Starting phenix.real_space_refine on Tue Sep 15 01:49:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.cif" model { file = "/net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r21_14244/09_2026/7r21_14244.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.181 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 61 5.49 5 S 69 5.16 5 C 22119 2.51 5 N 5999 2.21 5 O 6732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34980 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "D" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "E" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 860 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 8, 'TRANS': 99} Chain: "F" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "G" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "H" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 856 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 8, 'TRANS': 98} Chain: "I" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2597 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 321} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 2603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2603 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2596 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "M" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "P" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1936 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 16, 'TRANS': 223} Chain breaks: 2 Chain: "Q" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "R" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1320 Classifications: {'RNAv2': 62} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 19, 'rna3p_pyr': 18} Link IDs: {'rna2p': 24, 'rna3p': 37} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2597 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 322} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "T" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2350 Classifications: {'peptide': 304} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 290} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 7.51, per 1000 atoms: 0.21 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: 2.93 Conformation dependent library (CDL) restraints added in 1.4 seconds 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7956 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 57 sheets defined 37.2% alpha, 12.0% beta 0 base pairs and 5 stacking pairs defined. Time for finding SS restraints: 4.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.910A pdb=" N ILE A 8 " --> pdb=" O TRP A 4 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 33 Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.616A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 41 " --> pdb=" O GLN A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 59 removed outlier: 4.325A pdb=" N GLU A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 82 removed outlier: 3.929A pdb=" N GLU A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 4.024A pdb=" N LYS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 16 removed outlier: 3.706A pdb=" N VAL C 16 " --> pdb=" O LEU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 33 removed outlier: 4.283A pdb=" N VAL C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 50 removed outlier: 3.937A pdb=" N LEU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 61 removed outlier: 4.144A pdb=" N GLU C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 61 " --> pdb=" O LYS C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 82 removed outlier: 4.028A pdb=" N ILE C 74 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU C 79 " --> pdb=" O GLU C 75 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 98 removed outlier: 3.754A pdb=" N LEU C 90 " --> pdb=" O ASN C 86 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU C 93 " --> pdb=" O ASP C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.250A pdb=" N PHE C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA C 103 " --> pdb=" O TRP C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 103' Processing helix chain 'D' and resid 5 through 14 removed outlier: 3.508A pdb=" N TYR D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 33 Processing helix chain 'D' and resid 36 through 50 removed outlier: 3.669A pdb=" N LEU D 40 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU D 50 " --> pdb=" O LYS D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 60 removed outlier: 3.586A pdb=" N SER D 60 " --> pdb=" O LYS D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 82 removed outlier: 3.616A pdb=" N ILE D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU D 75 " --> pdb=" O PRO D 71 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA D 76 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU D 78 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 101 removed outlier: 3.938A pdb=" N LYS D 92 " --> pdb=" O LYS D 88 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 93 " --> pdb=" O ASP D 89 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ALA D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 removed outlier: 3.878A pdb=" N ASN E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR E 11 " --> pdb=" O ASN E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 16 No H-bonds generated for 'chain 'E' and resid 14 through 16' Processing helix chain 'E' and resid 24 through 33 removed outlier: 3.816A pdb=" N VAL E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 3.866A pdb=" N LEU E 50 " --> pdb=" O LYS E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 61 removed outlier: 3.872A pdb=" N GLU E 59 " --> pdb=" O LYS E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 100 removed outlier: 3.962A pdb=" N LYS E 92 " --> pdb=" O LYS E 88 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU E 97 " --> pdb=" O LEU E 93 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TRP E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 13 Processing helix chain 'F' and resid 14 through 16 No H-bonds generated for 'chain 'F' and resid 14 through 16' Processing helix chain 'F' and resid 24 through 33 removed outlier: 4.016A pdb=" N VAL F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 50 removed outlier: 3.959A pdb=" N LEU F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 61 removed outlier: 4.230A pdb=" N GLU F 59 " --> pdb=" O LYS F 55 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 82 removed outlier: 3.738A pdb=" N ILE F 74 " --> pdb=" O SER F 70 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU F 82 " --> pdb=" O GLU F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 100 removed outlier: 3.775A pdb=" N LEU F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS F 92 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TRP F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 103 No H-bonds generated for 'chain 'F' and resid 101 through 103' Processing helix chain 'G' and resid 5 through 15 removed outlier: 3.529A pdb=" N TYR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU G 15 " --> pdb=" O TYR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 33 removed outlier: 3.683A pdb=" N VAL G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 50 removed outlier: 4.102A pdb=" N LEU G 50 " --> pdb=" O LYS G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 60 removed outlier: 3.619A pdb=" N LEU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 59 " --> pdb=" O LYS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 98 removed outlier: 3.536A pdb=" N ALA G 98 " --> pdb=" O ALA G 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 removed outlier: 3.829A pdb=" N LEU H 15 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 33 removed outlier: 4.145A pdb=" N VAL H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 49 removed outlier: 3.728A pdb=" N LEU H 40 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 62 removed outlier: 4.216A pdb=" N GLU H 59 " --> pdb=" O LYS H 55 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER H 60 " --> pdb=" O LYS H 56 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 82 removed outlier: 3.891A pdb=" N LEU H 77 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU H 78 " --> pdb=" O ILE H 74 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU H 79 " --> pdb=" O GLU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 100 removed outlier: 3.926A pdb=" N LYS H 92 " --> pdb=" O LYS H 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU H 93 " --> pdb=" O ASP H 89 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 70 removed outlier: 3.699A pdb=" N LEU I 55 " --> pdb=" O THR I 51 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR I 70 " --> pdb=" O TYR I 66 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.632A pdb=" N LEU I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG I 82 " --> pdb=" O GLU I 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 77 through 82' Processing helix chain 'I' and resid 107 through 115 Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'I' and resid 144 through 152 Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 285 through 300 Processing helix chain 'I' and resid 324 through 333 Processing helix chain 'J' and resid 51 through 69 removed outlier: 3.632A pdb=" N LEU J 55 " --> pdb=" O THR J 51 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N THR J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 82 removed outlier: 3.629A pdb=" N LEU J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG J 82 " --> pdb=" O GLU J 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 77 through 82' Processing helix chain 'J' and resid 107 through 115 removed outlier: 3.565A pdb=" N ILE J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 121 Processing helix chain 'J' and resid 144 through 152 removed outlier: 3.587A pdb=" N GLU J 152 " --> pdb=" O ILE J 148 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 205 removed outlier: 3.557A