Starting phenix.real_space_refine on Mon Mar 18 06:41:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/03_2024/6gc0_4379.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/03_2024/6gc0_4379.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/03_2024/6gc0_4379.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/03_2024/6gc0_4379.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/03_2024/6gc0_4379.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc0_4379/03_2024/6gc0_4379.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.157 sd= 1.409 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 2847 5.49 5 S 64 5.16 5 C 41677 2.51 5 N 15706 2.21 5 O 23844 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 84138 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 58604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2729, 58604 Classifications: {'RNA': 2729} Modifications used: {'rna2p_pur': 260, 'rna2p_pyr': 141, 'rna3p_pur': 1323, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 401, 'rna3p': 2327} Chain breaks: 2 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 939 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 961 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 739 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} Chain: "U" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 410 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Residues with excluded nonbonded symmetry interactions: 100 residue: pdb=" P C A 840 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 840 " occ=0.00 residue: pdb=" P G A 841 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G A 841 " occ=0.00 residue: pdb=" P U A 842 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 842 " occ=0.00 residue: pdb=" P G A 843 " occ=0.00 ... (21 atoms not shown) pdb=" C4 G A 843 " occ=0.00 residue: pdb=" P A A 844 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 844 " occ=0.00 residue: pdb=" P A A 845 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 845 " occ=0.00 residue: pdb=" P U A 846 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 846 " occ=0.00 residue: pdb=" P U A 847 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 847 " occ=0.00 residue: pdb=" P C A 848 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 848 " occ=0.00 residue: pdb=" P A A 849 " occ=0.00 ... (20 atoms not shown) pdb=" C4 A A 849 " occ=0.00 residue: pdb=" P U A 850 " occ=0.00 ... (18 atoms not shown) pdb=" C6 U A 850 " occ=0.00 residue: pdb=" P C A 851 " occ=0.00 ... (18 atoms not shown) pdb=" C6 C A 851 " occ=0.00 ... (remaining 88 not shown) Time building chain proxies: 33.33, per 1000 atoms: 0.40 Number of scatterers: 84138 At special positions: 0 Unit cell: (243.04, 209.56, 221.96, 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 64 16.00 P 2847 15.00 O 23844 8.00 N 15706 7.00 C 41677 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 36.19 Conformation dependent library (CDL) restraints added in 3.4 seconds 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5374 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 44 sheets defined 27.2% alpha, 21.5% beta 659 base pairs and 1635 stacking pairs defined. Time for finding SS restraints: 29.26 Creating SS restraints... Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.096A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.797A pdb=" N HIS D 67 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE D 68 " --> pdb=" O GLU D 64 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 4.054A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASP D 103 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 126 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.652A pdb=" N VAL E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN E 30 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.512A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.532A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 removed outlier: 4.350A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.789A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.833A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 10 Processing helix chain 'F' and resid 10 through 19 removed outlier: 4.231A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.721A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.713A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 104 removed outlier: 3.790A pdb=" N TRP F 96 " --> pdb=" O GLY F 92 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR F 104 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 137 Processing helix chain 'F' and resid 161 through 171 removed outlier: 3.543A pdb=" N GLY F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F 167 " --> pdb=" O GLU F 163 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 80 removed outlier: 3.838A pdb=" N ALA G 67 " --> pdb=" O GLN G 63 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 149 removed outlier: 3.668A pdb=" N GLY