Starting phenix.real_space_refine on Sun Jun 29 20:03:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r21_14244/06_2025/7r21_14244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r21_14244/06_2025/7r21_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_14244/06_2025/7r21_14244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r21_14244/06_2025/7r21_14244.map" model { file = "/net/cci-nas-00/data/ceres_data/7r21_14244/06_2025/7r21_14244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r21_14244/06_2025/7r21_14244.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 69 5.16 5 C 22119 2.51 5 N 5999 2.21 5 O 6732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 34980 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1320 Classifications: {'RNA': 62} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 24, 'rna3p': 37} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "S" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2350 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 18.14, per 1000 atoms: 0.52 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: 7.51 Conformation dependent library (CDL) restraints added in 3.9 seconds 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7956 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 57 sheets defined 37.2% alpha, 12.0% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 9.93 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.910A pdb=" N ILE A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.616A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.325A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.929A pdb=" N GLU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 4.024A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.706A pdb=" N VAL C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 33 removed outlier: 4.283A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.937A pdb=" N LEU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 removed outlier: 4.144A pdb=" N GLU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 4.028A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.754A pdb=" N LEU C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.250A pdb=" N PHE C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 103 " --> pdb=" O TRP C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.508A pdb=" N TYR D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.669A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.586A pdb=" N SER D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.616A pdb=" N ILE D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.938A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.878A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.816A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.866A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 removed outlier: 3.872A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.962A pdb=" N LYS E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 24 through 33 removed outlier: 4.016A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.959A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 removed outlier: 4.230A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.738A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.775A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'G' and resid 5 through 15 removed outlier: 3.529A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 15 " --> pdb=" O TYR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.683A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 4.102A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 60 removed outlier: 3.619A pdb=" N LEU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.536A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 removed outlier: 3.829A pdb=" N LEU H 15 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.145A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.728A pdb=" N LEU H 40 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 62 removed outlier: 4.216A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.891A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 100 removed outlier: 3.926A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.699A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.632A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 285 through 300 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.632A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.629A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 removed outlier: 3.565A pdb=" N ILE J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 121 Processing helix chain 'J' and resid 144 through 152 removed outlier: 3.587A pdb=" N GLU J 152 " --> pdb=" O ILE J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 205 removed outlier: 3.557A pdb=" N VAL J 205 " --> pdb=" O LEU J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 202 through 205' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 241 through 246 removed outlier: 3.512A pdb=" N MET J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 301 Processing helix chain 'J' and resid 324 through 334 Processing helix chain 'K' and resid 51 through 69 removed outlier: 4.175A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.697A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 removed outlier: 3.539A pdb=" N ILE K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 242 through 247 removed outlier: 3.523A pdb=" N SER K 247 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'L' and resid 51 through 67 Processing helix chain 'L' and resid 77 through 83 removed outlier: 3.697A pdb=" N ARG L 82 " --> pdb=" O ARG L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.539A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 179 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.818A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 301 removed outlier: 3.687A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 299 " --> pdb=" O LYS L 295 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 300 " --> pdb=" O ASN L 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.632A pdb=" N MET L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.528A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.904A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.936A pdb=" N ILE M 111 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 Processing helix chain 'M' and resid 144 through 152 removed outlier: 3.823A pdb=" N GLU M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL M 151 " --> pdb=" O PHE M 147 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 removed outlier: 3.650A pdb=" N SER M 247 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 301 removed outlier: 3.661A pdb=" N LYS M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY M 301 " --> pdb=" O ALA M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.734A pdb=" N MET M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 69 removed outlier: 4.312A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.819A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 122 Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.680A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.667A pdb=" N ALA N 299 " --> pdb=" O LYS N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.906A pdb=" N LEU N 328 " --> pdb=" O SER N 324 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET N 335 " --> pdb=" O ASN N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 24 removed outlier: 3.529A pdb=" N THR O 24 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.532A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.559A pdb=" N LEU O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 82' Processing helix chain 'O' and resid 107 through 115 removed outlier: 3.653A pdb=" N ILE O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 122 Processing helix chain 'O' and resid 144 through 152 removed outlier: 3.761A pdb=" N GLU O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL O 151 " --> pdb=" O PHE O 147 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU O 152 " --> pdb=" O ILE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.674A pdb=" N LYS O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN O 296 " --> pdb=" O SER O 292 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA O 297 " --> pdb=" O ILE O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 3.834A pdb=" N LEU O 328 " --> pdb=" O SER O 324 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 46 removed outlier: 3.681A pdb=" N LEU P 38 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 51 removed outlier: 4.049A pdb=" N TYR P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 46 through 51' Processing helix chain 'P' and resid 54 through 69 removed outlier: 3.595A pdb=" N LYS