pdb=" N VAL J 205 " --> pdb=" O LEU J 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 202 through 205' Processing helix chain 'J' and resid 227 through 241 Processing helix chain 'J' and resid 241 through 246 removed outlier: 3.512A pdb=" N MET J 245 " --> pdb=" O ALA J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 301 Processing helix chain 'J' and resid 324 through 334 Processing helix chain 'K' and resid 51 through 69 removed outlier: 4.175A pdb=" N THR K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 82 removed outlier: 3.697A pdb=" N ARG K 82 " --> pdb=" O GLU K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 115 removed outlier: 3.539A pdb=" N ILE K 111 " --> pdb=" O ASP K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 122 Processing helix chain 'K' and resid 144 through 152 Processing helix chain 'K' and resid 227 through 241 Processing helix chain 'K' and resid 242 through 247 removed outlier: 3.523A pdb=" N SER K 247 " --> pdb=" O ILE K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 300 Processing helix chain 'K' and resid 324 through 335 Processing helix chain 'L' and resid 51 through 67 Processing helix chain 'L' and resid 77 through 83 removed outlier: 3.697A pdb=" N ARG L 82 " --> pdb=" O ARG L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 115 Processing helix chain 'L' and resid 115 through 122 Processing helix chain 'L' and resid 144 through 152 removed outlier: 3.539A pdb=" N GLU L 152 " --> pdb=" O ILE L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 179 Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 227 through 241 Processing helix chain 'L' and resid 241 through 246 removed outlier: 3.818A pdb=" N MET L 245 " --> pdb=" O ALA L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 301 removed outlier: 3.687A pdb=" N ALA L 289 " --> pdb=" O ASP L 285 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 299 " --> pdb=" O LYS L 295 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU L 300 " --> pdb=" O ASN L 296 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY L 301 " --> pdb=" O ALA L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 324 through 335 removed outlier: 3.632A pdb=" N MET L 335 " --> pdb=" O ASN L 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 20 through 24 Processing helix chain 'M' and resid 51 through 69 removed outlier: 3.528A pdb=" N LEU M 55 " --> pdb=" O THR M 51 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N THR M 69 " --> pdb=" O ASP M 65 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 82 removed outlier: 3.904A pdb=" N ARG M 82 " --> pdb=" O GLU M 78 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 115 removed outlier: 3.936A pdb=" N ILE M 111 " --> pdb=" O ASP M 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 122 Processing helix chain 'M' and resid 144 through 152 removed outlier: 3.823A pdb=" N GLU M 150 " --> pdb=" O ASP M 146 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL M 151 " --> pdb=" O PHE M 147 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N GLU M 152 " --> pdb=" O ILE M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 227 through 241 Processing helix chain 'M' and resid 242 through 247 removed outlier: 3.650A pdb=" N SER M 247 " --> pdb=" O ILE M 243 " (cutoff:3.500A) Processing helix chain 'M' and resid 285 through 301 removed outlier: 3.661A pdb=" N LYS M 295 " --> pdb=" O ARG M 291 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN M 296 " --> pdb=" O SER M 292 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY M 301 " --> pdb=" O ALA M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 324 through 335 removed outlier: 3.734A pdb=" N MET M 335 " --> pdb=" O ASN M 331 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 69 removed outlier: 4.312A pdb=" N THR N 69 " --> pdb=" O ASP N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 115 removed outlier: 3.819A pdb=" N ILE N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS N 113 " --> pdb=" O ALA N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 122 Processing helix chain 'N' and resid 144 through 151 removed outlier: 3.680A pdb=" N GLU N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 203 through 205 No H-bonds generated for 'chain 'N' and resid 203 through 205' Processing helix chain 'N' and resid 227 through 241 Processing helix chain 'N' and resid 285 through 301 removed outlier: 3.667A pdb=" N ALA N 299 " --> pdb=" O LYS N 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 324 through 335 removed outlier: 3.906A pdb=" N LEU N 328 " --> pdb=" O SER N 324 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET N 335 " --> pdb=" O ASN N 331 " (cutoff:3.500A) Processing helix chain 'O' and resid 20 through 24 removed outlier: 3.529A pdb=" N THR O 24 " --> pdb=" O GLY O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 69 removed outlier: 3.532A pdb=" N LEU O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR O 69 " --> pdb=" O ASP O 65 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 82 removed outlier: 3.559A pdb=" N LEU O 81 " --> pdb=" O THR O 77 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ARG O 82 " --> pdb=" O GLU O 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 77 through 82' Processing helix chain 'O' and resid 107 through 115 removed outlier: 3.653A pdb=" N ILE O 111 " --> pdb=" O ASP O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 116 through 122 Processing helix chain 'O' and resid 144 through 152 removed outlier: 3.761A pdb=" N GLU O 150 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL O 151 " --> pdb=" O PHE O 147 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU O 152 " --> pdb=" O ILE O 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 227 through 241 Processing helix chain 'O' and resid 285 through 301 removed outlier: 3.674A pdb=" N LYS O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN O 296 " --> pdb=" O SER O 292 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA O 297 " --> pdb=" O ILE O 293 " (cutoff:3.500A) Processing helix chain 'O' and resid 324 through 335 removed outlier: 3.834A pdb=" N LEU O 328 " --> pdb=" O SER O 324 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET O 335 " --> pdb=" O ASN O 331 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 46 removed outlier: 3.681A pdb=" N LEU P 38 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) Processing helix chain 'P' and resid 46 through 51 removed outlier: 4.049A pdb=" N TYR P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA P 51 " --> pdb=" O PRO P 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 46 through 51' Processing helix chain 'P' and resid 54 through 69 removed outlier: 3.595A pdb=" N LYS P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 129 through 141 removed outlier: 3.978A pdb=" N LEU P 135 " --> pdb=" O GLU P 131 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N MET P 141 " --> pdb=" O LEU P 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 20 through 24 removed outlier: 3.799A pdb=" N GLY Q 23 " --> pdb=" O GLY Q 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 69 removed outlier: 4.233A pdb=" N THR Q 69 " --> pdb=" O ASP Q 65 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.076A pdb=" N ARG Q 82 " --> pdb=" O GLU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 115 removed outlier: 3.970A pdb=" N ILE Q 111 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS Q 113 " --> pdb=" O ALA Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 122 removed outlier: 3.579A pdb=" N ASP Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 144 through 151 Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 227 through 241 Processing helix chain 'Q' and resid 285 through 301 Processing helix chain 'Q' and resid 325 through 335 removed outlier: 3.881A pdb=" N MET Q 335 " --> pdb=" O ASN Q 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 20 through 24 removed outlier: 3.714A pdb=" N GLY S 23 " --> pdb=" O GLY S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 69 removed outlier: 3.533A pdb=" N LEU S 55 " --> pdb=" O THR S 51 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 77 through 82 removed outlier: 3.857A pdb=" N ARG S 82 " --> pdb=" O GLU S 78 " (cutoff:3.500A) Processing helix chain 'S' and resid 107 through 115 removed outlier: 3.881A pdb=" N ILE S 111 " --> pdb=" O ASP S 107 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 122 Processing helix chain 'S' and resid 144 through 152 removed outlier: 4.329A pdb=" N GLU S 150 " --> pdb=" O ASP S 146 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL S 151 " --> pdb=" O PHE S 147 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLU S 152 " --> pdb=" O ILE S 148 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 227 through 241 Processing helix chain 'S' and resid 285 through 301 removed outlier: 3.557A pdb=" N ASN S 296 " --> pdb=" O SER S 292 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA S 297 " --> pdb=" O ILE S 293 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY S 301 " --> pdb=" O ALA S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 335 removed outlier: 3.782A pdb=" N MET S 335 " --> pdb=" O ASN S 331 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 24 removed outlier: 3.776A pdb=" N GLY T 23 " --> pdb=" O GLY T 20 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR T 24 " --> pdb=" O GLY T 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 20 through 24' Processing helix chain 'T' and resid 51 through 69 removed outlier: 3.764A pdb=" N LEU T 55 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR T 69 " --> pdb=" O ASP T 65 " (cutoff:3.500A) Processing helix chain 'T' and resid 70 through 75 removed outlier: 4.113A pdb=" N VAL T 74 " --> pdb=" O PRO T 71 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN T 75 " --> pdb=" O TYR T 72 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 82 removed outlier: 3.623A pdb=" N LEU T 81 " --> pdb=" O THR T 77 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG T 82 " --> pdb=" O GLU T 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 77 through 82' Processing helix chain 'T' and resid 107 through 115 removed outlier: 3.735A pdb=" N LYS T 113 " --> pdb=" O ALA T 109 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 122 removed outlier: 3.535A pdb=" N ASP T 119 " --> pdb=" O LEU T 115 " (cutoff:3.500A) Processing helix chain 'T' and resid 144 through 152 removed outlier: 3.603A pdb=" N ILE T 148 " --> pdb=" O THR T 144 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU T 152 " --> pdb=" O ILE T 148 " (cutoff:3.500A) Processing helix chain 'T' and resid 203 through 205 No H-bonds generated for 'chain 'T' and resid 203 through 205' Processing helix chain 'T' and resid 227 through 241 Processing helix chain 'T' and resid 285 through 301 removed outlier: 3.774A pdb=" N ALA T 297 " --> pdb=" O ILE T 293 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY T 301 " --> pdb=" O ALA T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 325 through 335 removed outlier: 4.283A pdb=" N MET T 335 " --> pdb=" O ASN T 331 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 2 through 12 current: chain 'I' and resid 193 through 201 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 193 through 201 current: chain 'I' and resid 305 through 309 Processing sheet with id=AA2, first strand: chain 'I' and resid 26 through 27 removed outlier: 3.606A pdb=" N GLU I 188 " --> pdb=" O ILE I 27 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N MET I 183 " --> pdb=" O ARG I 164 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 32 through 37 Processing sheet with id=AA4, first strand: chain 'I' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'I' and resid 123 through 125 removed outlier: 7.052A pdb=" N PHE I 123 " --> pdb=" O ARG I 131 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG I 131 " --> pdb=" O PHE I 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 3 through 14 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 3 through 14 current: chain 'J' and resid 184 through 200 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 184 through 200 current: chain 'J' and resid 305 through 309 removed outlier: 7.206A pdb=" N VAL J 306 " --> pdb=" O THR J 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 31 through 36 Processing sheet with id=AA8, first strand: chain 'J' and resid 94 through 96 Processing sheet with id=AA9, first strand: chain 'J' and resid 123 through 125 Processing sheet with id=AB1, first strand: chain 'K' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 2 through 14 current: chain 'K' and resid 183 through 201 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 183 through 201 current: chain 'K' and resid 304 through 309 removed outlier: 9.118A pdb=" N THR K 320 " --> pdb=" O ILE K 304 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL K 306 " --> pdb=" O THR K 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 31 through 36 Processing sheet with id=AB3, first strand: chain 'K' and resid 94 through 96 Processing sheet with id=AB4, first strand: chain 'K' and resid 123 through 124 Processing sheet with id=AB5, first strand: chain 'L' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 2 through 14 current: chain 'L' and resid 184 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 184 through 201 current: chain 'L' and resid 305 through 309 Processing sheet with id=AB6, first strand: chain 'L' and resid 31 through 36 Processing sheet with id=AB7, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AB8, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AB9, first strand: chain 'M' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 2 through 14 current: chain 'M' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 190 through 196 current: chain 'M' and resid 306 through 309 Processing sheet with id=AC1, first strand: chain 'M' and resid 26 through 27 Processing sheet with id=AC2, first strand: chain 'M' and resid 31 through 36 Processing sheet with id=AC3, first strand: chain 'M' and resid 94 through 96 Processing sheet with id=AC4, first strand: chain 'M' and resid 123 through 124 Processing sheet with id=AC5, first strand: chain 'M' and resid 213 through 215 Processing sheet with id=AC6, first strand: chain 'N' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 2 through 14 current: chain 'N' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 190 through 196 current: chain 'N' and resid 306 through 309 Processing sheet with id=AC7, first strand: chain 'N' and resid 26 through 27 Processing sheet with id=AC8, first strand: chain 'N' and resid 31 through 36 Processing sheet with id=AC9, first strand: chain 'N' and resid 94 through 96 Processing sheet with id=AD1, first strand: chain 'N' and resid 123 through 124 Processing sheet with id=AD2, first strand: chain 'N' and resid 213 through 215 Processing sheet with id=AD3, first strand: chain 'O' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 2 through 14 current: chain 'O' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 190 through 196 current: chain 'O' and resid 306 through 309 Processing sheet with id=AD4, first strand: chain 'O' and resid 26 through 27 Processing sheet with id=AD5, first strand: chain 'O' and resid 31 through 36 Processing sheet with id=AD6, first strand: chain 'O' and resid 94 through 96 Processing sheet with id=AD7, first strand: chain 'O' and resid 123 through 125 Processing sheet with id=AD8, first strand: chain 'O' and resid 213 through 215 Processing sheet with id=AD9, first strand: chain 'P' and resid 77 through 79 removed outlier: 3.517A pdb=" N LEU P 120 " --> pdb=" O ALA P 79 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP P 157 " --> pdb=" O CYS P 7 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ARG P 9 " --> pdb=" O PRO P 155 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'P' and resid 12 through 13 Processing sheet with id=AE2, first strand: chain 'P' and resid 168 through 169 removed outlier: 3.932A pdb=" N ALA P 168 " --> pdb=" O VAL P 240 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL P 240 " --> pdb=" O ALA P 168 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'P' and resid 197 through 199 Processing sheet with id=AE4, first strand: chain 'P' and resid 243 through 246 Processing sheet with id=AE5, first strand: chain 'Q' and resid 2 through 14 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 2 through 14 current: chain 'Q' and resid 190 through 196 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 190 through 196 current: chain 'Q' and resid 306 through 309 removed outlier: 6.864A pdb=" N VAL Q 306 " --> pdb=" O THR Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'Q' and resid 26 through 27 Processing sheet with id=AE7, first strand: chain 'Q' and resid 31 through 36 Processing sheet with id=AE8, first strand: chain 'Q' and resid 94 through 96 Processing sheet with id=AE9, first strand: chain 'Q' and resid 123 through 124 Processing sheet with id=AF1, first strand: chain 'Q' and resid 213 through 215 Processing sheet with id=AF2, first strand: chain 'S' and resid 2 through 10 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 2 through 10 current: chain 'S' and resid 193 through 196 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 193 through 196 current: chain 'S' and resid 306 through 309 Processing sheet with id=AF3, first strand: chain 'S' and resid 26 through 27 Processing sheet with id=AF4, first strand: chain 'S' and resid 31 through 36 Processing sheet with id=AF5, first strand: chain 'S' and resid 94 through 96 Processing sheet with id=AF6, first strand: chain 'S' and resid 123 through 124 Processing sheet with id=AF7, first strand: chain 'S' and resid 213 through 215 Processing sheet with id=AF8, first strand: chain 'T' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 2 through 12 current: chain 'T' and resid 192 through 196 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 192 through 196 current: chain 'T' and resid 306 through 309 removed outlier: 7.079A pdb=" N VAL T 306 " --> pdb=" O THR T 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'T' and resid 31 through 36 Processing sheet with id=AG1, first strand: chain 'T' and resid 94 through 96 Processing sheet with id=AG2, first strand: chain 'T' and resid 123 through 124 Processing sheet with id=AG3, first strand: chain 'T' and resid 213 through 215 1036 hydrogen bonds defined for protein. 2967 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 5 stacking parallelities Total time for adding SS restraints: 6.83 Time building geometry restraints manager: 3.89 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: 48390 2.99 - 5.97: 399 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: 20922 35.52 - 71.04: 477 71.04 - 106.55: 39 106.55 - 142.07: 1 142.07 - 177.59: 3 Dihedral angle restraints: 21442 sinusoidal: 9032 harmonic: 12410 Sorted by residual: dihedral pdb=" C4' G R 8 " pdb=" C3' G R 8 " pdb=" C2' G R 8 " pdb=" C1' G R 8 " ideal model delta sinusoidal sigma weight residual 36.35 -36.92 73.26 1 3.10e+00 1.04e-01 7.11e+02 dihedral pdb=" C4' G R 14 " pdb=" C3' G R 14 " pdb=" C2' G R 14 " pdb=" C1' G R 14 " ideal model delta sinusoidal sigma weight residual 36.34 -36.55 72.90 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' U R 2 " pdb=" C3' U R 2 " pdb=" C2' U R 2 " pdb=" C1' U R 2 " ideal model delta sinusoidal sigma weight residual 36.35 -36.45 72.80 1 3.10e+00 1.04e-01 7.04e+02 ... (remaining 21439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 4809 0.067 - 0.134: 668 0.134 - 0.201: 18 0.201 - 0.268: 82 0.268 - 0.335: 25 Chirality restraints: 5602 Sorted by residual: chirality pdb=" P C R 58 " pdb=" OP1 C R 58 " pdb=" OP2 C R 58 " pdb=" O5' C R 58 " both_signs ideal model delta sigma weight residual True 2.17 -2.51 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" P U R 2 " pdb=" OP1 U R 2 " pdb=" OP2 U R 2 " pdb=" O5' U R 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C3' G