G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA G 144 " --> pdb=" O ILE G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 47 Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.677A pdb=" N ALA J 29 " --> pdb=" O LEU J 25 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.812A pdb=" N ILE J 93 " --> pdb=" O PHE J 89 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 108 removed outlier: 4.375A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 120 Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.565A pdb=" N GLN J 135 " --> pdb=" O HIS J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 111 No H-bonds generated for 'chain 'K' and resid 109 through 111' Processing helix chain 'K' and resid 112 through 118 removed outlier: 3.668A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.776A pdb=" N THR L 5 " --> pdb=" O ARG L 2 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 6' Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.795A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 74 removed outlier: 3.592A pdb=" N THR L 74 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.559A pdb=" N ARG L 132 " --> pdb=" O THR L 128 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.759A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA N 25 " --> pdb=" O PHE N 21 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 45 removed outlier: 3.546A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 55 Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.608A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.599A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.985A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 82 through 87' Processing helix chain 'O' and resid 5 through 11 removed outlier: 3.768A pdb=" N ARG O 9 " --> pdb=" O SER O 5 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA O 11 " --> pdb=" O ARG O 7 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 22 removed outlier: 3.634A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.870A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 84 removed outlier: 3.518A pdb=" N ALA O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS O 76 " --> pdb=" O ALA O 72 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 113 removed outlier: 3.634A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.807A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.723A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.907A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS Q 13 " --> pdb=" O ALA Q 9 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 4.191A pdb=" N ARG Q 27 " --> pdb=" O TYR Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 3.969A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 92 through 101 removed outlier: 3.540A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.725A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.591A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 36 removed outlier: 4.649A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.534A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 69 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 3 through 8 removed outlier: 3.745A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU T 8 " --> pdb=" O GLU T 4 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 3 through 8' Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.521A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'V' and resid 12 through 23 removed outlier: 4.246A pdb=" N ALA V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.214A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 62 removed outlier: 3.852A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 74 removed outlier: 3.503A pdb=" N LEU X 67 " --> pdb=" O ILE X 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.519A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 32 removed outlier: 3.698A pdb=" N LEU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 56 removed outlier: 3.686A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 27 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.526A pdb=" N GLY Z 45 " --> pdb=" O PRO Z 41 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N MET Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 14 Processing helix chain '0' and resid 15 through 19 removed outlier: 4.397A pdb=" N HIS 0 18 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 removed outlier: 3.523A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 38 removed outlier: 3.842A pdb=" N VAL 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU 2 31 " --> pdb=" O GLY 2 27 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 36 through 43 removed outlier: 3.706A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU 3 43 " --> pdb=" O ARG 3 39 " (cutoff:3.500A) Processing helix chain '3' and resid 50 through 53 removed outlier: 3.536A pdb=" N ASP 3 53 " --> pdb=" O SER 3 50 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 50 through 53' Processing helix chain '3' and