P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.978A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 24 removed outlier: 3.799A pdb=" N GLY Q 23 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 69 removed outlier: 4.233A pdb=" N THR Q 69 " --> pdb=" O ASP Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.076A pdb=" N ARG Q 82 " --> pdb=" O GLU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 115 removed outlier: 3.970A pdb=" N ILE Q 111 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS Q 113 " --> pdb=" O ALA Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 122 removed outlier: 3.579A pdb=" N ASP Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 151 Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 227 through 241 Processing helix chain 'Q' and resid 285 through 301 Processing helix chain 'Q' and resid 325 through 335 removed outlier: 3.881A pdb=" N MET Q 335 " --> pdb=" O ASN Q 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 removed outlier: 3.714A pdb=" N GLY S 23 " --> pdb=" O GLY S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 69 removed outlier: 3.533A pdb=" N LEU S 55 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 82 removed outlier: 3.857A pdb=" N ARG S 82 " --> pdb=" O GLU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 115 removed outlier: 3.881A pdb=" N ILE S 111 " --> pdb=" O ASP S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 122 Processing helix chain 'S' and resid 144 through 152 removed outlier: 4.329A pdb=" N GLU S 150 " --> pdb=" O ASP S 146 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL S 151 " --> pdb=" O PHE S 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU S 152 " --> pdb=" O ILE S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 227 through 241 Processing helix chain 'S' and resid 285 through 301 removed outlier: 3.557A pdb=" N ASN S 296 " --> pdb=" O SER S 292 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 297 " --> pdb=" O ILE S 293 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY S 301 " --> pdb=" O ALA S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 335 removed outlier: 3.782A pdb=" N MET S 335 " --> pdb=" O ASN S 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 24 removed outlier: 3.776A pdb=" N GLY T 23 " --> pdb=" O GLY T 20 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR T 24 " --> pdb=" O GLY T 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 20 through 24' Processing helix chain 'T' and resid 51 through 69 removed outlier: 3.764A pdb=" N LEU T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 75 removed outlier: 4.113A pdb=" N VAL T 74 " --> pdb=" O PRO T 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN T 75 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.623A pdb=" N LEU T 81 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG T 82 " --> pdb=" O GLU T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.735A pdb=" N LYS T 113 " --> pdb=" O ALA T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 122 removed outlier: 3.535A pdb=" N ASP T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 152 removed outlier: 3.603A pdb=" N ILE T 148 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU T 152 " --> pdb=" O ILE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 203 through 205 No H-bonds generated for 'chain 'T' and resid 203 through 205' Processing helix chain 'T' and resid 227 through 241 Processing helix chain 'T' and resid 285 through 301 removed outlier: 3.774A pdb=" N ALA T 297 " --> pdb=" O ILE T 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY T 301 " --> pdb=" O ALA T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 335 removed outlier: 4.283A pdb=" N MET T 335 " --> pdb=" O ASN T 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 12 current: chain 'I' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 193 through 201 current: chain 'I' and resid 305 through 309 Processing sheet with id=AA2, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.606A pdb=" N GLU I 188 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET I 183 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AA4, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'I' and resid 123 through 125 removed outlier: 7.052A pdb=" N PHE I 123 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG I 131 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 3 through 14 current: chain 'J' and resid 184 through 200 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 200 current: chain 'J' and resid 305 through 309 removed outlier: 7.206A pdb=" N VAL J 306 " --> pdb=" O THR J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AA8, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'J' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 304 through 309 removed outlier: 9.118A pdb=" N THR K 320 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB3, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'K' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 184 through 201 current: chain 'L' and resid 305 through 309 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AB7, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AB8, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AB9, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 190 through 196 current: chain 'M' and resid 306 through 309 Processing sheet with id=AC1, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC2, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AC3, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AC4, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AC5, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AC6, first strand: chain 'N' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 14 current: chain 'N' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 190 through 196 current: chain 'N' and resid 306 through 309 Processing sheet with id=AC7, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AC9, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'N' and resid 123 through 124 Processing sheet with id=AD2, first strand: chain 'N' and resid 213 through 215 Processing sheet with id=AD3, first strand: chain 'O' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 2 through 14 current: chain 'O' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 190 through 196 current: chain 'O' and resid 306 through 309 Processing sheet with id=AD4, first strand: chain 'O' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'O' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AD7, first strand: chain 'O' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'O' and resid 213 through 215 Processing sheet with id=AD9, first strand: chain 'P' and resid 77 through 79 removed outlier: 3.517A pdb=" N LEU P 120 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG P 9 " --> pdb=" O PRO P 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 12 through 13 Processing sheet with id=AE2, first strand: chain 'P' and resid 168 through 169 removed outlier: 3.932A pdb=" N ALA P 168 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL P 240 " --> pdb=" O ALA P 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 197 through 199 Processing sheet with id=AE4, first strand: chain 'P' and resid 243 through 246 Processing sheet with id=AE5, first strand: chain 'Q' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 2 through 14 current: chain 'Q' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 190 through 196 current: chain 'Q' and resid 306 through 309 removed outlier: 6.864A pdb=" N VAL Q 306 " --> pdb=" O THR Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'Q' and resid 26 through 27 Processing sheet with id=AE7, first strand: chain 'Q' and resid 31 through 36 Processing sheet with id=AE8, first strand: chain 'Q' and resid 94 through 96 Processing sheet with id=AE9, first strand: chain 'Q' and resid 123 through 124 Processing sheet with id=AF1, first strand: chain 'Q' and resid 213 through 215 Processing sheet with id=AF2, first strand: chain 'S' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 2 through 10 current: chain 'S' and resid 193 through 196 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 193 through 196 current: chain 'S' and resid 306 through 309 Processing sheet with id=AF3, first strand: chain 'S' and resid 26 through 27 Processing sheet with id=AF4, first strand: chain 'S' and resid 31 through 36 Processing sheet with id=AF5, first strand: chain 'S' and resid 94 through 96 Processing sheet with id=AF6, first strand: chain 'S' and resid 123 through 124 Processing sheet with id=AF7, first strand: chain 'S' and resid 213 through 215 Processing sheet with id=AF8, first strand: chain 'T' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 2 through 12 current: chain 'T' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 192 through 196 current: chain 'T' and resid 306 through 309 removed outlier: 7.079A pdb=" N VAL T 306 " --> pdb=" O THR T 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'T' and resid 31 through 36 Processing sheet with id=AG1, first strand: chain 'T' and resid 94 through 96 Processing sheet with id=AG2, first strand: chain 'T' and resid 123 through 124 Processing sheet with id=AG3, first strand: chain 'T' and resid 213 through 215 1036 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 10.38 Time building geometry restraints manager: 9.01 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: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.230 Check model and map are aligned: 0.260 Set scattering table: 0.270 Process input model: 73.690 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.830 ------------------------------------------------------------------------------- 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 : 10.