R 14 " pdb=" C4' G R 14 " pdb=" O3' G R 14 " pdb=" C2' G R 14 " both_signs ideal model delta sigma weight residual False -2.50 -2.80 0.30 2.00e-01 2.50e+01 2.29e+00 ... (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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 34.730 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 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= 0.133 Angle : 0.631 14.936 48824 Z= 0.321 Chirality : 0.055 0.335 5602 Planarity : 0.005 0.150 6062 Dihedral : 15.360 177.588 13465 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.12 % Rotamer: Outliers : 0.06 % Allowed : 0.56 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.13), residues: 4275 helix: 0.43 (0.15), residues: 1354 sheet: -0.52 (0.21), residues: 683 loop : -1.13 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 67 TYR 0.030 0.001 TYR G 45 PHE 0.013 0.001 PHE P 12 TRP 0.027 0.002 TRP C 4 HIS 0.004 0.001 HIS J 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.13 (35792) covalent geometry : angle 0.63124 / 0.32 (48810) SS BOND : bond 0.00289 / 0.18 ( 7) SS BOND : angle 0.79006 / 0.43 ( 14) hydrogen bonds : bond 0.14885 / 9.64 ( 1036) hydrogen bonds : angle 5.94515 / 4.25 ( 2967) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 1.402 Fit side-chains REVERT: A 57 LYS cc_start: 0.7718 (tttt) cc_final: 0.7459 (tppt) REVERT: A 72 GLU cc_start: 0.6983 (pm20) cc_final: 0.6738 (pm20) REVERT: E 80 LYS cc_start: 0.8349 (mmmm) cc_final: 0.8131 (mmmm) REVERT: K 112 ILE cc_start: 0.9014 (pt) cc_final: 0.8794 (pt) REVERT: L 93 THR cc_start: 0.7766 (m) cc_final: 0.7508 (m) REVERT: M 27 ILE cc_start: 0.8528 (pt) cc_final: 0.8224 (pt) REVERT: O 274 PRO cc_start: 0.8350 (Cg_exo) cc_final: 0.8077 (Cg_endo) REVERT: O 288 GLU cc_start: 0.7320 (tp30) cc_final: 0.6982 (tp30) REVERT: S 237 SER cc_start: 0.8013 (p) cc_final: 0.7775 (p) REVERT: T 130 ARG cc_start: 0.4954 (mmp80) cc_final: 0.4232 (mmp80) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.2473 time to fit residues: 197.0952 Evaluate side-chains 434 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 0.9990 chunk 424 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 37 GLN L 162 HIS N 296 ASN O 296 ASN Q 12 ASN ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 296 ASN T 17 ASN T 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.170257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.128644 restraints weight = 46374.022| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.06 r_work: 0.3310 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35799 Z= 0.147 Angle : 0.788 22.810 48824 Z= 0.358 Chirality : 0.069 0.995 5602 Planarity : 0.005 0.073 6062 Dihedral : 9.718 179.156 5430 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 0.67 % Allowed : 8.40 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4275 helix: 0.62 (0.15), residues: 1366 sheet: -0.46 (0.20), residues: 688 loop : -1.18 (0.13), residues: 2221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 155 TYR 0.024 0.001 TYR P 231 PHE 0.014 0.001 PHE L 258 TRP 0.020 0.002 TRP C 4 HIS 0.005 0.001 HIS N 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (35792) covalent geometry : angle 0.78794 / 0.36 (48810) SS BOND : bond 0.00379 / 0.24 ( 7) SS BOND : angle 0.95305 / 0.53 ( 14) hydrogen bonds : bond 0.04071 / 2.63 ( 1036) hydrogen bonds : angle 4.67373 / 3.34 ( 2967) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 491 time to evaluate : 1.329 Fit side-chains REVERT: A 57 LYS cc_start: 0.7482 (tttt) cc_final: 0.7250 (tppt) REVERT: A 72 GLU cc_start: 0.7186 (pm20) cc_final: 0.6754 (pm20) REVERT: C 20 PHE cc_start: 0.5965 (m-10) cc_final: 0.5736 (m-80) REVERT: E 80 LYS cc_start: 0.8316 (mmmm) cc_final: 0.8085 (mmmm) REVERT: F 22 GLU cc_start: 0.7710 (tm-30) cc_final: 0.6984 (tm-30) REVERT: F 42 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7777 (mt-10) REVERT: F 88 LYS cc_start: 0.8189 (tptp) cc_final: 0.7883 (tppt) REVERT: G 67 ARG cc_start: 0.8202 (mtp-110) cc_final: 0.7962 (ttm110) REVERT: H 67 ARG cc_start: 0.7313 (tmt170) cc_final: 0.7108 (tmt170) REVERT: H 80 LYS cc_start: 0.7872 (tptm) cc_final: 0.7577 (tppt) REVERT: I 83 TYR cc_start: 0.7109 (m-10) cc_final: 0.6844 (m-10) REVERT: J 54 MET cc_start: 0.8592 (mmm) cc_final: 0.8370 (tpp) REVERT: K 112 ILE cc_start: 0.9168 (pt) cc_final: 0.8937 (pt) REVERT: M 27 ILE cc_start: 0.8781 (pt) cc_final: 0.8550 (pt) REVERT: M 312 ASP cc_start: 0.7329 (p0) cc_final: 0.7054 (p0) REVERT: O 151 VAL cc_start: 0.7331 (m) cc_final: 0.6979 (m) REVERT: O 288 GLU cc_start: 0.7978 (tp30) cc_final: 0.7670 (tp30) REVERT: P 231 TYR cc_start: 0.3734 (p90) cc_final: 0.3444 (p90) REVERT: S 68 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8050 (pttp) REVERT: S 237 SER cc_start: 0.8258 (p) cc_final: 0.8008 (p) REVERT: S 309 TYR cc_start: 0.8051 (t80) cc_final: 0.7846 (t80) REVERT: T 11 LEU cc_start: 0.7016 (mt) cc_final: 0.6728 (tt) REVERT: T 70 THR cc_start: 0.8211 (t) cc_final: 0.7778 (p) REVERT: T 130 ARG cc_start: 0.5502 (mmp80) cc_final: 0.5267 (mmp80) REVERT: T 131 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.6613 (ptp90) REVERT: T 245 MET cc_start: 0.7040 (mmp) cc_final: 0.6462 (mmp) outliers start: 24 outliers final: 14 residues processed: 504 average time/residue: 0.2413 time to fit residues: 192.1478 Evaluate side-chains 454 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 440 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 89 ASP Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 284 GLU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 36 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain T residue 139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 243 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 313 optimal weight: 0.0770 chunk 218 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 252 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 204 optimal weight: 3.9990 chunk 370 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 278 optimal weight: 3.9990 overall best weight: 1.6744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 182 GLN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 17 ASN T 290 ASN T 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.165182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.123921 restraints weight = 46586.470| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.12 r_work: 0.3218 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35799 Z= 0.182 Angle : 0.700 11.926 48824 Z= 0.336 Chirality : 0.061 0.862 5602 Planarity : 0.005 0.074 6062 Dihedral : 10.230 176.404 5430 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.37 % Favored : 92.56 % Rotamer: Outliers : 1.29 % Allowed : 12.26 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.13), residues: 4275 helix: 0.31 (0.15), residues: 1425 sheet: -0.69 (0.21), residues: 658 loop : -1.09 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 49 TYR 0.025 0.002 TYR P 231 PHE 0.025 0.002 PHE I 258 TRP 0.019 0.002 TRP C 4 HIS 0.012 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 (35792) covalent geometry : angle 0.70020 / 0.34 (48810) SS BOND : bond 0.00142 / 0.10 ( 7) SS BOND : angle 0.96838 / 0.58 ( 14) hydrogen bonds : bond 0.03978 / 2.59 ( 1036) hydrogen bonds : angle 4.58235 / 3.27 ( 2967) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 458 time to evaluate : 1.124 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7423 (tttt) cc_final: 0.7161 (tppt) REVERT: A 72 GLU cc_start: 0.7392 (pm20) cc_final: 0.7155 (pm20) REVERT: E 80 LYS cc_start: 0.8303 (mmmm) cc_final: 0.8006 (mmmm) REVERT: F 22 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7720 (tm-30) REVERT: F 88 LYS cc_start: 0.8250 (tptp) cc_final: 0.7907 (tppt) REVERT: G 4 TRP cc_start: 0.6544 (t60) cc_final: 0.6179 (t60) REVERT: G 67 ARG cc_start: 0.8260 (mtp-110) cc_final: 0.7968 (ttm110) REVERT: H 67 ARG cc_start: 0.7319 (tmt170) cc_final: 0.7104 (tmt170) REVERT: H 72 GLU cc_start: 0.7325 (pm20) cc_final: 0.7035 (pm20) REVERT: H 80 LYS cc_start: 0.7764 (tptm) cc_final: 0.7419 (tppt) REVERT: I 83 TYR cc_start: 0.7592 (m-10) cc_final: 0.7149 (m-10) REVERT: I 131 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6966 (ptt90) REVERT: I 298 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6801 (mtt180) REVERT: I 308 THR cc_start: 0.7790 (p) cc_final: 0.7563 (p) REVERT: J 54 MET cc_start: 0.8854 (mmm) cc_final: 0.8640 (tpp) REVERT: J 258 PHE cc_start: 0.8891 (t80) cc_final: 0.8681 (t80) REVERT: K 1 MET cc_start: 0.8750 (tmm) cc_final: 0.8540 (ttp) REVERT: K 112 ILE cc_start: 0.9291 (pt) cc_final: 0.9045 (pt) REVERT: K 114 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.7986 (pm20) REVERT: L 54 MET cc_start: 0.9225 (tpp) cc_final: 0.8704 (tpp) REVERT: L 219 GLN cc_start: 0.7181 (mm110) cc_final: 0.6547 (mm110) REVERT: O 288 GLU cc_start: 0.8233 (tp30) cc_final: 0.7925 (tp30) REVERT: P 110 ARG cc_start: 0.7463 (tmm-80) cc_final: 0.7165 (tmm-80) REVERT: P 123 TYR cc_start: 0.6042 (m-80) cc_final: 0.5697 (m-80) REVERT: S 68 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8091 (pttp) REVERT: S 240 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8286 (mtmt) REVERT: S 253 ASN cc_start: 0.7812 (t0) cc_final: 0.7477 (t0) REVERT: S 309 TYR cc_start: 0.8117 (t80) cc_final: 0.7629 (t80) REVERT: T 131 ARG cc_start: 0.8076 (ptm-80) cc_final: 0.6852 (ptp90) REVERT: T 242 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7087 (tt) REVERT: T 245 MET cc_start: 0.7103 (mmp) cc_final: 0.6688 (mmp) outliers start: 46 outliers final: 29 residues processed: 485 average time/residue: 0.2463 time to fit residues: 187.6265 Evaluate side-chains 461 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 430 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 294 ILE Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 253 ILE Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 134 SER Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 182 optimal weight: 1.9990 chunk 404 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 