resid 54 through 59 removed outlier: 3.939A pdb=" N ALA 3 59 " --> pdb=" O GLY 3 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.624A pdb=" N GLU C 34 " --> pdb=" O TYR C 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.670A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 128 through 130 Processing sheet with id=AA5, first strand: chain 'C' and resid 162 through 165 removed outlier: 6.756A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET C 180 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 4 through 14 removed outlier: 5.692A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.234A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 117 through 118 removed outlier: 3.735A pdb=" N GLY D 117 " --> pdb=" O MET D 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.392A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU E 147 " --> pdb=" O VAL E 187 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N THR E 189 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE E 149 " --> pdb=" O THR E 189 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 65 through 67 removed outlier: 4.337A pdb=" N CYS F 86 " --> pdb=" O MET F 37 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET F 37 " --> pdb=" O CYS F 86 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 90 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR F 34 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR F 127 " --> pdb=" O ILE F 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 8 through 9 removed outlier: 3.638A pdb=" N VAL G 8 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 16 through 18 removed outlier: 3.649A pdb=" N LYS G 17 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 24 " --> pdb=" O LYS G 17 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 121 through 123 removed outlier: 3.569A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN G 87 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG G 162 " --> pdb=" O GLN G 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 95 through 98 removed outlier: 3.964A pdb=" N LYS G 98 " --> pdb=" O VAL G 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.325A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 73 through 76 removed outlier: 3.548A pdb=" N LYS J 85 " --> pdb=" O HIS J 76 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.896A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.115A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 69 through 70 removed outlier: 4.115A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.829A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N THR P 24 " --> pdb=" O VAL P 85 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL P 85 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU P 26 " --> pdb=" O ILE P 83 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE P 83 " --> pdb=" O GLU P 26 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N LYS P 28 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC4, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.542A pdb=" N ILE N 113 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 25 through 30 removed outlier: 3.724A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN O 38 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 89 through 90 removed outlier: 4.261A pdb=" N LYS P 110 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.783A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 19 through 22 removed outlier: 7.403A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.164A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 2 through 10 removed outlier: 3.526A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP S 94 " --> pdb=" O ILE S 85 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE S 85 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE S 96 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N LYS S 83 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.152A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 11 through 14 removed outlier: 4.152A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.900A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD6, first strand: chain 'U' and resid 82 through 86 removed outlier: 3.920A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 2 through 8 removed outlier: 8.346A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU V 38 " --> pdb=" O ILE V 30 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE V 30 " --> pdb=" O LEU V 38 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN V 78 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ILE V 89 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASP V 76 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N PHE V 91 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ALA V 74 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG V 93 " --> pdb=" O VAL V 72 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL V 72 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 