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.13), residues: 4275 helix: 0.43 (0.15), residues: 1354 sheet: -0.52 (0.21), residues: 683 loop : -1.13 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 4 HIS 0.004 0.001 HIS J 280 PHE 0.013 0.001 PHE P 12 TYR 0.030 0.001 TYR G 45 ARG 0.013 0.000 ARG G 67 Details of bonding type rmsd hydrogen bonds : bond 0.14885 ( 1036) hydrogen bonds : angle 5.94515 ( 2967) SS BOND : bond 0.00289 ( 7) SS BOND : angle 0.79006 ( 14) covalent geometry : bond 0.00327 (35792) covalent geometry : angle 0.58406 (48810) *********************** 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 : 4.207 Fit side-chains REVERT: A 57 LYS cc_start: 0.7718 (tttt) cc_final: 0.7459 (tppt) REVERT: A 72 GLU cc_start: 0.6983 (pm20) cc_final: 0.6738 (pm20) REVERT: E 80 LYS cc_start: 0.8348 (mmmm) cc_final: 0.8130 (mmmm) REVERT: K 112 ILE cc_start: 0.9014 (pt) cc_final: 0.8794 (pt) REVERT: L 93 THR cc_start: 0.7766 (m) cc_final: 0.7508 (m) REVERT: M 27 ILE cc_start: 0.8528 (pt) cc_final: 0.8224 (pt) REVERT: O 274 PRO cc_start: 0.8350 (Cg_exo) cc_final: 0.8078 (Cg_endo) REVERT: O 288 GLU cc_start: 0.7319 (tp30) cc_final: 0.6982 (tp30) REVERT: S 237 SER cc_start: 0.8013 (p) cc_final: 0.7775 (p) REVERT: T 130 ARG cc_start: 0.4954 (mmp80) cc_final: 0.4232 (mmp80) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.5345 time to fit residues: 426.2296 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 : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 360 optimal weight: 5.9990 chunk 323 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 218 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 334 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 387 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 37 GLN J 162 HIS J 182 GLN L 162 HIS N 296 ASN O 296 ASN Q 12 ASN S 253 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN T 296 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.161660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.119252 restraints weight = 46421.969| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.12 r_work: 0.3173 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 35799 Z= 0.267 Angle : 0.712 10.579 48824 Z= 0.369 Chirality : 0.050 0.255 5602 Planarity : 0.006 0.087 6062 Dihedral : 13.353 177.149 5670 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.88 % Rotamer: Outliers : 1.20 % Allowed : 10.86 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.13), residues: 4275 helix: -0.02 (0.14), residues: 1422 sheet: -0.77 (0.20), residues: 668 loop : -1.21 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 4 HIS 0.009 0.002 HIS N 57 PHE 0.037 0.003 PHE I 258 TYR 0.025 0.002 TYR P 231 ARG 0.007 0.001 ARG I 10 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 1036) hydrogen bonds : angle 4.85673 ( 2967) SS BOND : bond 0.00614 ( 7) SS BOND : angle 1.38334 ( 14) covalent geometry : bond 0.00640 (35792) covalent geometry : angle 0.71183 (48810) *********************** 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 529 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 486 time to evaluate : 3.498 Fit side-chains REVERT: A 57 LYS cc_start: 0.7442 (tttt) cc_final: 0.7207 (tppt) REVERT: A 72 GLU cc_start: 0.7266 (pm20) cc_final: 0.6789 (pm20) REVERT: D 14 TYR cc_start: 0.7560 (m-80) cc_final: 0.7312 (m-80) REVERT: E 22 GLU cc_start: 0.8022 (tp30) cc_final: 0.7697 (tp30) REVERT: E 35 ARG cc_start: 0.8195 (tpp-160) cc_final: 0.7863 (tpp80) REVERT: E 80 LYS cc_start: 0.8320 (mmmm) cc_final: 0.8012 (mmmm) REVERT: F 22 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7844 (tm-30) REVERT: F 42 GLU cc_start: 0.8415 (mt-10) cc_final: 0.8027 (mt-10) REVERT: F 55 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7686 (mtmt) REVERT: F 88 LYS cc_start: 0.8317 (tptp) cc_final: 0.7984 (tppt) REVERT: G 67 ARG cc_start: 0.8347 (mtp-110) cc_final: 0.8013 (ttm110) REVERT: H 80 LYS cc_start: 0.7770 (tptm) cc_final: 0.7475 (tppt) REVERT: I 83 TYR cc_start: 0.7744 (m-10) cc_final: 0.7517 (m-10) REVERT: I 131 ARG cc_start: 0.7427 (ptm-80) cc_final: 0.7112 (ptt90) REVERT: I 298 ARG cc_start: 0.7312 (ttm-80) cc_final: 0.6686 (mtt180) REVERT: J 37 ARG cc_start: 0.6486 (mmm-85) cc_final: 0.6034 (mmm-85) REVERT: J 245 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8204 (ttt) REVERT: K 112 ILE cc_start: 0.9343 (pt) cc_final: 0.9103 (pt) REVERT: L 65 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8409 (m-30) REVERT: L 164 ARG cc_start: 0.7505 (mtt-85) cc_final: 0.7118 (ptp-110) REVERT: L 230 GLU cc_start: 0.8541 (tt0) cc_final: 0.8299 (tt0) REVERT: M 312 ASP cc_start: 0.7772 (p0) cc_final: 0.7412 (p0) REVERT: N 285 ASP cc_start: 0.9169 (p0) cc_final: 0.8784 (p0) REVERT: O 258 PHE cc_start: 0.8741 (t80) cc_final: 0.8525 (t80) REVERT: O 288 GLU cc_start: 0.8263 (tp30) cc_final: 0.7946 (tp30) REVERT: S 83 TYR cc_start: 0.8350 (m-10) cc_final: 0.8104 (m-10) REVERT: S 93 THR cc_start: 0.7210 (p) cc_final: 0.6722 (p) REVERT: S 240 LYS cc_start: 0.8544 (mtpt) cc_final: 0.8261 (mtmt) REVERT: S 309 TYR cc_start: 0.8101 (t80) cc_final: 0.7667 (t80) REVERT: T 131 ARG cc_start: 0.8052 (ptm-80) cc_final: 0.6825 (ptp90) REVERT: T 242 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7098 (tt) REVERT: T 245 MET cc_start: 0.7109 (mmp) cc_final: 0.6520 (mmp) REVERT: T 265 GLU cc_start: 0.6989 (mp0) cc_final: 0.6725 (mp0) outliers start: 43 outliers final: 25 residues processed: 508 average time/residue: 0.5012 time to fit residues: 398.4956 Evaluate side-chains 471 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 442 time to evaluate : 3.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 227 ASP Chi-restraints excluded: chain L residue 65 ASP Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain 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 334 LYS Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 311 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 372 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 360 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 334 optimal weight: 0.6980 chunk 216 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 309 optimal weight: 30.0000 chunk 52 optimal weight: 0.4980 chunk 48 optimal weight: 4.9990 chunk 409 optimal weight: 4.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 7 ASN J 162 HIS J 296 ASN O 162 HIS ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN T 296 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.163668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121417 restraints weight = 46549.538| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.10 r_work: 0.3216 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1527 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= 0.158 Angle : 0.592 9.753 48824 Z= 0.306 Chirality : 0.046 0.241 5602 Planarity : 0.005 0.079 6062 Dihedral : 13.285 179.376 5670 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 1.79 % Allowed : 13.69 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.13), residues: 4275 helix: 0.28 (0.15), residues: 1375 sheet: -0.81 (0.20), residues: 658 loop : -1.26 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 4 HIS 0.010 0.002 HIS L 162 PHE 0.024 0.002 PHE I 258 TYR 0.025 0.001 TYR P 231 ARG 0.006 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 1036) hydrogen bonds : angle 4.60744 ( 2967) SS BOND : bond 0.00165 ( 7) SS BOND : angle 0.95521 ( 14) covalent geometry : bond 0.00369 (35792) covalent geometry : angle 0.59190 (48810) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 460 time to evaluate : 3.477 Fit side-chains REVERT: A 57 LYS cc_start: 0.7376 (tttt) cc_final: 0.7106 (tppt) REVERT: A 72 GLU cc_start: 0.7329 (pm20) cc_final: 0.7068 (pm20) REVERT: E 80 LYS cc_start: 0.8329 (mmmm) cc_final: 0.8018 (mmmm) REVERT: F 22 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7829 (tm-30) REVERT: F 39 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7406 (tt0) REVERT: F 88 LYS cc_start: 