272 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 406 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 7 ASN ** S 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 253 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.165737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.124944 restraints weight = 46358.182| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.12 r_work: 0.3224 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 35799 Z= 0.146 Angle : 0.654 10.603 48824 Z= 0.315 Chirality : 0.058 0.718 5602 Planarity : 0.005 0.074 6062 Dihedral : 10.292 175.073 5430 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.23 % Favored : 92.70 % Rotamer: Outliers : 1.88 % Allowed : 13.89 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4275 helix: 0.39 (0.15), residues: 1417 sheet: -0.61 (0.20), residues: 672 loop : -1.11 (0.13), residues: 2186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 49 TYR 0.014 0.001 TYR T 309 PHE 0.021 0.001 PHE I 258 TRP 0.020 0.002 TRP C 4 HIS 0.009 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 (35792) covalent geometry : angle 0.65365 / 0.31 (48810) SS BOND : bond 0.00132 / 0.09 ( 7) SS BOND : angle 0.87376 / 0.52 ( 14) hydrogen bonds : bond 0.03490 / 2.28 ( 1036) hydrogen bonds : angle 4.42445 / 3.16 ( 2967) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 466 time to evaluate : 1.328 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7551 (tttt) cc_final: 0.7308 (tppt) REVERT: A 72 GLU cc_start: 0.7116 (pm20) cc_final: 0.6788 (pm20) REVERT: D 78 GLU cc_start: 0.6432 (mp0) cc_final: 0.6162 (mp0) REVERT: E 35 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7933 (tpp80) REVERT: E 80 LYS cc_start: 0.8313 (mmmm) cc_final: 0.8018 (mmmm) REVERT: F 22 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7722 (tm-30) REVERT: F 88 LYS cc_start: 0.8294 (tptp) cc_final: 0.8011 (tppt) REVERT: G 4 TRP cc_start: 0.6549 (t60) cc_final: 0.6186 (t60) REVERT: G 38 GLU cc_start: 0.7881 (mp0) cc_final: 0.7658 (mp0) REVERT: G 67 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7936 (ttm110) REVERT: H 37 GLN cc_start: 0.7799 (tp40) cc_final: 0.7590 (tp40) REVERT: H 67 ARG cc_start: 0.7306 (tmt170) cc_final: 0.7046 (tmt170) REVERT: H 72 GLU cc_start: 0.7291 (pm20) cc_final: 0.6984 (pm20) REVERT: I 83 TYR cc_start: 0.7468 (m-10) cc_final: 0.7062 (m-10) REVERT: I 131 ARG cc_start: 0.7223 (ptm-80) cc_final: 0.6973 (ptm-80) REVERT: I 298 ARG cc_start: 0.7257 (ttm-80) cc_final: 0.6743 (mtt180) REVERT: I 308 THR cc_start: 0.7771 (p) cc_final: 0.7535 (p) REVERT: J 37 ARG cc_start: 0.6287 (mmm-85) cc_final: 0.6051 (mmm-85) REVERT: J 236 GLU cc_start: 0.8273 (mp0) cc_final: 0.7887 (mp0) REVERT: J 258 PHE cc_start: 0.8834 (t80) cc_final: 0.8593 (t80) REVERT: J 294 ILE cc_start: 0.9312 (mt) cc_final: 0.9096 (mt) REVERT: K 1 MET cc_start: 0.8756 (tmm) cc_final: 0.8291 (ttp) REVERT: K 112 ILE cc_start: 0.9278 (pt) cc_final: 0.9019 (pt) REVERT: L 54 MET cc_start: 0.9178 (tpp) cc_final: 0.8957 (tpp) REVERT: M 86 THR cc_start: 0.8267 (OUTLIER) cc_final: 0.7881 (p) REVERT: M 312 ASP cc_start: 0.7662 (p0) cc_final: 0.7220 (p0) REVERT: N 285 ASP cc_start: 0.9181 (p0) cc_final: 0.8860 (p0) REVERT: O 157 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8113 (mp) REVERT: O 288 GLU cc_start: 0.8197 (tp30) cc_final: 0.7879 (tp30) REVERT: P 50 TYR cc_start: 0.2619 (m-80) cc_final: 0.1202 (m-80) REVERT: P 176 TYR cc_start: 0.4072 (OUTLIER) cc_final: 0.2560 (m-10) REVERT: S 68 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8107 (pttp) REVERT: S 240 LYS cc_start: 0.8536 (mtpt) cc_final: 0.8284 (mtmt) REVERT: S 253 ASN cc_start: 0.7865 (t0) cc_final: 0.7472 (t0) REVERT: S 309 TYR cc_start: 0.8120 (t80) cc_final: 0.7636 (t80) REVERT: T 242 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7045 (tt) REVERT: T 245 MET cc_start: 0.7147 (mmp) cc_final: 0.6650 (mmm) outliers start: 67 outliers final: 40 residues processed: 509 average time/residue: 0.2436 time to fit residues: 195.8743 Evaluate side-chains 482 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 438 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL 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 N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU 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 294 ILE Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain O residue 334 LYS Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 176 TYR Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 237 SER Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 258 optimal weight: 0.9980 chunk 306 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 313 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 406 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 261 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 17 ASN M 59 HIS O 17 ASN O 53 ASN ** 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 = 0.3961 r_free = 0.3961 target = 0.166682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125456 restraints weight = 46503.759| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.18 r_work: 0.3226 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35799 Z= 0.123 Angle : 0.624 10.705 48824 Z= 0.301 Chirality : 0.055 0.616 5602 Planarity : 0.004 0.071 6062 Dihedral : 10.275 177.567 5430 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.07 % Allowed : 15.82 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.13), residues: 4275 helix: 0.63 (0.15), residues: 1369 sheet: -0.58 (0.20), residues: 672 loop : -1.14 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 130 TYR 0.028 0.001 TYR P 231 PHE 0.015 0.001 PHE K 258 TRP 0.024 0.002 TRP C 4 HIS 0.006 0.001 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (35792) covalent geometry : angle 0.62435 / 0.30 (48810) SS BOND : bond 0.00115 / 0.08 ( 7) SS BOND : angle 0.83060 / 0.49 ( 14) hydrogen bonds : bond 0.03196 / 2.09 ( 1036) hydrogen bonds : angle 4.31368 / 3.08 ( 2967) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 460 time to evaluate : 1.328 Fit side-chains REVERT: A 57 LYS cc_start: 0.7493 (tttt) cc_final: 0.7245 (tppt) REVERT: A 72 GLU cc_start: 0.7384 (pm20) cc_final: 0.6827 (pm20) REVERT: D 78 GLU cc_start: 0.6419 (mp0) cc_final: 0.6088 (mp0) REVERT: E 80 LYS cc_start: 0.8351 (mmmm) cc_final: 0.8045 (mmmm) REVERT: F 88 LYS cc_start: 0.8232 (tptp) cc_final: 0.7937 (tppt) REVERT: G 4 TRP cc_start: 0.6408 (t60) cc_final: 0.6080 (t60) REVERT: G 67 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7833 (ttm110) REVERT: H 37 GLN cc_start: 0.7759 (tp40) cc_final: 0.7517 (tp40) REVERT: H 67 ARG cc_start: 0.7254 (tmt170) cc_final: 0.6994 (tmt170) REVERT: H 72 GLU cc_start: 0.7250 (pm20) cc_final: 0.6947 (pm20) REVERT: I 83 TYR cc_start: 0.7148 (m-10) cc_final: 0.6929 (m-10) REVERT: I 131 ARG cc_start: 0.7057 (ptm-80) cc_final: 0.6784 (ptm-80) REVERT: I 298 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6660 (mtt180) REVERT: J 1 MET cc_start: 0.8617 (tpp) cc_final: 0.8182 (tpt) REVERT: J 258 PHE cc_start: 0.8630 (t80) cc_final: 0.8417 (t80) REVERT: J 294 ILE cc_start: 0.9257 (mt) cc_final: 0.9052 (mt) REVERT: K 1 MET cc_start: 0.8683 (tmm) cc_final: 0.8203 (ttp) REVERT: K 112 ILE cc_start: 0.9205 (pt) cc_final: 0.8939 (pt) REVERT: K 114 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8034 (pm20) REVERT: M 86 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7827 (p) REVERT: M 239 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8799 (mm) REVERT: M 316 ASP cc_start: 0.7394 (p0) cc_final: 0.7146 (p0) REVERT: N 285 ASP cc_start: 0.8896 (p0) cc_final: 0.8627 (p0) REVERT: N 306 VAL cc_start: 0.9225 (OUTLIER) cc_final: 0.8760 (t) REVERT: O 157 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7980 (mp) REVERT: O 288 GLU cc_start: 0.7844 (tp30) cc_final: 0.7528 (tp30) REVERT: P 50 TYR cc_start: 0.2460 (m-80) cc_final: 0.1136 (m-80) REVERT: P 176 TYR cc_start: 0.3561 (m-10) cc_final: 0.2564 (m-10) REVERT: S 68 LYS cc_start: 0.8770 (mmmt) cc_final: 0.8095 (pttp) REVERT: S 236 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: S 240 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8185 (mtmt) REVERT: S 253 ASN cc_start: 0.7667 (t0) cc_final: 0.7312 (t0) REVERT: S 261 PHE cc_start: 0.8453 (t80) cc_final: 0.8055 (t80) REVERT: S 309 TYR cc_start: 0.8080 (t80) cc_final: 0.7623 (t80) REVERT: T 131 ARG cc_start: 0.7773 (ptm-80) cc_final: 0.6705 (ptp90) REVERT: T 242 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.6966 (tt) REVERT: T 245 MET cc_start: 0.7088 (mmp) cc_final: 0.6586 (mmm) REVERT: T 265 GLU cc_start: 0.7174 (mp0) cc_final: 0.6916 (mp0) outliers start: 74 outliers final: 47 residues processed: 505 average time/residue: 0.2454 time to fit residues: 195.9288 Evaluate side-chains 492 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 438 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 F residue 16 VAL Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE 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 114 GLU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 199 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 284 GLU Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain Q residue 36 VAL Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 417 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 253 optimal weight: 0.8980 chunk 367 optimal weight: 4.9990 chunk 6 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 355 optimal weight: 0.9990 chunk 316 optimal weight: 0.7980 chunk 404 optimal weight: 7.