18 through 19 removed outlier: 3.501A pdb=" N GLY W 18 " --> pdb=" O ARG W 35 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.739A pdb=" N GLY W 61 " --> pdb=" O VAL W 27 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS W 68 " --> pdb=" O ARG W 73 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG W 73 " --> pdb=" O LYS W 68 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 12 through 17 removed outlier: 3.640A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR X 24 " --> pdb=" O ASN X 16 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 32 through 38 Processing sheet with id=AE3, first strand: chain 'Z' and resid 34 through 38 removed outlier: 3.533A pdb=" N VAL Z 35 " --> pdb=" O ILE Z 6 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AE5, first strand: chain '0' and resid 47 through 48 Processing sheet with id=AE6, first strand: chain '1' and resid 6 through 11 removed outlier: 3.766A pdb=" N GLU 1 6 " --> pdb=" O LYS 1 24 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR 1 20 " --> pdb=" O LEU 1 10 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '1' and resid 36 through 39 removed outlier: 3.620A pdb=" N LYS 1 37 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '3' and resid 14 through 15 removed outlier: 3.609A pdb=" N LYS 3 14 " --> pdb=" O LYS 3 22 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS 3 23 " --> pdb=" O ALA 3 47 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 3 47 " --> pdb=" O HIS 3 23 " (cutoff:3.500A) 659 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1553 hydrogen bonds 2414 hydrogen bond angles 0 basepair planarities 659 basepair parallelities 1635 stacking parallelities Total time for adding SS restraints: 125.73 Time building geometry restraints manager: 38.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 15650 1.34 - 1.46: 37866 1.46 - 1.58: 32461 1.58 - 1.70: 5691 1.70 - 1.82: 118 Bond restraints: 91786 Sorted by residual: bond pdb=" C ALA E 128 " pdb=" N PRO E 129 " ideal model delta sigma weight residual 1.334 1.483 -0.149 2.34e-02 1.83e+03 4.03e+01 bond pdb=" C ARG 3 44 " pdb=" N PRO 3 45 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.91e+00 bond pdb=" N PHE F 176 " pdb=" CA PHE F 176 " ideal model delta sigma weight residual 1.459 1.484 -0.026 1.16e-02 7.43e+03 4.90e+00 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.64e+00 bond pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.34e+00 ... (remaining 91781 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.43: 17081 106.43 - 113.71: 56387 113.71 - 120.99: 38731 120.99 - 128.27: 21460 128.27 - 135.55: 4411 Bond angle restraints: 138070 Sorted by residual: angle pdb=" C LYS 1 49 " pdb=" N GLU 1 50 " pdb=" CA GLU 1 50 " ideal model delta sigma weight residual 121.31 132.48 -11.17 1.49e+00 4.50e-01 5.62e+01 angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 121.54 135.55 -14.01 1.91e+00 2.74e-01 5.38e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 134.02 -12.32 1.80e+00 3.09e-01 4.68e+01 angle pdb=" C CYS N 100 " pdb=" N GLY N 101 " pdb=" CA GLY N 101 " ideal model delta sigma weight residual 121.41 132.57 -11.16 1.96e+00 2.60e-01 3.24e+01 angle pdb=" C GLN P 14 " pdb=" N ASP P 15 " pdb=" CA ASP P 15 " ideal model delta sigma weight residual 124.82 134.63 -9.81 1.78e+00 3.16e-01 3.04e+01 ... (remaining 138065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 52056 35.93 - 71.86: 5974 71.86 - 107.80: 723 107.80 - 143.73: 4 143.73 - 179.66: 14 Dihedral angle restraints: 58771 sinusoidal: 50418 harmonic: 8353 Sorted by residual: dihedral pdb=" CA THR D 151 " pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta harmonic sigma weight residual -180.00 -116.29 -63.71 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA VAL H 31 " pdb=" C VAL H 31 " pdb=" N PRO H 32 " pdb=" CA PRO H 32 " ideal model delta harmonic sigma weight residual -180.00 -119.84 -60.16 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA GLY C 11 " pdb=" C GLY C 11 " pdb=" N ARG C 12 " pdb=" CA ARG C 12 " ideal model delta harmonic sigma weight residual -180.00 -131.52 -48.48 0 5.00e+00 4.00e-02 9.40e+01 ... (remaining 58768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 16879 0.060 - 0.119: 722 0.119 - 0.179: 117 0.179 - 0.238: 11 0.238 - 0.298: 8 Chirality restraints: 17737 Sorted by residual: chirality pdb=" C3' A A1938 " pdb=" C4' A A1938 " pdb=" O3' A A1938 " pdb=" C2' A A1938 " both_signs ideal model delta sigma weight residual False -2.74 -2.45 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" CB ILE E 149 " pdb=" CA ILE E 149 " pdb=" CG1 ILE E 149 " pdb=" CG2 ILE E 149 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' G A 271 " pdb=" C4' G A 271 " pdb=" O3' G A 271 " pdb=" C2' G A 271 " both_signs ideal model delta sigma weight residual False -2.74 -2.46 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 17734 not shown) Planarity restraints: 6884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO H 32 