0.8289 (tptp) cc_final: 0.7972 (tppt) REVERT: G 53 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8744 (ttmt) REVERT: G 67 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7961 (ttm110) REVERT: H 72 GLU cc_start: 0.7153 (pm20) cc_final: 0.6880 (pm20) REVERT: H 80 LYS cc_start: 0.7795 (tptm) cc_final: 0.7438 (tppt) REVERT: I 83 TYR cc_start: 0.7618 (m-10) cc_final: 0.7348 (m-10) REVERT: I 131 ARG cc_start: 0.7350 (ptm-80) cc_final: 0.7098 (ptm-80) REVERT: I 298 ARG cc_start: 0.7268 (ttm-80) cc_final: 0.6689 (mtt180) REVERT: J 221 ARG cc_start: 0.6965 (mmp80) cc_final: 0.6749 (mmp80) REVERT: K 112 ILE cc_start: 0.9333 (pt) cc_final: 0.9081 (pt) REVERT: K 114 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: L 65 ASP cc_start: 0.8690 (t0) cc_final: 0.8416 (m-30) REVERT: L 154 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7177 (tm-30) REVERT: L 164 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.7081 (ptp-110) REVERT: L 219 GLN cc_start: 0.7075 (mm110) cc_final: 0.6379 (mm110) REVERT: L 230 GLU cc_start: 0.8473 (tt0) cc_final: 0.8249 (tt0) REVERT: M 86 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8355 (p) REVERT: N 90 GLN cc_start: 0.8179 (tp40) cc_final: 0.7436 (tp-100) REVERT: N 285 ASP cc_start: 0.9130 (p0) cc_final: 0.8779 (p0) REVERT: O 157 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8232 (mp) REVERT: O 288 GLU cc_start: 0.8163 (tp30) cc_final: 0.7834 (tp30) REVERT: P 110 ARG cc_start: 0.7467 (tmm-80) cc_final: 0.7153 (tmm-80) REVERT: S 1 MET cc_start: 0.7759 (tpp) cc_final: 0.7448 (tpt) REVERT: S 83 TYR cc_start: 0.8369 (m-10) cc_final: 0.8155 (m-10) REVERT: S 240 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8196 (mtmt) REVERT: S 309 TYR cc_start: 0.8126 (t80) cc_final: 0.7643 (t80) REVERT: T 131 ARG cc_start: 0.8063 (ptm-80) cc_final: 0.6850 (ptp90) REVERT: T 242 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7055 (tt) REVERT: T 245 MET cc_start: 0.7188 (mmp) cc_final: 0.6712 (mmm) outliers start: 64 outliers final: 38 residues processed: 502 average time/residue: 0.5188 time to fit residues: 406.8559 Evaluate side-chains 478 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 436 time to evaluate : 3.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain H residue 36 THR 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 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 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 N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 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 199 VAL 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 222 GLU Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 237 SER 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 57 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 120 optimal weight: 10.0000 chunk 326 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 371 optimal weight: 0.6980 chunk 358 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 61 optimal weight: 0.0170 overall best weight: 1.1222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 GLN M 59 HIS Q 17 ASN S 17 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.163207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.121769 restraints weight = 46592.726| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.17 r_work: 0.3181 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1639 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= 0.138 Angle : 0.568 9.568 48824 Z= 0.294 Chirality : 0.045 0.238 5602 Planarity : 0.005 0.076 6062 Dihedral : 13.222 178.864 5670 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.42 % Favored : 92.51 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 4275 helix: 0.43 (0.15), residues: 1369 sheet: -0.74 (0.21), residues: 656 loop : -1.21 (0.13), residues: 2250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 4 HIS 0.009 0.002 HIS L 162 PHE 0.019 0.001 PHE I 258 TYR 0.022 0.001 TYR G 45 ARG 0.005 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03484 ( 1036) hydrogen bonds : angle 4.42183 ( 2967) SS BOND : bond 0.00130 ( 7) SS BOND : angle 0.92712 ( 14) covalent geometry : bond 0.00321 (35792) covalent geometry : angle 0.56802 (48810) *********************** 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 554 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 469 time to evaluate : 3.839 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7522 (tttt) cc_final: 0.7281 (tppt) REVERT: D 78 GLU cc_start: 0.6449 (mp0) cc_final: 0.6194 (mp0) REVERT: E 35 ARG cc_start: 0.8096 (tpp80) cc_final: 0.7858 (tpp80) REVERT: E 78 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6917 (mm-30) REVERT: E 80 LYS cc_start: 0.8356 (mmmm) cc_final: 0.8064 (mmmm) REVERT: F 22 GLU cc_start: 0.7935 (tm-30) cc_final: 0.7694 (tm-30) REVERT: F 73 ASP cc_start: 0.7650 (p0) cc_final: 0.7191 (p0) REVERT: F 88 LYS cc_start: 0.8276 (tptp) cc_final: 0.7978 (tppt) REVERT: G 67 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7970 (ttm110) REVERT: G 80 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7428 (mtpp) REVERT: H 72 GLU cc_start: 0.7141 (pm20) cc_final: 0.6827 (pm20) REVERT: H 80 LYS cc_start: 0.7737 (tptm) cc_final: 0.7373 (tppt) REVERT: I 83 TYR cc_start: 0.7466 (m-10) cc_final: 0.7134 (m-10) REVERT: I 131 ARG cc_start: 0.7347 (ptm-80) cc_final: 0.7072 (ptm-80) REVERT: I 165 VAL cc_start: 0.7158 (OUTLIER) cc_final: 0.6943 (m) REVERT: I 230 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: I 298 ARG cc_start: 0.7297 (ttm-80) cc_final: 0.6761 (mtt180) REVERT: J 221 ARG cc_start: 0.7062 (mmp80) cc_final: 0.6808 (mmp80) REVERT: J 236 GLU cc_start: 0.8287 (mp0) cc_final: 0.7847 (mp0) REVERT: J 309 TYR cc_start: 0.8709 (t80) cc_final: 0.8429 (t80) REVERT: K 112 ILE cc_start: 0.9271 (pt) cc_final: 0.9022 (pt) REVERT: K 114 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7951 (pm20) REVERT: L 65 ASP cc_start: 0.8686 (t0) cc_final: 0.8437 (m-30) REVERT: L 154 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7044 (tm-30) REVERT: L 164 ARG cc_start: 0.7453 (mtt-85) cc_final: 0.7244 (ptp-110) REVERT: L 219 GLN cc_start: 0.7196 (mm110) cc_final: 0.6993 (mm110) REVERT: L 230 GLU cc_start: 0.8469 (tt0) cc_final: 0.8242 (tt0) REVERT: M 312 ASP cc_start: 0.7674 (p0) cc_final: 0.7222 (p0) REVERT: N 90 GLN cc_start: 0.8120 (tp40) cc_final: 0.7444 (tp-100) REVERT: O 157 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8185 (mp) REVERT: O 183 MET cc_start: 0.4168 (OUTLIER) cc_final: 0.3028 (ptp) REVERT: O 288 GLU cc_start: 0.8143 (tp30) cc_final: 0.7837 (tp30) REVERT: P 136 TYR cc_start: 0.3784 (m-10) cc_final: 0.3246 (m-10) REVERT: S 1 MET cc_start: 0.7718 (tpp) cc_final: 0.7415 (tpt) REVERT: S 240 LYS cc_start: 0.8501 (mtpt) cc_final: 0.8247 (mtmt) REVERT: S 261 PHE cc_start: 0.8437 (t80) cc_final: 0.8033 (t80) REVERT: S 309 TYR cc_start: 0.8223 (t80) cc_final: 0.7769 (t80) REVERT: T 131 ARG cc_start: 0.8062 (ptm-80) cc_final: 0.6864 (ptp90) REVERT: T 242 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7058 (tt) REVERT: T 245 MET cc_start: 0.7147 (mmp) cc_final: 0.6680 (mmm) outliers start: 85 outliers final: 52 residues processed: 528 average time/residue: 0.5250 time to fit residues: 438.3985 Evaluate side-chains 503 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 444 time to evaluate : 4.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 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 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 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 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 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 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 204 LEU 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 238 optimal weight: 0.8980 chunk 350 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 386 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 269 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 17 ASN Q 17 ASN S 17 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 296 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.120857 restraints weight = 46469.521| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.19 r_work: 0.3166 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1806 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= 0.154 Angle : 0.581 9.629 48824 Z= 0.299 Chirality : 0.045 0.240 5602 Planarity : 0.005 0.078 6062 Dihedral : 13.239 179.208 5670 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.39 % Favored : 92.54 % Rotamer: Outliers : 2.97 % Allowed : 16.63 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.13), residues: 4275 helix: 0.46 (0.15), residues: 1362 sheet: -0.76 (0.21), residues: 656 loop : -1.18 (0.13), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 4 HIS 0.010 0.002 HIS L 162 PHE 0.021 0.002 PHE I 258 TYR 0.028 0.001 TYR P 231 ARG 0.006 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1036) hydrogen bonds : angle 4.40179 ( 2967) SS BOND : bond 0.00139 ( 7) SS BOND : angle 0.95453 ( 14) covalent geometry : bond 0.00362 (35792) covalent geometry : angle 0.58130 (48810) *********************** 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 554 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 448 time to evaluate : 3.