305 GLU cc_start: 0.8292 (mm-30) cc_final: 0.8080 (mm-30) REVERT: J 1 MET cc_start: 0.8836 (tpp) cc_final: 0.8512 (tpt) REVERT: J 83 TYR cc_start: 0.8724 (m-10) cc_final: 0.8491 (m-10) REVERT: J 236 GLU cc_start: 0.8311 (mp0) cc_final: 0.8068 (mp0) REVERT: K 112 ILE cc_start: 0.9302 (pt) cc_final: 0.9050 (pt) REVERT: K 114 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8090 (pm20) REVERT: K 246 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8737 (mm) REVERT: M 86 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8350 (p) REVERT: M 239 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8912 (mm) REVERT: M 312 ASP cc_start: 0.7300 (p0) cc_final: 0.6974 (p0) REVERT: N 285 ASP cc_start: 0.9125 (p0) cc_final: 0.8773 (p0) REVERT: N 306 VAL cc_start: 0.9315 (OUTLIER) cc_final: 0.8888 (t) REVERT: O 157 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8199 (mp) REVERT: O 164 ARG cc_start: 0.7451 (ptp-170) cc_final: 0.6975 (ttp-170) REVERT: O 288 GLU cc_start: 0.8149 (tp30) cc_final: 0.7848 (tp30) REVERT: P 50 TYR cc_start: 0.2667 (m-80) cc_final: 0.1214 (m-80) REVERT: P 136 TYR cc_start: 0.3617 (m-10) cc_final: 0.3128 (m-10) REVERT: P 141 MET cc_start: 0.6913 (OUTLIER) cc_final: 0.6471 (mtm) REVERT: P 176 TYR cc_start: 0.4345 (m-80) cc_final: 0.3407 (m-10) REVERT: P 218 TYR cc_start: 0.3709 (t80) cc_final: 0.3396 (t80) REVERT: S 240 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8204 (mtmt) REVERT: S 309 TYR cc_start: 0.8187 (t80) cc_final: 0.7736 (t80) REVERT: T 131 ARG cc_start: 0.7905 (ptm-80) cc_final: 0.6972 (ptp90) REVERT: T 209 GLN cc_start: 0.6193 (OUTLIER) cc_final: 0.5664 (mm-40) REVERT: T 242 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7010 (tt) REVERT: T 245 MET cc_start: 0.7258 (mmp) cc_final: 0.6769 (mmm) outliers start: 80 outliers final: 61 residues processed: 492 average time/residue: 0.2447 time to fit residues: 190.8476 Evaluate side-chains 499 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 427 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 39 GLU Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 209 GLN Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 351 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 137 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 348 optimal weight: 3.9990 chunk 376 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 398 optimal weight: 0.7980 chunk 354 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 19 GLN M 219 GLN Q 17 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.161722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.120843 restraints weight = 46421.948| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.11 r_work: 0.3168 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 35799 Z= 0.162 Angle : 0.599 10.102 48824 Z= 0.306 Chirality : 0.046 0.261 5602 Planarity : 0.005 0.073 6062 Dihedral : 13.178 179.576 5670 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.46 % Favored : 92.51 % Rotamer: Outliers : 2.41 % Allowed : 18.59 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.13), residues: 4275 helix: 0.63 (0.15), residues: 1350 sheet: -0.76 (0.19), residues: 759 loop : -1.17 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 49 TYR 0.025 0.001 TYR G 45 PHE 0.024 0.002 PHE I 258 TRP 0.024 0.002 TRP C 4 HIS 0.011 0.002 HIS L 162 Details of bonding type rmsd covalent geometry : bond 0.00386 (35792) covalent geometry : angle 0.59900 (48810) SS BOND : bond 0.00133 ( 7) SS BOND : angle 0.97788 ( 14) hydrogen bonds : bond 0.03329 ( 1036) hydrogen bonds : angle 4.31245 ( 2967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10165.72 seconds wall clock time: 174 minutes 48.01 seconds (10488.01 seconds total)