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 219 GLN O 17 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.167349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.126579 restraints weight = 46323.458| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.08 r_work: 0.3254 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 35799 Z= 0.114 Angle : 0.614 10.225 48824 Z= 0.296 Chirality : 0.053 0.586 5602 Planarity : 0.004 0.069 6062 Dihedral : 10.228 179.284 5430 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 1.96 % Allowed : 16.74 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.13), residues: 4275 helix: 0.73 (0.15), residues: 1370 sheet: -0.55 (0.20), residues: 672 loop : -1.10 (0.13), residues: 2233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 130 TYR 0.014 0.001 TYR P 231 PHE 0.014 0.001 PHE K 258 TRP 0.026 0.002 TRP C 4 HIS 0.005 0.001 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (35792) covalent geometry : angle 0.61369 / 0.30 (48810) SS BOND : bond 0.00300 / 0.18 ( 7) SS BOND : angle 0.84046 / 0.49 ( 14) hydrogen bonds : bond 0.03028 / 1.99 ( 1036) hydrogen bonds : angle 4.23931 / 3.02 ( 2967) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 453 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7475 (tttt) cc_final: 0.7246 (tppt) REVERT: A 72 GLU cc_start: 0.7178 (pm20) cc_final: 0.6864 (pm20) REVERT: D 78 GLU cc_start: 0.6422 (mp0) cc_final: 0.6023 (mp0) REVERT: E 80 LYS cc_start: 0.8354 (mmmm) cc_final: 0.7958 (mmmm) REVERT: F 88 LYS cc_start: 0.8254 (tptp) cc_final: 0.7967 (tppt) REVERT: G 4 TRP cc_start: 0.6560 (t60) cc_final: 0.6249 (t60) REVERT: G 67 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7931 (ttm110) REVERT: H 37 GLN cc_start: 0.7790 (tp40) cc_final: 0.7527 (tp40) REVERT: H 67 ARG cc_start: 0.7274 (tmt170) cc_final: 0.6899 (tmt170) REVERT: H 72 GLU cc_start: 0.7312 (pm20) cc_final: 0.6938 (pm20) REVERT: I 83 TYR cc_start: 0.7230 (m-10) cc_final: 0.6768 (m-10) REVERT: I 131 ARG cc_start: 0.7153 (ptm-80) cc_final: 0.6863 (ptt90) REVERT: I 294 ILE cc_start: 0.7718 (pt) cc_final: 0.7455 (pt) REVERT: I 298 ARG cc_start: 0.7128 (ttm-80) cc_final: 0.6689 (mtt180) REVERT: J 1 MET cc_start: 0.8702 (tpp) cc_final: 0.8332 (tpt) REVERT: J 54 MET cc_start: 0.8704 (mmm) cc_final: 0.8492 (tpp) REVERT: J 236 GLU cc_start: 0.8291 (mp0) cc_final: 0.7914 (mp0) REVERT: J 294 ILE cc_start: 0.9321 (mt) cc_final: 0.9118 (mt) REVERT: K 1 MET cc_start: 0.8760 (tmm) cc_final: 0.8355 (ttp) REVERT: K 112 ILE cc_start: 0.9305 (pt) cc_final: 0.9059 (pt) REVERT: K 114 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: M 86 THR cc_start: 0.8236 (OUTLIER) cc_final: 0.7892 (p) REVERT: M 239 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8891 (mm) REVERT: M 312 ASP cc_start: 0.7624 (p0) cc_final: 0.7121 (p0) REVERT: N 285 ASP cc_start: 0.9143 (p0) cc_final: 0.8833 (p0) REVERT: O 151 VAL cc_start: 0.7386 (m) cc_final: 0.7002 (m) REVERT: O 157 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mp) REVERT: O 288 GLU cc_start: 0.8120 (tp30) cc_final: 0.7803 (tp30) REVERT: P 50 TYR cc_start: 0.2536 (m-80) cc_final: 0.1174 (m-80) REVERT: P 136 TYR cc_start: 0.3772 (m-10) cc_final: 0.3196 (m-10) REVERT: P 176 TYR cc_start: 0.3355 (m-10) cc_final: 0.2550 (m-10) REVERT: S 17 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7007 (t0) REVERT: S 68 LYS cc_start: 0.8829 (mmmt) cc_final: 0.8075 (pttp) REVERT: S 236 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7179 (mp0) REVERT: S 240 LYS cc_start: 0.8519 (mtpt) cc_final: 0.8251 (mtmt) REVERT: S 253 ASN cc_start: 0.7765 (t0) cc_final: 0.7367 (t0) REVERT: S 254 LEU cc_start: 0.6015 (OUTLIER) cc_final: 0.5610 (mm) REVERT: S 261 PHE cc_start: 0.8511 (t80) cc_final: 0.8141 (t80) REVERT: S 309 TYR cc_start: 0.8135 (t80) cc_final: 0.7658 (t80) REVERT: T 10 ARG cc_start: 0.6809 (mtm180) cc_final: 0.6399 (mtp180) REVERT: T 131 ARG cc_start: 0.7975 (ptm-80) cc_final: 0.6809 (ptp90) REVERT: T 242 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7017 (tt) REVERT: T 245 MET cc_start: 0.7127 (mmp) cc_final: 0.6636 (mmm) outliers start: 70 outliers final: 46 residues processed: 501 average time/residue: 0.2427 time to fit residues: 193.2962 Evaluate side-chains 491 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 437 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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 F residue 16 VAL 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 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 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 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 198 ILE 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 157 ILE Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 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 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain S residue 17 ASN Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 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 225 VAL Chi-restraints excluded: chain T residue 242 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 222 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 323 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 170 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 81 optimal weight: 6.9990 chunk 233 optimal weight: 0.0670 chunk 301 optimal weight: 9.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 17 ASN S 209 GLN ** 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 = 0.3969 r_free = 0.3969 target = 0.167331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125789 restraints weight = 46490.285| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.17 r_work: 0.3255 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1871 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= 0.115 Angle : 0.612 10.502 48824 Z= 0.295 Chirality : 0.053 0.539 5602 Planarity : 0.004 0.068 6062 Dihedral : 10.234 179.388 5430 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer: Outliers : 2.18 % Allowed : 17.30 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.13), residues: 4275 helix: 0.80 (0.15), residues: 1363 sheet: -0.56 (0.20), residues: 678 loop : -1.07 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 130 TYR 0.027 0.001 TYR P 231 PHE 0.018 0.001 PHE J 258 TRP 0.023 0.001 TRP C 4 HIS 0.005 0.001 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (35792) covalent geometry : angle 0.61163 / 0.29 (48810) SS BOND : bond 0.00106 / 0.07 ( 7) SS BOND : angle 0.81483 / 0.47 ( 14) hydrogen bonds : bond 0.02972 / 1.95 ( 1036) hydrogen bonds : angle 4.19763 / 2.99 ( 2967) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 452 time to evaluate : 1.274 Fit side-chains REVERT: A 57 LYS cc_start: 0.7513 (tttt) cc_final: 0.7289 (tppt) REVERT: A 72 GLU cc_start: 0.7111 (pm20) cc_final: 0.6792 (pm20) REVERT: C 79 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5200 (pm20) REVERT: D 78 GLU cc_start: 0.6516 (mp0) cc_final: 0.6203 (mp0) REVERT: E 80 LYS cc_start: 0.8333 (mmmm) cc_final: 0.7949 (mmmm) REVERT: F 22 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7265 (tm-30) REVERT: F 88 LYS cc_start: 0.8238 (tptp) cc_final: 0.7939 (tppt) REVERT: G 4 TRP cc_start: 0.6408 (t60) cc_final: 0.6110 (t60) REVERT: G 67 ARG cc_start: 0.8180 (mtp-110) cc_final: 0.7922 (ttm110) REVERT: H 37 GLN cc_start: 0.7785 (tp40) cc_final: 0.7515 (tp40) REVERT: H 55 LYS cc_start: 0.8063 (mttp) cc_final: 0.7729 (mtmt) REVERT: H 67 ARG cc_start: 0.7308 (tmt170) cc_final: 0.6926 (tmt170) REVERT: I 83 TYR cc_start: 0.7218 (m-10) cc_final: 0.6722 (m-10) REVERT: I 131 ARG cc_start: 0.7174 (ptm-80) cc_final: 0.6824 (ptt90) REVERT: I 298 ARG cc_start: 0.7115 (ttm-80) cc_final: 0.6682 (mtt180) REVERT: J 1 MET cc_start: 0.8677 (tpp) cc_final: 0.8324 (tpt) REVERT: J 37 ARG cc_start: 0.6187 (mmm-85) cc_final: 0.5952 (mmm-85) REVERT: J 236 GLU cc_start: 0.8267 (mp0) cc_final: 0.7894 (mp0) REVERT: K 1 MET cc_start: 0.8781 (tmm) cc_final: 0.8406 (ttp) REVERT: K 112 ILE cc_start: 0.9301 (pt) cc_final: 0.9053 (pt) REVERT: K 114 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: L 54 MET cc_start: 0.9331 (tpp) cc_final: 0.8512 (tpt) REVERT: M 86 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7924 (p) REVERT: M 162 HIS cc_start: 0.8300 (OUTLIER) cc_final: 0.7985 (p90) REVERT: M 239 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8900 (mm) REVERT: M 316 ASP cc_start: 0.7729 (p0) cc_final: 0.7456 (p0) REVERT: N 285 ASP cc_start: 0.9161 (p0) cc_final: 0.8845 (p0) REVERT: N 306 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.8849 (t) REVERT: O 151 VAL cc_start: 0.7330 (m) cc_final: 0.6934 (m) REVERT: O 157 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.8084 (mp) REVERT: O 288 GLU cc_start: 0.8159 (tp30) cc_final: 0.7821 (tp30) REVERT: P 50 TYR cc_start: 0.2369 (m-80) cc_final: 0.1050 (m-80) REVERT: P 136 TYR cc_start: 0.3582 (m-10) cc_final: 0.3173 (m-10) REVERT: P 176 TYR cc_start: 0.3559 (m-10) cc_final: 0.2598 (m-10) REVERT: S 28 GLU cc_start: 0.6585 (pm20) cc_final: 0.5664 (pm20) REVERT: S 68 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8082 (pttp) REVERT: S 131 ARG cc_start: 0.8484 (ptp90) cc_final: 0.8250 (ptp90) REVERT: S 236 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7087 (mp0) REVERT: S 240 LYS cc_start: 0.8525 (mtpt) cc_final: 0.8258 (mtmt) REVERT: S 253 ASN cc_start: 0.7750 (t0) cc_final: 0.7354 (t0) REVERT: S 254 LEU cc_start: 0.5578 (OUTLIER) cc_final: 0.5154 (mm) REVERT: S 261 PHE cc_start: 0.8522 (t80) cc_final: 0.8145 (t80) REVERT: S 309 TYR cc_start: 0.8122 (t80) cc_final: 0.7653 (t80) REVERT: T 131 ARG cc_start: 0.8013 (ptm-80) cc_final: 0.6828 (ptp90) REVERT: T 242 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7005 (tt) REVERT: T 245 MET cc_start: 0.7241 (mmp) cc_final: 0.6774 (mmm) outliers start: 78 outliers final: 58 residues processed: 507 average time/residue: 0.2354 time to fit residues: 190.8525 Evaluate side-chains 504 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 436 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL 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 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 162 HIS Chi-restraints excluded: chain M residue 165 VAL Chi-restraints excluded: chain M residue 239 LEU Chi-restraints excluded: chain M residue 306 VAL Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 246 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU 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 332 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 