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7541 (tttt) cc_final: 0.7300 (tppt) REVERT: A 72 GLU cc_start: 0.7046 (pm20) cc_final: 0.6766 (pm20) REVERT: D 78 GLU cc_start: 0.6472 (mp0) cc_final: 0.6099 (mp0) REVERT: E 14 TYR cc_start: 0.8808 (m-80) cc_final: 0.8585 (m-80) REVERT: E 35 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7799 (tpp80) REVERT: E 68 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8557 (mm) REVERT: E 78 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6792 (mm-30) REVERT: E 80 LYS cc_start: 0.8330 (mmmm) cc_final: 0.7935 (mmmm) REVERT: F 22 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7663 (tm-30) REVERT: F 42 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8146 (mt-10) REVERT: F 55 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7969 (mtmt) REVERT: F 88 LYS cc_start: 0.8276 (tptp) cc_final: 0.7979 (tppt) REVERT: G 67 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7966 (ttm110) REVERT: G 80 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7526 (mtpp) REVERT: H 72 GLU cc_start: 0.7200 (pm20) cc_final: 0.6928 (pm20) REVERT: H 80 LYS cc_start: 0.7762 (tptm) cc_final: 0.7378 (tppt) REVERT: I 83 TYR cc_start: 0.7518 (m-10) cc_final: 0.7179 (m-10) REVERT: I 131 ARG cc_start: 0.7424 (ptm-80) cc_final: 0.7144 (ptm-80) REVERT: I 165 VAL cc_start: 0.7149 (OUTLIER) cc_final: 0.6913 (m) REVERT: I 230 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: I 298 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.6781 (mtt180) REVERT: J 1 MET cc_start: 0.8846 (tpp) cc_final: 0.8397 (tpt) REVERT: J 221 ARG cc_start: 0.7097 (mmp80) cc_final: 0.6810 (mmp80) REVERT: J 309 TYR cc_start: 0.8723 (t80) cc_final: 0.8448 (t80) REVERT: K 112 ILE cc_start: 0.9274 (pt) cc_final: 0.9021 (pt) REVERT: K 114 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: L 65 ASP cc_start: 0.8659 (t0) cc_final: 0.8415 (m-30) REVERT: L 154 GLU cc_start: 0.7336 (tm-30) cc_final: 0.6981 (tm-30) REVERT: L 219 GLN cc_start: 0.7294 (mm110) cc_final: 0.7066 (mm110) REVERT: M 239 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8864 (mm) REVERT: M 316 ASP cc_start: 0.7813 (p0) cc_final: 0.7499 (p0) REVERT: N 90 GLN cc_start: 0.8124 (tp40) cc_final: 0.7596 (tp-100) REVERT: N 285 ASP cc_start: 0.9112 (p0) cc_final: 0.8873 (p0) REVERT: O 157 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8211 (mp) REVERT: O 183 MET cc_start: 0.4157 (OUTLIER) cc_final: 0.3034 (ptp) REVERT: O 288 GLU cc_start: 0.8256 (tp30) cc_final: 0.7968 (tp30) REVERT: P 136 TYR cc_start: 0.3820 (m-10) cc_final: 0.3210 (m-10) REVERT: P 176 TYR cc_start: 0.4007 (OUTLIER) cc_final: 0.2935 (m-10) REVERT: P 195 MET cc_start: 0.4658 (tpp) cc_final: 0.4301 (tpt) REVERT: S 240 LYS cc_start: 0.8510 (mtpt) cc_final: 0.8259 (mtmt) REVERT: S 309 TYR cc_start: 0.8316 (t80) cc_final: 0.7884 (t80) REVERT: T 11 LEU cc_start: 0.6259 (tp) cc_final: 0.6031 (tt) REVERT: T 131 ARG cc_start: 0.8085 (ptm-80) cc_final: 0.6909 (ptp90) REVERT: T 242 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7052 (tt) REVERT: T 245 MET cc_start: 0.7134 (mmp) cc_final: 0.6651 (mmm) REVERT: T 265 GLU cc_start: 0.7343 (mp0) cc_final: 0.7030 (mp0) outliers start: 106 outliers final: 72 residues processed: 522 average time/residue: 0.4995 time to fit residues: 416.0752 Evaluate side-chains 514 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 431 time to evaluate : 3.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 12 ASN 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 158 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 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 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 222 GLU 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 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 158 THR Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 4 optimal weight: 8.9990 chunk 415 optimal weight: 1.9990 chunk 198 optimal weight: 0.9980 chunk 367 optimal weight: 5.9990 chunk 359 optimal weight: 6.9990 chunk 318 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 GLN L 99 ASN L 310 ASN Q 17 ASN S 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.161113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.120099 restraints weight = 46763.769| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.12 r_work: 0.3154 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35799 Z= 0.168 Angle : 0.594 9.736 48824 Z= 0.306 Chirality : 0.046 0.242 5602 Planarity : 0.005 0.079 6062 Dihedral : 13.257 179.411 5670 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.72 % Favored : 92.23 % Rotamer: Outliers : 3.19 % Allowed : 17.64 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4275 helix: 0.50 (0.15), residues: 1350 sheet: -0.78 (0.20), residues: 656 loop : -1.18 (0.13), residues: 2269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 4 HIS 0.011 0.002 HIS L 162 PHE 0.021 0.002 PHE I 258 TYR 0.017 0.001 TYR P 231 ARG 0.006 0.000 ARG L 164 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 1036) hydrogen bonds : angle 4.39426 ( 2967) SS BOND : bond 0.00151 ( 7) SS BOND : angle 1.06781 ( 14) covalent geometry : bond 0.00399 (35792) covalent geometry : angle 0.59355 (48810) *********************** 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 560 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 446 time to evaluate : 3.591 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7412 (tttt) cc_final: 0.7173 (tppt) REVERT: C 79 GLU cc_start: 0.5988 (OUTLIER) cc_final: 0.5654 (pm20) REVERT: D 78 GLU cc_start: 0.6523 (mp0) cc_final: 0.6203 (mp0) REVERT: E 14 TYR cc_start: 0.8870 (m-80) cc_final: 0.8619 (m-80) REVERT: E 35 ARG cc_start: 0.8093 (tpp80) cc_final: 0.7777 (tpp80) REVERT: E 68 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8530 (mm) REVERT: E 80 LYS cc_start: 0.8352 (mmmm) cc_final: 0.7941 (mmmm) REVERT: E 82 GLU cc_start: 0.6009 (tp30) cc_final: 0.5680 (pt0) REVERT: F 22 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7752 (tm-30) REVERT: F 42 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8189 (mt-10) REVERT: F 55 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7966 (mtmt) REVERT: F 88 LYS cc_start: 0.8236 (tptp) cc_final: 0.7952 (tppt) REVERT: G 4 TRP cc_start: 0.6949 (t60) cc_final: 0.6744 (t60) REVERT: G 67 ARG cc_start: 0.8248 (mtp-110) cc_final: 0.7974 (ttm110) REVERT: G 80 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7392 (mtpp) REVERT: H 70 SER cc_start: 0.7479 (t) cc_final: 0.7212 (t) REVERT: H 72 GLU cc_start: 0.7194 (pm20) cc_final: 0.6949 (pm20) REVERT: H 80 LYS cc_start: 0.7779 (tptm) cc_final: 0.7382 (tppt) REVERT: I 83 TYR cc_start: 0.7560 (m-10) cc_final: 0.7279 (m-10) REVERT: I 131 ARG cc_start: 0.7483 (ptm-80) cc_final: 0.7166 (ptm-80) REVERT: I 165 VAL cc_start: 0.7219 (OUTLIER) cc_final: 0.6965 (m) REVERT: I 230 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7334 (tt0) REVERT: I 294 ILE cc_start: 0.7669 (pt) cc_final: 0.7450 (pt) REVERT: I 298 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6774 (mtt180) REVERT: J 1 MET cc_start: 0.8822 (tpp) cc_final: 0.8370 (tpt) REVERT: J 221 ARG cc_start: 0.7059 (mmp80) cc_final: 0.6741 (mmp80) REVERT: J 309 TYR cc_start: 0.8745 (t80) cc_final: 0.8482 (t80) REVERT: K 112 ILE cc_start: 0.9301 (pt) cc_final: 0.9054 (pt) REVERT: K 114 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: K 246 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8823 (mm) REVERT: L 65 ASP cc_start: 0.8702 (t0) cc_final: 0.8378 (m-30) REVERT: L 154 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6973 (tm-30) REVERT: L 219 GLN cc_start: 0.7387 (mm110) cc_final: 0.7107 (mm110) REVERT: L 326 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7834 (mm-30) REVERT: M 239 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8924 (mm) REVERT: M 312 ASP cc_start: 0.7624 (p0) cc_final: 0.7096 (p0) REVERT: M 316 ASP cc_start: 0.7874 (p0) cc_final: 0.7494 (p0) REVERT: N 90 GLN cc_start: 0.8154 (tp40) cc_final: 0.7562 (tp40) REVERT: N 306 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8850 (t) REVERT: O 157 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8240 (mp) REVERT: O 183 MET cc_start: 0.4196 (OUTLIER) cc_final: 0.3051 (ptp) REVERT: O 288 GLU cc_start: 0.8250 (tp30) cc_final: 0.7948 (tp30) REVERT: P 136 TYR cc_start: 0.4071 (m-10) cc_final: 0.3765 (m-10) REVERT: P 176 TYR cc_start: 0.4180 (OUTLIER) cc_final: 0.3132 (m-10) REVERT: P 195 MET cc_start: 0.5063 (tpp) cc_final: 0.4850 (tpt) REVERT: S 1 MET cc_start: 0.7416 (tpp) cc_final: 0.6964 (tpt) REVERT: S 240 LYS cc_start: 0.8534 (mtpt) cc_final: 0.8270 (mtmt) REVERT: S 254 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5728 (mm) REVERT: S 309 TYR cc_start: 0.8307 (t80) cc_final: 0.7883 (t80) REVERT: T 131 ARG cc_start: 0.7997 (ptm-80) cc_final: 0.7037 (ptp90) REVERT: T 242 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7051 (tt) REVERT: T 245 MET cc_start: 0.7244 (mmp) cc_final: 0.6792 (mmm) REVERT: T 291 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7033 (ttm110) outliers start: 114 outliers final: 79 residues processed: 525 average time/residue: 0.4989 time to fit residues: 418.8965 Evaluate side-chains 532 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 437 time to evaluate : 3.