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" C PRO H 32 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO H 32 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN H 33 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL H 31 " 0.060 5.00e-02 4.00e+02 9.00e-02 1.29e+01 pdb=" N PRO H 32 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.057 5.00e-02 4.00e+02 8.68e-02 1.21e+01 pdb=" N PRO D 152 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.048 5.00e-02 4.00e+02 ... (remaining 6881 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 20276 2.81 - 3.33: 65993 3.33 - 3.85: 176196 3.85 - 4.38: 208195 4.38 - 4.90: 272397 Nonbonded interactions: 743057 Sorted by model distance: nonbonded pdb=" OD1 ASN D 136 " pdb=" OG SER D 139 " model vdw 2.283 2.440 nonbonded pdb=" O2' A A 911 " pdb=" O2' C A2263 " model vdw 2.290 2.440 nonbonded pdb=" O2' G A1792 " pdb=" OP1 C A1830 " model vdw 2.292 2.440 nonbonded pdb=" OP1 G A1296 " pdb=" O2' G A2709 " model vdw 2.294 2.440 nonbonded pdb=" O2' U A2343 " pdb=" O2' G A2373 " model vdw 2.301 2.440 ... (remaining 743052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 7.400 Check model and map are aligned: 0.940 Set scattering table: 0.590 Process input model: 283.070 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 297.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 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 : 0.002 0.149 91786 Z= 0.133 Angle : 0.523 16.019 138070 Z= 0.290 Chirality : 0.028 0.298 17737 Planarity : 0.005 0.090 6884 Dihedral : 22.053 179.660 53397 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 0.04 % Allowed : 1.05 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.12), residues: 2898 helix: -4.74 (0.06), residues: 675 sheet: -1.43 (0.20), residues: 586 loop : -2.51 (0.12), residues: 1637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP C 212 HIS 0.006 0.001 HIS N 16 PHE 0.019 0.002 PHE U 94 TYR 0.019 0.002 TYR N 112 ARG 0.006 0.000 ARG F 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1114 time to evaluate : 3.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 102 TYR cc_start: 0.7776 (m-80) cc_final: 0.7484 (m-80) REVERT: E 101 TYR cc_start: 0.7138 (t80) cc_final: 0.6857 (t80) REVERT: E 159 LEU cc_start: 0.4906 (tp) cc_final: 0.4699 (tp) REVERT: G 74 MET cc_start: -0.0613 (mtp) cc_final: -0.0920 (mmm) REVERT: J 101 ILE cc_start: 0.7218 (mm) cc_final: 0.6996 (mm) REVERT: L 54 GLN cc_start: 0.6643 (tt0) cc_final: 0.5899 (tt0) REVERT: L 55 MET cc_start: 0.7572 (tpp) cc_final: 0.7218 (tpp) REVERT: N 52 ILE cc_start: 0.7729 (mt) cc_final: 0.7446 (mt) REVERT: N 107 ASN cc_start: 0.8263 (t0) cc_final: 0.7952 (t0) REVERT: O 26 LEU cc_start: 0.7408 (tp) cc_final: 0.7107 (tt) REVERT: P 4 ILE cc_start: 0.6770 (mt) cc_final: 0.6321 (mt) REVERT: Q 31 TYR cc_start: 0.7325 (t80) cc_final: 0.6850 (t80) REVERT: Q 80 ASN cc_start: 0.6374 (t0) cc_final: 0.6083 (t0) REVERT: R 89 HIS cc_start: 0.6920 (t-90) cc_final: 0.6640 (t-90) REVERT: U 17 ASP cc_start: 0.5453 (p0) cc_final: 0.4864 (p0) REVERT: U 27 VAL cc_start: 0.7020 (p) cc_final: 0.6235 (t) REVERT: U 94 PHE cc_start: 0.4721 (p90) cc_final: 0.4460 (p90) REVERT: X 31 ASN cc_start: 0.5315 (t0) cc_final: 0.4964 (t0) REVERT: X 77 TYR cc_start: 0.7125 (p90) cc_final: 0.6558 (p90) REVERT: Y 50 VAL cc_start: 0.7854 (t) cc_final: 0.7459 (p) REVERT: 1 8 ILE cc_start: 0.7860 (pt) cc_final: 0.7389 (pt) REVERT: 2 8 SER cc_start: 0.7336 (t) cc_final: 0.6970 (m) REVERT: 2 21 ARG cc_start: 0.8415 (mmt90) cc_final: 0.7921 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 1115 average time/residue: 0.9367 time to fit residues: 1667.2238 Evaluate side-chains 659 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 659 time to evaluate : 3.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 479 optimal weight: 2.9990 chunk 430 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 230 optimal weight: 10.0000 chunk 445 optimal weight: 1.9990 chunk 172 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 331 optimal weight: 0.7980 chunk 515 optimal weight: 20.0000 overall best weight: 5.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 ASN C 116 GLN C 199 HIS ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 242 HIS D 67 HIS D 134 HIS ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 62 GLN E 165 HIS ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN H 43 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 74 GLN Q 43 GLN Q 71 ASN R 87 GLN R 91 GLN S 9 HIS T 48 GLN U 68 ASN V 75 GLN W 8 ASN W 53 HIS X 35 HIS Y 15 ASN Z 19 HIS 2 26 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 91786 Z= 0.298 Angle : 0.665 14.567 138070 Z= 0.339 Chirality : 0.037 0.297 17737 Planarity : 0.006 0.098 6884 Dihedral : 23.007 178.093 47637 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 5.31 % Allowed : 15.15 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.13), residues: 2898 helix: -2.59 (0.15), residues: 713 sheet: -1.03 (0.20), residues: 598 loop : -1.92 (0.13), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 212 HIS 0.015 0.002 HIS J 80 PHE 0.028 0.003 PHE O 92 TYR 0.022 0.003 TYR J 16 ARG 0.010 0.001 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 719 time to evaluate : 3.