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 117 optimal weight: 2.9990 chunk 321 optimal weight: 10.0000 chunk 326 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 chunk 350 optimal weight: 0.0980 chunk 34 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 236 optimal weight: 5.9990 chunk 363 optimal weight: 5.9990 chunk 425 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 17 ASN L 99 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.164844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.123620 restraints weight = 46487.487| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.14 r_work: 0.3211 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 35799 Z= 0.157 Angle : 0.650 11.697 48824 Z= 0.315 Chirality : 0.055 0.635 5602 Planarity : 0.005 0.071 6062 Dihedral : 10.306 179.437 5430 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer: Outliers : 2.55 % Allowed : 17.55 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.13), residues: 4275 helix: 0.56 (0.15), residues: 1396 sheet: -0.64 (0.20), residues: 678 loop : -1.04 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 130 TYR 0.019 0.001 TYR Q 309 PHE 0.021 0.002 PHE L 258 TRP 0.022 0.002 TRP A 4 HIS 0.009 0.002 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (35792) covalent geometry : angle 0.65014 / 0.32 (48810) SS BOND : bond 0.00125 / 0.08 ( 7) SS BOND : angle 0.93926 / 0.56 ( 14) hydrogen bonds : bond 0.03364 / 2.21 ( 1036) hydrogen bonds : angle 4.29073 / 3.06 ( 2967) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 439 time to evaluate : 1.368 Fit side-chains REVERT: A 57 LYS cc_start: 0.7507 (tttt) cc_final: 0.7279 (tppt) REVERT: A 72 GLU cc_start: 0.7225 (pm20) cc_final: 0.6822 (pm20) REVERT: C 79 GLU cc_start: 0.5680 (OUTLIER) cc_final: 0.5105 (pm20) REVERT: D 78 GLU cc_start: 0.6343 (mp0) cc_final: 0.5982 (mp0) REVERT: E 80 LYS cc_start: 0.8446 (mmmm) cc_final: 0.8079 (mmmm) REVERT: F 22 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7126 (tm-30) REVERT: F 78 GLU cc_start: 0.7444 (mt-10) cc_final: 0.7207 (mt-10) REVERT: F 88 LYS cc_start: 0.8208 (tptp) cc_final: 0.7918 (tppt) REVERT: G 67 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7843 (ttm110) REVERT: H 67 ARG cc_start: 0.7283 (tmt170) cc_final: 0.6992 (tmt170) REVERT: H 72 GLU cc_start: 0.7490 (mp0) cc_final: 0.7276 (pm20) REVERT: I 131 ARG cc_start: 0.7195 (ptm-80) cc_final: 0.6899 (ptm-80) REVERT: I 294 ILE cc_start: 0.7708 (pt) cc_final: 0.7483 (pt) REVERT: I 298 ARG cc_start: 0.7133 (ttm-80) cc_final: 0.6744 (mtt180) REVERT: J 1 MET cc_start: 0.8644 (tpp) cc_final: 0.8285 (tpt) REVERT: J 37 ARG cc_start: 0.6105 (mmm-85) cc_final: 0.5837 (mmm-85) REVERT: J 221 ARG cc_start: 0.6731 (mmp80) cc_final: 0.6514 (mmp80) REVERT: K 1 MET cc_start: 0.8713 (tmm) cc_final: 0.8352 (ttp) REVERT: K 112 ILE cc_start: 0.9266 (pt) cc_final: 0.9015 (pt) REVERT: K 114 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: L 54 MET cc_start: 0.9276 (tpp) cc_final: 0.8308 (tpt) REVERT: M 162 HIS cc_start: 0.8282 (OUTLIER) cc_final: 0.7973 (p90) REVERT: M 239 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8772 (mm) REVERT: M 312 ASP cc_start: 0.7282 (p0) cc_final: 0.7044 (p0) REVERT: M 316 ASP cc_start: 0.7669 (p0) cc_final: 0.7292 (p0) REVERT: N 285 ASP cc_start: 0.8888 (p0) cc_final: 0.8598 (p0) REVERT: N 306 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8790 (t) REVERT: O 157 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7986 (mp) REVERT: O 288 GLU cc_start: 0.7844 (tp30) cc_final: 0.7533 (tp30) REVERT: P 50 TYR cc_start: 0.2431 (m-80) cc_final: 0.1112 (m-80) REVERT: P 136 TYR cc_start: 0.3593 (m-10) cc_final: 0.3177 (m-10) REVERT: P 176 TYR cc_start: 0.3785 (m-10) cc_final: 0.2857 (m-10) REVERT: P 222 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.4851 (pm20) REVERT: S 68 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8092 (pttp) REVERT: S 236 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: S 240 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8213 (mtmt) REVERT: S 253 ASN cc_start: 0.7778 (t0) cc_final: 0.7346 (t0) REVERT: S 254 LEU cc_start: 0.5471 (OUTLIER) cc_final: 0.5062 (mm) REVERT: S 309 TYR cc_start: 0.8181 (t80) cc_final: 0.7784 (t80) REVERT: T 131 ARG cc_start: 0.7845 (ptm-80) cc_final: 0.6662 (ptp90) REVERT: T 242 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6802 (tt) REVERT: T 245 MET cc_start: 0.7235 (mmp) cc_final: 0.6771 (mmm) outliers start: 91 outliers final: 69 residues processed: 505 average time/residue: 0.2373 time to fit residues: 190.7055 Evaluate side-chains 507 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 428 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 245 MET Chi-restraints excluded: chain I residue 311 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 158 THR Chi-restraints excluded: chain J residue 162 HIS Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 245 MET Chi-restraints excluded: chain J residue 311 VAL Chi-restraints excluded: chain K residue 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 99 ASN Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 162 HIS 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 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 114 GLU Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL 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 36 VAL Chi-restraints excluded: chain Q residue 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 296 ASN Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 180 optimal weight: 1.9990 chunk 415 optimal weight: 5.9990 chunk 368 optimal weight: 0.1980 chunk 252 optimal weight: 0.0870 chunk 414 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 421 optimal weight: 7.9990 chunk 71 optimal weight: 0.0670 chunk 386 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 99 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 209 GLN T 296 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126030 restraints weight = 46248.055| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.06 r_work: 0.3246 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35799 Z= 0.115 Angle : 0.620 10.232 48824 Z= 0.301 Chirality : 0.053 0.558 5602 Planarity : 0.004 0.070 6062 Dihedral : 10.263 178.282 5430 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 2.52 % Allowed : 17.72 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4275 helix: 0.81 (0.15), residues: 1350 sheet: -0.60 (0.20), residues: 680 loop : -1.06 (0.13), residues: 2245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 130 TYR 0.019 0.001 TYR Q 309 PHE 0.016 0.001 PHE I 258 TRP 0.036 0.002 TRP C 4 HIS 0.005 0.001 HIS M 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (35792) covalent geometry : angle 0.61947 / 0.30 (48810) SS BOND : bond 0.00114 / 0.07 ( 7) SS BOND : angle 0.82147 / 0.49 ( 14) hydrogen bonds : bond 0.02977 / 1.95 ( 1036) hydrogen bonds : angle 4.21612 / 3.00 ( 2967) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 441 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 57 LYS cc_start: 0.7504 (tttt) cc_final: 0.7277 (tppt) REVERT: A 72 GLU cc_start: 0.6987 (pm20) cc_final: 0.6588 (pm20) REVERT: A 91 ARG cc_start: 0.7068 (mtp180) cc_final: 0.6716 (tpt90) REVERT: C 79 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5081 (pm20) REVERT: D 78 GLU cc_start: 0.6315 (mp0) cc_final: 0.5913 (mp0) REVERT: E 80 LYS cc_start: 0.8265 (mmmm) cc_final: 0.7850 (mmmm) REVERT: F 22 GLU cc_start: 0.7859 (tm-30) cc_final: 0.7260 (tm-30) REVERT: F 78 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7326 (mt-10) REVERT: G 67 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7946 (ttm110) REVERT: H 55 LYS cc_start: 0.8088 (mttp) cc_final: 0.7747 (mtmt) REVERT: H 67 ARG cc_start: 0.7278 (tmt170) cc_final: 0.6957 (tmt170) REVERT: I 83 TYR cc_start: 0.7274 (m-10) cc_final: 0.6817 (m-10) REVERT: I 131 ARG cc_start: 0.7238 (ptm-80) cc_final: 0.6770 (ptt90) REVERT: I 294 ILE cc_start: 0.7650 (pt) cc_final: 0.7401 (pt) REVERT: I 298 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6726 (mtt180) REVERT: J 1 MET cc_start: 0.8666 (tpp) cc_final: 0.8364 (tpt) REVERT: J 37 ARG cc_start: 0.6144 (mmm-85) cc_final: 0.5821 (mmm-85) REVERT: J 221 ARG cc_start: 0.6993 (mmp80) cc_final: 0.6781 (mmp80) REVERT: J 236 GLU cc_start: 0.8334 (mp0) cc_final: 0.8023 (mp0) REVERT: K 1 MET cc_start: 0.8781 (tmm) cc_final: 0.8426 (ttp) REVERT: K 112 ILE cc_start: 0.9303 (pt) cc_final: 0.9051 (pt) REVERT: K 114 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: L 54 MET cc_start: 0.9304 (tpp) cc_final: 0.8524 (tpt) REVERT: M 86 THR cc_start: 0.8401 (OUTLIER) cc_final: 0.8077 (p) REVERT: M 162 HIS cc_start: 0.8307 (OUTLIER) cc_final: 0.7952 (p90) REVERT: M 239 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8924 (mm) REVERT: M 316 ASP cc_start: 0.7793 (p0) cc_final: 0.7433 (p0) REVERT: N 285 ASP cc_start: 0.9132 (p0) cc_final: 0.8795 (p0) REVERT: N 306 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.8863 (t) REVERT: O 151 VAL cc_start: 0.7415 (m) cc_final: 0.7041 (m) REVERT: O 157 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8109 (mp) REVERT: O 288 GLU cc_start: 0.8139 (tp30) cc_final: 0.7821 (tp30) REVERT: P 50 TYR cc_start: 0.2483 (m-80) cc_final: 0.1125 (m-80) REVERT: P 136 TYR cc_start: 0.3630 (m-10) cc_final: 0.3182 (m-10) REVERT: P 176 TYR cc_start: 0.4186 (m-10) cc_final: 0.3312 (m-10) REVERT: Q 310 ASN cc_start: 0.8369 (t0) cc_final: 0.8118 (t0) REVERT: S 54 MET cc_start: 0.8054 (tpt) cc_final: 0.7784 (mmt) REVERT: S 236 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7078 (mp0) REVERT: S 240 LYS cc_start: 0.8528 (mtpt) cc_final: 0.8287 (mtmt) REVERT: S 253 ASN cc_start: 0.7768 (t0) cc_final: 0.7334 (t0) REVERT: S 309 TYR cc_start: 0.8199 (t80) cc_final: 0.7764 (t80) REVERT: T 131 ARG cc_start: 0.8060 (ptm-80) cc_final: 0.6852 (ptp90) REVERT: T 209 GLN cc_start: 0.5843 (OUTLIER) cc_final: 0.5211 (mm-40) REVERT: T 242 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7000 (tt) REVERT: T 245 MET cc_start: 0.7230 (mmp) cc_final: 0.6772 (mmm) REVERT: T 291 ARG cc_start: 0.7294 (ttm110) cc_final: 0.6932 (ttm110) outliers start: 90 outliers final: 66 residues processed: 506 average time/residue: 0.2386 time to fit residues: 193.4356 Evaluate side-chains 504 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 428 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 141 ILE 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 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 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 162 HIS 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 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 199 VAL Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL 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 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 209 GLN Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 216 optimal weight: 0.9990 chunk 376 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 chunk 426 optimal weight: 3.9990 chunk 209 optimal weight: 0.0070 chunk 341 optimal weight: 0.3980 chunk 221 optimal weight: 0.8980 chunk 223 optimal weight: 0.5980 chunk 159 optimal weight: 4.9990 chunk 372 optimal weight: 0.8980 chunk 218 optimal weight: 8.