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 12 ASN 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 158 THR Chi-restraints excluded: chain K residue 246 LEU Chi-restraints excluded: chain K residue 267 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 267 VAL Chi-restraints excluded: chain L residue 326 GLU Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 184 LEU Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 267 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain N residue 312 ASP Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 70 THR Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 183 MET Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 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 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 158 THR Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 55 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 199 VAL Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 262 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 349 optimal weight: 0.0770 chunk 165 optimal weight: 0.9980 chunk 358 optimal weight: 9.9990 chunk 232 optimal weight: 0.2980 chunk 373 optimal weight: 2.9990 chunk 246 optimal weight: 0.0570 chunk 119 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 99 ASN O 17 ASN Q 17 ASN S 17 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.124305 restraints weight = 46460.294| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.10 r_work: 0.3219 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 35799 Z= 0.105 Angle : 0.544 9.382 48824 Z= 0.278 Chirality : 0.043 0.225 5602 Planarity : 0.004 0.072 6062 Dihedral : 13.147 178.498 5670 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.41 % Favored : 93.52 % Rotamer: Outliers : 2.10 % Allowed : 19.40 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.13), residues: 4275 helix: 0.57 (0.15), residues: 1396 sheet: -0.60 (0.20), residues: 672 loop : -1.17 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 4 HIS 0.006 0.001 HIS N 280 PHE 0.014 0.001 PHE I 88 TYR 0.030 0.001 TYR P 231 ARG 0.013 0.000 ARG S 131 Details of bonding type rmsd hydrogen bonds : bond 0.02838 ( 1036) hydrogen bonds : angle 4.18902 ( 2967) SS BOND : bond 0.00122 ( 7) SS BOND : angle 0.80485 ( 14) covalent geometry : bond 0.00231 (35792) covalent geometry : angle 0.54406 (48810) *********************** 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 535 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 460 time to evaluate : 4.303 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7466 (tttt) cc_final: 0.7237 (tppt) REVERT: A 72 GLU cc_start: 0.6767 (pm20) cc_final: 0.6503 (pm20) REVERT: C 5 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.5996 (pt) REVERT: C 79 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5202 (pm20) REVERT: D 78 GLU cc_start: 0.6387 (mp0) cc_final: 0.5984 (mp0) REVERT: E 14 TYR cc_start: 0.8787 (m-80) cc_final: 0.8549 (m-80) REVERT: E 35 ARG cc_start: 0.8082 (tpp80) cc_final: 0.7853 (tpp80) REVERT: E 80 LYS cc_start: 0.8291 (mmmm) cc_final: 0.7849 (mmmm) REVERT: E 82 GLU cc_start: 0.5883 (tp30) cc_final: 0.5438 (pt0) REVERT: F 22 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7621 (tm-30) REVERT: F 42 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8098 (mt-10) REVERT: F 73 ASP cc_start: 0.7442 (p0) cc_final: 0.7035 (p0) REVERT: F 88 LYS cc_start: 0.8194 (tptp) cc_final: 0.7904 (tppt) REVERT: G 67 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7945 (ttm110) REVERT: G 80 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7483 (mtpp) REVERT: H 72 GLU cc_start: 0.7166 (pm20) cc_final: 0.6736 (pm20) REVERT: H 80 LYS cc_start: 0.7747 (tptm) cc_final: 0.7344 (tppt) REVERT: I 83 TYR cc_start: 0.7215 (m-10) cc_final: 0.6769 (m-10) REVERT: I 131 ARG cc_start: 0.7301 (ptm-80) cc_final: 0.6988 (ptt90) REVERT: I 230 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7363 (tt0) REVERT: I 298 ARG cc_start: 0.7157 (ttm-80) cc_final: 0.6719 (mtt180) REVERT: J 1 MET cc_start: 0.8788 (tpp) cc_final: 0.8400 (tpt) REVERT: J 37 ARG cc_start: 0.6493 (mmm-85) cc_final: 0.6124 (mmm-85) REVERT: J 221 ARG cc_start: 0.7040 (mmp80) cc_final: 0.6757 (mmp80) REVERT: J 236 GLU cc_start: 0.8269 (mp0) cc_final: 0.7841 (mp0) REVERT: K 112 ILE cc_start: 0.9281 (pt) cc_final: 0.9018 (pt) REVERT: K 114 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: L 65 ASP cc_start: 0.8645 (t0) cc_final: 0.8440 (m-30) REVERT: L 219 GLN cc_start: 0.7400 (mm110) cc_final: 0.7172 (mm110) REVERT: L 326 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7652 (mm-30) REVERT: M 86 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8186 (p) REVERT: M 239 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8918 (mm) REVERT: M 316 ASP cc_start: 0.7799 (p0) cc_final: 0.7427 (p0) REVERT: N 90 GLN cc_start: 0.7996 (tp40) cc_final: 0.7497 (tp-100) REVERT: N 285 ASP cc_start: 0.9073 (p0) cc_final: 0.8800 (p0) REVERT: N 306 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.8897 (t) REVERT: O 157 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8194 (mp) REVERT: O 288 GLU cc_start: 0.8185 (tp30) cc_final: 0.7889 (tp30) REVERT: P 50 TYR cc_start: 0.2666 (m-80) cc_final: 0.1224 (m-80) REVERT: P 136 TYR cc_start: 0.3943 (m-10) cc_final: 0.3627 (m-10) REVERT: P 141 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6671 (mtm) REVERT: P 176 TYR cc_start: 0.4087 (OUTLIER) cc_final: 0.2860 (m-10) REVERT: S 1 MET cc_start: 0.7784 (tpp) cc_final: 0.7305 (tpt) REVERT: S 240 LYS cc_start: 0.8500 (mtpt) cc_final: 0.8249 (mtmt) REVERT: S 309 TYR cc_start: 0.8242 (t80) cc_final: 0.7780 (t80) REVERT: T 131 ARG cc_start: 0.7851 (ptm-80) cc_final: 0.6922 (ptp90) REVERT: T 242 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6984 (tt) REVERT: T 245 MET cc_start: 0.7213 (mmp) cc_final: 0.6748 (mmm) REVERT: T 291 ARG cc_start: 0.7335 (ttm110) cc_final: 0.6945 (ttm110) outliers start: 75 outliers final: 39 residues processed: 509 average time/residue: 0.5327 time to fit residues: 430.1561 Evaluate side-chains 493 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 441 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain 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 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 326 GLU Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 326 GLU Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 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 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 296 ASN 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 239 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 269 optimal weight: 4.9990 chunk 365 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 190 optimal weight: 0.4980 chunk 378 optimal weight: 0.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 0.0670 chunk 151 optimal weight: 0.6980 chunk 394 optimal weight: 3.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 53 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124549 restraints weight = 46374.593| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.12 r_work: 0.3217 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 35799 Z= 0.106 Angle : 0.543 9.326 48824 Z= 0.278 Chirality : 0.043 0.230 5602 Planarity : 0.004 0.071 6062 Dihedral : 13.109 177.873 5670 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.69 % Favored : 93.24 % Rotamer: Outliers : 2.04 % Allowed : 19.82 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.13), residues: 4275 helix: 0.58 (0.15), residues: 1414 sheet: -0.62 (0.21), residues: 658 loop : -1.12 (0.13), residues: 2203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP C 4 HIS 0.005 0.001 HIS O 280 PHE 0.015 0.001 PHE J 258 TYR 0.015 0.001 TYR P 231 ARG 0.007 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.02890 ( 1036) hydrogen bonds : angle 4.15093 ( 2967) SS BOND : bond 0.00113 ( 7) SS BOND : angle 0.84867 ( 14) covalent geometry : bond 0.00238 (35792) covalent geometry : angle 0.54293 (48810) *********************** 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 516 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 443 time to evaluate : 3.