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 200 MET cc_start: 0.6842 (ptm) cc_final: 0.6636 (ptp) REVERT: E 101 TYR cc_start: 0.7381 (t80) cc_final: 0.6961 (t80) REVERT: E 198 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6465 (mm-30) REVERT: F 47 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.4800 (ttpp) REVERT: N 107 ASN cc_start: 0.8636 (t0) cc_final: 0.8228 (t0) REVERT: R 1 MET cc_start: 0.5508 (tpt) cc_final: 0.4995 (tpt) REVERT: V 29 ILE cc_start: 0.6888 (tp) cc_final: 0.6650 (tp) REVERT: V 91 PHE cc_start: 0.5859 (m-80) cc_final: 0.5519 (m-80) REVERT: W 39 THR cc_start: 0.7146 (p) cc_final: 0.6851 (p) REVERT: X 77 TYR cc_start: 0.7198 (p90) cc_final: 0.6700 (p90) REVERT: 2 8 SER cc_start: 0.7452 (t) cc_final: 0.6997 (m) REVERT: 3 48 MET cc_start: 0.8160 (mmm) cc_final: 0.7918 (mmm) outliers start: 127 outliers final: 89 residues processed: 777 average time/residue: 0.8269 time to fit residues: 1091.6267 Evaluate side-chains 716 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 626 time to evaluate : 3.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 73 ILE Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 138 LEU Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 4 ASN Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 78 VAL Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 74 LYS Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 29 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 286 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 351 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 516 optimal weight: 5.9990 chunk 558 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 512 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 chunk 414 optimal weight: 0.1980 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 GLN C 199 HIS ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN P 40 GLN R 12 HIS S 61 ASN T 28 ASN Y 58 ASN 0 18 HIS 1 45 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 91786 Z= 0.285 Angle : 0.659 16.348 138070 Z= 0.338 Chirality : 0.037 0.301 17737 Planarity : 0.006 0.099 6884 Dihedral : 23.185 178.149 47637 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 6.99 % Allowed : 17.24 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.14), residues: 2898 helix: -1.67 (0.17), residues: 714 sheet: -0.94 (0.20), residues: 585 loop : -1.80 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP F 96 HIS 0.013 0.002 HIS F 4 PHE 0.021 0.003 PHE O 92 TYR 0.017 0.002 TYR H 25 ARG 0.015 0.001 ARG V 9 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 675 time to evaluate : 3.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 LYS cc_start: 0.7437 (tppt) cc_final: 0.7093 (tptt) REVERT: D 165 MET cc_start: 0.7189 (OUTLIER) cc_final: 0.6507 (tpp) REVERT: E 101 TYR cc_start: 0.7384 (t80) cc_final: 0.7113 (t80) REVERT: E 189 THR cc_start: 0.6237 (t) cc_final: 0.5862 (t) REVERT: F 47 LYS cc_start: 0.5891 (OUTLIER) cc_final: 0.5171 (ttpp) REVERT: F 121 PHE cc_start: 0.5497 (m-80) cc_final: 0.5294 (m-10) REVERT: J 131 ASN cc_start: 0.7511 (p0) cc_final: 0.7300 (p0) REVERT: L 110 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7320 (m) REVERT: N 2 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7020 (mtp85) REVERT: N 8 ARG cc_start: 0.7373 (ptp-170) cc_final: 0.7132 (ptp-170) REVERT: Q 12 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7088 (ttp80) REVERT: R 1 MET cc_start: 0.6239 (tpt) cc_final: 0.5012 (tpt) REVERT: V 55 GLU cc_start: 0.6050 (pm20) cc_final: 0.5777 (pm20) REVERT: W 39 THR cc_start: 0.7445 (p) cc_final: 0.7213 (p) REVERT: X 77 TYR cc_start: 0.7168 (p90) cc_final: 0.6745 (p90) REVERT: 2 8 SER cc_start: 0.7678 (t) cc_final: 0.7374 (m) REVERT: 2 45 SER cc_start: 0.7429 (p) cc_final: 0.7149 (p) REVERT: 3 48 MET cc_start: 0.8369 (mmm) cc_final: 0.8081 (mmm) outliers start: 167 outliers final: 131 residues processed: 766 average time/residue: 0.8075 time to fit residues: 1047.6738 Evaluate side-chains 744 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 609 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 40 GLN Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 26 PHE Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 26 SER Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 18 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 510 optimal weight: 9.9990 chunk 388 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 518 optimal weight: 3.9990 chunk 549 optimal weight: 0.0470 chunk 270 optimal weight: 10.0000 chunk 491 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 overall best weight: 6.