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 99 ASN O 53 ASN S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.167507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.125952 restraints weight = 46499.873| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.15 r_work: 0.3256 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35799 Z= 0.112 Angle : 0.610 9.672 48824 Z= 0.295 Chirality : 0.052 0.520 5602 Planarity : 0.004 0.068 6062 Dihedral : 10.221 177.859 5430 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.97 % Favored : 92.98 % Rotamer: Outliers : 2.21 % Allowed : 18.20 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.13), residues: 4275 helix: 0.82 (0.15), residues: 1343 sheet: -0.64 (0.19), residues: 760 loop : -1.05 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 130 TYR 0.019 0.001 TYR Q 309 PHE 0.017 0.001 PHE J 258 TRP 0.034 0.002 TRP C 4 HIS 0.005 0.001 HIS O 280 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (35792) covalent geometry : angle 0.60975 / 0.30 (48810) SS BOND : bond 0.00114 / 0.08 ( 7) SS BOND : angle 0.82102 / 0.49 ( 14) hydrogen bonds : bond 0.02907 / 1.90 ( 1036) hydrogen bonds : angle 4.17963 / 2.98 ( 2967) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8550 Ramachandran restraints generated. 4275 Oldfield, 0 Emsley, 4275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 435 time to evaluate : 1.384 Fit side-chains REVERT: A 57 LYS cc_start: 0.7500 (tttt) cc_final: 0.7282 (tppt) REVERT: A 72 GLU cc_start: 0.6989 (pm20) cc_final: 0.6592 (pm20) REVERT: A 91 ARG cc_start: 0.7001 (mtp180) cc_final: 0.6705 (tpt90) REVERT: C 79 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.5072 (pm20) REVERT: D 78 GLU cc_start: 0.6437 (mp0) cc_final: 0.6076 (mp0) REVERT: E 78 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6623 (mm-30) REVERT: E 80 LYS cc_start: 0.8178 (mmmm) cc_final: 0.7735 (mmmm) REVERT: F 22 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 78 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7326 (mt-10) REVERT: G 67 ARG cc_start: 0.8210 (mtp-110) cc_final: 0.7961 (ttm110) REVERT: H 55 LYS cc_start: 0.8072 (mttp) cc_final: 0.7744 (mtmt) REVERT: H 67 ARG cc_start: 0.7273 (tmt170) cc_final: 0.6942 (tmt170) REVERT: I 131 ARG cc_start: 0.7084 (ptm-80) cc_final: 0.6634 (ptt90) REVERT: I 294 ILE cc_start: 0.7749 (pt) cc_final: 0.7491 (pt) REVERT: I 298 ARG cc_start: 0.7123 (ttm-80) cc_final: 0.6666 (mtt180) REVERT: J 1 MET cc_start: 0.8641 (tpp) cc_final: 0.8357 (tpt) REVERT: J 37 ARG cc_start: 0.6037 (mmm-85) cc_final: 0.5812 (mmm-85) REVERT: J 221 ARG cc_start: 0.7015 (mmp80) cc_final: 0.6787 (mmp80) REVERT: J 236 GLU cc_start: 0.8328 (mp0) cc_final: 0.7986 (mp0) REVERT: K 1 MET cc_start: 0.8782 (tmm) cc_final: 0.8432 (ttp) REVERT: K 112 ILE cc_start: 0.9297 (pt) cc_final: 0.9038 (pt) REVERT: K 114 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.8047 (pm20) REVERT: L 54 MET cc_start: 0.9252 (tpp) cc_final: 0.8413 (tpt) REVERT: M 86 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (p) REVERT: M 162 HIS cc_start: 0.8267 (OUTLIER) cc_final: 0.7910 (p90) REVERT: M 239 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8927 (mm) REVERT: M 312 ASP cc_start: 0.7487 (p0) cc_final: 0.7217 (p0) REVERT: M 316 ASP cc_start: 0.7794 (p0) cc_final: 0.7436 (p0) REVERT: N 285 ASP cc_start: 0.9145 (p0) cc_final: 0.8806 (p0) REVERT: N 306 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8851 (t) REVERT: O 151 VAL cc_start: 0.7338 (m) cc_final: 0.6944 (m) REVERT: O 157 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.7935 (mp) REVERT: O 288 GLU cc_start: 0.8144 (tp30) cc_final: 0.7816 (tp30) REVERT: P 50 TYR cc_start: 0.2687 (m-80) cc_final: 0.1405 (m-80) REVERT: P 136 TYR cc_start: 0.3620 (m-10) cc_final: 0.3173 (m-10) REVERT: P 176 TYR cc_start: 0.4190 (m-10) cc_final: 0.3254 (m-10) REVERT: P 222 GLU cc_start: 0.5219 (OUTLIER) cc_final: 0.4719 (pm20) REVERT: Q 310 ASN cc_start: 0.8323 (t0) cc_final: 0.8072 (t0) REVERT: S 54 MET cc_start: 0.8014 (tpt) cc_final: 0.7755 (mmt) REVERT: S 236 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7045 (mp0) REVERT: S 240 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8295 (mtmt) REVERT: S 253 ASN cc_start: 0.7742 (t0) cc_final: 0.7286 (t0) REVERT: S 254 LEU cc_start: 0.5501 (OUTLIER) cc_final: 0.5009 (mm) REVERT: S 309 TYR cc_start: 0.8287 (t80) cc_final: 0.7830 (t80) REVERT: T 131 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.6840 (ptp90) REVERT: T 242 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6999 (tt) REVERT: T 245 MET cc_start: 0.7228 (mmp) cc_final: 0.6754 (mmm) REVERT: T 291 ARG cc_start: 0.7286 (ttm110) cc_final: 0.6913 (ttm110) outliers start: 79 outliers final: 65 residues processed: 493 average time/residue: 0.2400 time to fit residues: 189.8166 Evaluate side-chains 502 residues out of total 3591 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 426 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 CYS Chi-restraints excluded: chain C residue 5 ILE Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain I residue 45 VAL Chi-restraints excluded: chain I residue 54 MET Chi-restraints excluded: chain I residue 141 ILE 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 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 99 ASN Chi-restraints excluded: chain L residue 162 HIS Chi-restraints excluded: chain L residue 199 VAL Chi-restraints excluded: chain L residue 201 ASP Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 162 HIS 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 86 THR Chi-restraints excluded: chain N residue 163 ASN Chi-restraints excluded: chain N residue 184 LEU Chi-restraints excluded: chain N residue 198 ILE Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 213 VAL Chi-restraints excluded: chain N residue 306 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 157 ILE Chi-restraints excluded: chain O residue 267 VAL Chi-restraints excluded: chain O residue 308 THR Chi-restraints excluded: chain P residue 15 VAL Chi-restraints excluded: chain P residue 38 LEU Chi-restraints excluded: chain P residue 84 LEU Chi-restraints excluded: chain P residue 121 VAL Chi-restraints excluded: chain P residue 141 MET Chi-restraints excluded: chain P residue 161 VAL Chi-restraints excluded: chain P residue 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 77 THR Chi-restraints excluded: chain Q residue 86 THR Chi-restraints excluded: chain Q residue 131 ARG Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 211 LEU Chi-restraints excluded: chain Q residue 284 GLU Chi-restraints excluded: chain Q residue 300 LEU Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 105 LEU Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain S residue 245 MET Chi-restraints excluded: chain S residue 254 LEU Chi-restraints excluded: chain S residue 265 GLU Chi-restraints excluded: chain S residue 332 LEU Chi-restraints excluded: chain S residue 336 VAL Chi-restraints excluded: chain T residue 139 SER Chi-restraints excluded: chain T residue 225 VAL Chi-restraints excluded: chain T residue 242 LEU Chi-restraints excluded: chain T residue 306 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 351 optimal weight: 0.9990 chunk 313 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 348 optimal weight: 0.9980 chunk 376 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 398 optimal weight: 7.9990 chunk 354 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... S 17 ASN ** T 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.164991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.122636 restraints weight = 46520.474| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.30 r_work: 0.3204 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2104 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= 0.152 Angle : 0.634 10.682 48824 Z= 0.307 Chirality : 0.054 0.554 5602 Planarity : 0.004 0.069 6062 Dihedral : 10.250 178.474 5430 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 2.24 % Allowed : 18.37 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.13), residues: 4275 helix: 0.59 (0.15), residues: 1392 sheet: -0.68 (0.19), residues: 760 loop : -1.01 (0.14), residues: 2123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 130 TYR 0.019 0.001 TYR Q 309 PHE 0.020 0.001 PHE J 258 TRP 0.032 0.002 TRP C 4 HIS 0.008 0.001 HIS L 162 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 (35792) covalent geometry : angle 0.63426 / 0.31 (48810) SS BOND : bond 0.00129 / 0.09 ( 7) SS BOND : angle 0.89905 / 0.54 ( 14) hydrogen bonds : bond 0.03134 / 2.05 ( 1036) hydrogen bonds : angle 4.21782 / 3.01 ( 2967) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10028.36 seconds wall clock time: 172 minutes 13.81 seconds (10333.81 seconds total)