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.6888 (pm20) cc_final: 0.6582 (pm20) REVERT: C 5 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6052 (pt) REVERT: C 79 GLU cc_start: 0.5743 (OUTLIER) cc_final: 0.5185 (pm20) REVERT: D 78 GLU cc_start: 0.6374 (mp0) cc_final: 0.5967 (mp0) REVERT: E 14 TYR cc_start: 0.8754 (m-80) cc_final: 0.8508 (m-80) REVERT: E 35 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7894 (tpp80) REVERT: E 80 LYS cc_start: 0.8269 (mmmm) cc_final: 0.7830 (mmmm) REVERT: E 82 GLU cc_start: 0.5855 (tp30) cc_final: 0.5458 (pt0) REVERT: F 22 GLU cc_start: 0.7856 (tm-30) cc_final: 0.6842 (tm-30) REVERT: F 42 GLU cc_start: 0.8433 (mt-10) cc_final: 0.8187 (mt-10) REVERT: F 73 ASP cc_start: 0.7407 (p0) cc_final: 0.6985 (p0) REVERT: G 67 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7945 (ttm110) REVERT: G 80 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7353 (mtpp) REVERT: H 72 GLU cc_start: 0.7154 (pm20) cc_final: 0.6716 (pm20) REVERT: H 80 LYS cc_start: 0.7854 (tptm) cc_final: 0.7452 (tppt) REVERT: I 83 TYR cc_start: 0.7198 (m-10) cc_final: 0.6726 (m-10) REVERT: I 131 ARG cc_start: 0.7294 (ptm-80) cc_final: 0.6815 (ptt90) REVERT: I 298 ARG cc_start: 0.7179 (ttm-80) cc_final: 0.6762 (mtt180) REVERT: I 305 GLU cc_start: 0.8290 (mm-30) cc_final: 0.8059 (mm-30) REVERT: J 1 MET cc_start: 0.8760 (tpp) cc_final: 0.8370 (tpt) REVERT: J 221 ARG cc_start: 0.7023 (mmp80) cc_final: 0.6740 (mmp80) REVERT: K 112 ILE cc_start: 0.9288 (pt) cc_final: 0.9024 (pt) REVERT: K 114 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8036 (pm20) REVERT: L 65 ASP cc_start: 0.8663 (t0) cc_final: 0.8458 (m-30) REVERT: L 219 GLN cc_start: 0.7423 (mm110) cc_final: 0.7189 (mm110) REVERT: M 86 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8242 (p) REVERT: M 239 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8923 (mm) REVERT: M 312 ASP cc_start: 0.7564 (p0) cc_final: 0.7226 (p0) REVERT: M 316 ASP cc_start: 0.7817 (p0) cc_final: 0.7434 (p0) REVERT: N 306 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.8888 (t) REVERT: O 157 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8179 (mp) REVERT: O 164 ARG cc_start: 0.7469 (ptp-170) cc_final: 0.7042 (ttp-170) REVERT: O 209 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8295 (mt0) REVERT: O 288 GLU cc_start: 0.8216 (tp30) cc_final: 0.7922 (tp30) REVERT: P 50 TYR cc_start: 0.2672 (m-80) cc_final: 0.1244 (m-80) REVERT: P 136 TYR cc_start: 0.3927 (m-10) cc_final: 0.3606 (m-10) REVERT: S 1 MET cc_start: 0.7784 (tpp) cc_final: 0.7379 (tpt) REVERT: S 240 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8243 (mtmt) REVERT: S 254 LEU cc_start: 0.5860 (OUTLIER) cc_final: 0.5520 (mm) REVERT: S 309 TYR cc_start: 0.8216 (t80) cc_final: 0.7762 (t80) REVERT: T 70 THR cc_start: 0.8486 (OUTLIER) cc_final: 0.7971 (p) REVERT: T 131 ARG cc_start: 0.7806 (ptm-80) cc_final: 0.6869 (ptp90) REVERT: T 209 GLN cc_start: 0.6180 (OUTLIER) cc_final: 0.5796 (mm-40) REVERT: T 242 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.6985 (tt) REVERT: T 245 MET cc_start: 0.7237 (mmp) cc_final: 0.6747 (mmm) outliers start: 73 outliers final: 51 residues processed: 494 average time/residue: 0.5248 time to fit residues: 409.8695 Evaluate side-chains 503 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 440 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain I residue 45 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 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain 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 46 GLU Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 284 GLU Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 326 GLU 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 222 GLU Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 70 THR 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 Chi-restraints excluded: chain T residue 336 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 330 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 134 optimal weight: 0.2980 chunk 151 optimal weight: 0.8980 chunk 321 optimal weight: 0.7980 chunk 300 optimal weight: 0.8980 chunk 372 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 17 ASN S 17 ASN S 209 GLN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 GLN T 296 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.164738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.123894 restraints weight = 46496.577| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.10 r_work: 0.3199 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35799 Z= 0.117 Angle : 0.553 10.740 48824 Z= 0.283 Chirality : 0.044 0.226 5602 Planarity : 0.004 0.069 6062 Dihedral : 13.108 177.982 5670 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.95 % Favored : 93.01 % Rotamer: Outliers : 2.38 % Allowed : 19.32 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4275 helix: 0.62 (0.15), residues: 1390 sheet: -0.64 (0.20), residues: 664 loop : -1.08 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 4 HIS 0.006 0.001 HIS L 162 PHE 0.017 0.001 PHE I 258 TYR 0.012 0.001 TYR P 231 ARG 0.007 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.02944 ( 1036) hydrogen bonds : angle 4.14954 ( 2967) SS BOND : bond 0.00117 ( 7) SS BOND : angle 0.84940 ( 14) covalent geometry : bond 0.00268 (35792) covalent geometry : angle 0.55295 (48810) *********************** 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 510 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 425 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.7124 (pm20) cc_final: 0.6783 (pm20) REVERT: C 5 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6246 (pt) REVERT: C 79 GLU cc_start: 0.5751 (OUTLIER) cc_final: 0.5199 (pm20) REVERT: D 78 GLU cc_start: 0.6358 (mp0) cc_final: 0.5933 (mp0) REVERT: E 14 TYR cc_start: 0.8839 (m-80) cc_final: 0.8590 (m-80) REVERT: E 35 ARG cc_start: 0.8111 (tpp80) cc_final: 0.7823 (tpp80) REVERT: E 68 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8515 (mm) REVERT: E 80 LYS cc_start: 0.8280 (mmmm) cc_final: 0.7841 (mmmm) REVERT: E 82 GLU cc_start: 0.5857 (tp30) cc_final: 0.5466 (pt0) REVERT: F 22 GLU cc_start: 0.7854 (tm-30) cc_final: 0.6827 (tm-30) REVERT: F 42 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8195 (mt-10) REVERT: F 55 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7897 (mtmt) REVERT: F 73 ASP cc_start: 0.7430 (p0) cc_final: 0.7014 (p0) REVERT: G 67 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7995 (ttm110) REVERT: G 80 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7505 (mtpp) REVERT: H 72 GLU cc_start: 0.7164 (pm20) cc_final: 0.6722 (pm20) REVERT: H 80 LYS cc_start: 0.7794 (tptm) cc_final: 0.7369 (tppt) REVERT: I 83 TYR cc_start: 0.7219 (m-10) cc_final: 0.6727 (m-10) REVERT: I 131 ARG cc_start: 0.7342 (ptm-80) cc_final: 0.6862 (ptt90) REVERT: I 165 VAL cc_start: 0.7209 (OUTLIER) cc_final: 0.6979 (m) REVERT: I 298 ARG cc_start: 0.7172 (ttm-80) cc_final: 0.6785 (mtt180) REVERT: I 305 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8089 (mm-30) REVERT: J 1 MET cc_start: 0.8759 (tpp) cc_final: 0.8368 (tpt) REVERT: J 221 ARG cc_start: 0.7041 (mmp80) cc_final: 0.6754 (mmp80) REVERT: J 236 GLU cc_start: 0.8325 (mp0) cc_final: 0.7919 (mp0) REVERT: K 112 ILE cc_start: 0.9286 (pt) cc_final: 0.9034 (pt) REVERT: K 114 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: L 65 ASP cc_start: 0.8676 (t0) cc_final: 0.8455 (m-30) REVERT: L 219 GLN cc_start: 0.7451 (mm110) cc_final: 0.7224 (mm110) REVERT: M 86 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8331 (p) REVERT: M 239 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8912 (mm) REVERT: M 316 ASP cc_start: 0.7835 (p0) cc_final: 0.7443 (p0) REVERT: N 285 ASP cc_start: 0.9078 (p0) cc_final: 0.8830 (p0) REVERT: N 306 VAL cc_start: 0.9282 (OUTLIER) cc_final: 0.8864 (t) REVERT: O 157 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8184 (mp) REVERT: O 164 ARG cc_start: 0.7471 (ptp-170) cc_final: 0.7053 (ttp-170) REVERT: O 209 GLN cc_start: 0.8532 (mm-40) cc_final: 0.8295 (mt0) REVERT: O 288 GLU cc_start: 0.8232 (tp30) cc_final: 0.7941 (tp30) REVERT: P 50 TYR cc_start: 0.2660 (m-80) cc_final: 0.1223 (m-80) REVERT: P 136 TYR cc_start: 0.3935 (m-10) cc_final: 0.3616 (m-10) REVERT: S 1 MET cc_start: 0.7805 (tpp) cc_final: 0.7444 (tpt) REVERT: S 240 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8295 (mtmt) REVERT: S 254 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5470 (mm) REVERT: S 309 TYR cc_start: 0.8330 (t80) cc_final: 0.7871 (t80) REVERT: T 70 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.7988 (p) REVERT: T 131 ARG cc_start: 0.7840 (ptm-80) cc_final: 0.6894 (ptp90) REVERT: T 209 GLN cc_start: 0.5949 (OUTLIER) cc_final: 0.5280 (mm-40) REVERT: T 242 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6981 (tt) REVERT: T 245 MET cc_start: 0.7231 (mmp) cc_final: 0.6746 (mmm) REVERT: T 291 ARG cc_start: 0.7323 (ttm110) cc_final: 0.6962 (ttm110) outliers start: 85 outliers final: 64 residues processed: 488 average time/residue: 0.5080 time to fit residues: 392.2351 Evaluate side-chains 499 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 420 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain 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 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 306 VAL 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 O residue 326 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 222 GLU 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 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 70 THR 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 296 ASN Chi-restraints excluded: chain T residue 306 VAL Chi-restraints excluded: chain T residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 85 optimal weight: 0.1980 chunk 346 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 407 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 17 ASN S 17 ASN ** 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 = 0.3949 r_free = 0.3949 target = 0.163188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.114666 restraints weight = 46504.385| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.57 r_work: 0.3204 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 35799 Z= 0.130 Angle : 0.560 9.800 48824 Z= 0.286 Chirality : 0.044 0.247 5602 Planarity : 0.004 0.069 6062 Dihedral : 13.117 178.221 5670 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.09 % Favored : 92.87 % Rotamer: Outliers : 2.41 % Allowed : 19.23 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4275 helix: 0.59 (0.15), residues: 1392 sheet: -0.72 (0.19), residues: 744 loop : -1.10 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 4 HIS 0.007 0.001 HIS L 162 PHE 0.018 0.001 PHE I 258 TYR 0.014 0.001 TYR Q 309 ARG 0.007 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03014 ( 1036) hydrogen bonds : angle 4.16442 ( 2967) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.88274 ( 14) covalent geometry : bond 0.00303 (35792) covalent geometry : angle 0.55984 (48810) ********************** 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 515 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 429 time to evaluate : 4.763 Fit side-chains revert: symmetry clash REVERT: A 72 GLU cc_start: 0.6836 (pm20) cc_final: 0.6577 (pm20) REVERT: C 5 ILE cc_start: 0.6792 (OUTLIER) cc_final: 0.5945 (pt) REVERT: C 79 GLU cc_start: 0.5676 (OUTLIER) cc_final: 0.5178 (pm20) REVERT: D 78 GLU cc_start: 0.6009 (mp0) cc_final: 0.5631 (mp0) REVERT: E 14 TYR cc_start: 0.8644 (m-80) cc_final: 0.8318 (m-80) REVERT: E 35 ARG cc_start: 0.8262 (tpp80) cc_final: 0.7871 (tpp80) REVERT: E 68 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8427 (mm) REVERT: E 80 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7511 (mmmm) REVERT: E 82 GLU cc_start: 0.5987 (tp30) cc_final: 0.5426 (pt0) REVERT: F 22 GLU cc_start: 0.8077 (tm-30) cc_final: 0.6890 (tm-30) REVERT: F 42 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7922 (mt-10) REVERT: F 55 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7552 (mtmt) REVERT: F 73 ASP cc_start: 0.7046 (p0) cc_final: 0.6734 (p0) REVERT: G 67 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.7927 (ttm110) REVERT: G 80 LYS cc_start: 0.7610 (OUTLIER) cc_final: 0.7054 (mtpp) REVERT: H 72 GLU cc_start: 0.7172 (pm20) cc_final: 0.6704 (pm20) REVERT: H 80 LYS cc_start: 0.7521 (tptm) cc_final: 0.7159 (tppt) REVERT: I 83 TYR cc_start: 0.7154 (m-10) cc_final: 0.6813 (m-10) REVERT: I 131 ARG cc_start: 0.7191 (ptm-80) cc_final: 0.6676 (ptt90) REVERT: I 165 VAL cc_start: 0.6968 (OUTLIER) cc_final: 0.6745 (m) REVERT: I 298 ARG cc_start: 0.6766 (ttm-80) cc_final: 0.6251 (mtt180) REVERT: I 305 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7754 (mm-30) REVERT: J 1 MET cc_start: 0.8520 (tpp) cc_final: 0.8075 (tpt) REVERT: J 221 ARG cc_start: 0.6929 (mmp80) cc_final: 0.6542 (mmp80) REVERT: J 236 GLU cc_start: 0.8270 (mp0) cc_final: 0.7573 (mp0) REVERT: K 112 ILE cc_start: 0.9393 (pt) cc_final: 0.9107 (pt) REVERT: K 114 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8024 (pm20) REVERT: L 65 ASP cc_start: 0.8947 (t0) cc_final: 0.8602 (m-30) REVERT: L 219 GLN cc_start: 0.7382 (mm110) cc_final: 0.7059 (mm110) REVERT: L 265 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8254 (pt0) REVERT: M 86 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8254 (p) REVERT: M 239 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8859 (mm) REVERT: M 316 ASP cc_start: 0.7683 (p0) cc_final: 0.7366 (p0) REVERT: N 306 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.8978 (t) REVERT: O 90 GLN cc_start: 0.8426 (tp40) cc_final: 0.8087 (tm-30) REVERT: O 157 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8188 (mp) REVERT: O 164 ARG cc_start: 0.7370 (ptp-170) cc_final: 0.6959 (ttp-170) REVERT: O 209 GLN cc_start: 0.8645 (mm-40) cc_final: 0.8311 (mt0) REVERT: O 288 GLU cc_start: 0.8089 (tp30) cc_final: 0.7756 (tp30) REVERT: P 50 TYR cc_start: 0.2117 (m-80) cc_final: 0.0917 (m-80) REVERT: P 136 TYR cc_start: 0.3916 (m-10) cc_final: 0.3632 (m-10) REVERT: P 222 GLU cc_start: 0.4931 (OUTLIER) cc_final: 0.4352 (pm20) REVERT: S 1 MET cc_start: 0.7620 (tpp) cc_final: 0.7311 (tpt) REVERT: S 240 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7953 (mtmt) REVERT: S 254 LEU cc_start: 0.4876 (OUTLIER) cc_final: 0.4594 (mm) REVERT: S 309 TYR cc_start: 0.7941 (t80) cc_final: 0.7481 (t80) REVERT: T 70 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.7885 (p) REVERT: T 131 ARG cc_start: 0.7637 (ptm-80) cc_final: 0.6617 (ptp90) REVERT: T 242 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6862 (tt) REVERT: T 245 MET cc_start: 0.7042 (mmp) cc_final: 0.6556 (mmm) outliers start: 86 outliers final: 64 residues processed: 488 average time/residue: 0.5655 time to fit residues: 438.4247 Evaluate side-chains 510 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 430 time to evaluate : 5.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 55 LYS Chi-restraints excluded: chain F residue 80 LYS Chi-restraints excluded: chain G residue 80 LYS Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 198 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain L residue 265 GLU Chi-restraints excluded: chain 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 46 GLU Chi-restraints excluded: chain N residue 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 267 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 O residue 326 GLU Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 42 LEU Chi-restraints excluded: chain P residue 94 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 222 GLU 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 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 224 ILE Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain Q residue 336 VAL Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 70 THR 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 Chi-restraints excluded: chain T residue 336 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 136 optimal weight: 3.9990 chunk 333 optimal weight: 2.9990 chunk 364 optimal weight: 0.8980 chunk 350 optimal weight: 0.0570 chunk 282 optimal weight: 4.9990 chunk 342 optimal weight: 40.0000 chunk 231 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 335 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 238 optimal weight: 0.8980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.164196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.123506 restraints weight = 46454.190| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.14 r_work: 0.3202 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35799 Z= 0.123 Angle : 0.561 9.516 48824 Z= 0.287 Chirality : 0.044 0.228 5602 Planarity : 0.004 0.070 6062 Dihedral : 13.132 177.944 5670 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.04 % Favored : 92.91 % Rotamer: Outliers : 2.41 % Allowed : 19.65 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4275 helix: 0.59 (0.15), residues: 1392 sheet: -0.72 (0.19), residues: 744 loop : -1.09 (0.13), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 4 HIS 0.007 0.001 HIS L 162 PHE 0.018 0.001 PHE I 258 TYR 0.020 0.001 TYR Q 309 ARG 0.007 0.000 ARG E 49 Details of bonding type rmsd hydrogen bonds : bond 0.03001 ( 1036) hydrogen bonds : angle 4.15632 ( 2967) SS BOND : bond 0.00125 ( 7) SS BOND : angle 0.86156 ( 14) covalent geometry : bond 0.00285 (35792) covalent geometry : angle 0.56138 (48810) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22100.05 seconds wall clock time: 378 minutes 29.44 seconds (22709.44 seconds total)