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 44 HIS V 51 GLN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN 3 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 91786 Z= 0.326 Angle : 0.705 15.082 138070 Z= 0.360 Chirality : 0.039 0.288 17737 Planarity : 0.006 0.101 6884 Dihedral : 23.318 179.415 47637 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.42 % Favored : 91.51 % Rotamer: Outliers : 7.45 % Allowed : 18.83 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.14), residues: 2898 helix: -1.32 (0.18), residues: 715 sheet: -1.04 (0.20), residues: 599 loop : -1.84 (0.14), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP F 96 HIS 0.017 0.002 HIS C 199 PHE 0.029 0.002 PHE W 22 TYR 0.021 0.002 TYR S 38 ARG 0.008 0.001 ARG L 123 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 665 time to evaluate : 3.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 216 ARG cc_start: 0.7110 (mtp-110) cc_final: 0.6884 (ttp-110) REVERT: D 89 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6620 (mm-30) REVERT: D 127 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.6104 (m-10) REVERT: D 159 LYS cc_start: 0.7312 (tppt) cc_final: 0.6963 (tptt) REVERT: D 165 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6492 (tpp) REVERT: E 101 TYR cc_start: 0.7506 (t80) cc_final: 0.7220 (t80) REVERT: J 131 ASN cc_start: 0.7584 (p0) cc_final: 0.7181 (p0) REVERT: K 28 SER cc_start: 0.8564 (t) cc_final: 0.8355 (p) REVERT: N 2 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6915 (mtp85) REVERT: N 8 ARG cc_start: 0.7046 (ptp-170) cc_final: 0.6643 (ptp-170) REVERT: N 20 MET cc_start: 0.8295 (tpp) cc_final: 0.7964 (tpp) REVERT: P 55 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.6232 (m90) REVERT: R 1 MET cc_start: 0.6528 (tpt) cc_final: 0.5059 (tpt) REVERT: V 75 GLN cc_start: 0.6233 (pm20) cc_final: 0.5852 (mp10) REVERT: W 39 THR cc_start: 0.7587 (p) cc_final: 0.7296 (p) REVERT: 2 8 SER cc_start: 0.7842 (t) cc_final: 0.7468 (m) REVERT: 2 35 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7259 (mtm-85) REVERT: 3 48 MET cc_start: 0.8249 (mmm) cc_final: 0.7564 (mmt) outliers start: 178 outliers final: 136 residues processed: 761 average time/residue: 0.8174 time to fit residues: 1058.0486 Evaluate side-chains 762 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 622 time to evaluate : 3.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 53 THR Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 44 HIS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 457 optimal weight: 1.9990 chunk 311 optimal weight: 10.0000 chunk 7 optimal weight: 10.0000 chunk 408 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 468 optimal weight: 10.0000 chunk 379 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 chunk 492 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN H 11 ASN J 135 GLN ** K 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS ** N 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN P 9 GLN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN Z 33 HIS 0 18 HIS 3 27 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 91786 Z= 0.401 Angle : 0.793 14.991 138070 Z= 0.402 Chirality : 0.043 0.305 17737 Planarity : 0.006 0.100 6884 Dihedral : 23.588 178.934 47637 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 24.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.94 % Favored : 89.96 % Rotamer: Outliers : 8.87 % Allowed : 19.96 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.14), residues: 2898 helix: -1.29 (0.18), residues: 705 sheet: -1.03 (0.21), residues: 574 loop : -2.03 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP F 96 HIS 0.040 0.002 HIS V 44 PHE 0.029 0.003 PHE W 22 TYR 0.026 0.003 TYR S 38 ARG 0.012 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 847 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 635 time to evaluate : 3.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7710 (p0) REVERT: C 220 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6785 (ptt180) REVERT: D 13 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.5841 (ptp90) REVERT: D 159 LYS cc_start: 0.7286 (tppt) cc_final: 0.6924 (tptt) REVERT: D 165 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6707 (tpp) REVERT: F 36 ASN cc_start: 0.5449 (OUTLIER) cc_final: 0.4869 (t0) REVERT: F 70 ARG cc_start: 0.3662 (OUTLIER) cc_final: 0.2213 (ttp-170) REVERT: J 131 ASN cc_start: 0.7774 (p0) cc_final: 0.7282 (p0) REVERT: K 3 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6263 (pt0) REVERT: N 2 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7314 (mtp85) REVERT: N 8 ARG cc_start: 0.7156 (ptp-170) cc_final: 0.6763 (ptp-170) REVERT: P 55 HIS cc_start: 0.6448 (OUTLIER) cc_final: 0.5865 (m90) REVERT: P 109 ILE cc_start: 0.6797 (mm) cc_final: 0.6585 (mm) REVERT: S 82 MET cc_start: 0.5696 (OUTLIER) cc_final: 0.5111 (mtt) REVERT: U 25 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6422 (mttm) REVERT: V 18 ARG cc_start: 0.4887 (mmm-85) cc_final: 0.4651 (mmm-85) REVERT: W 39 THR cc_start: 0.7781 (p) cc_final: 0.7556 (p) REVERT: X 45 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6720 (m-10) REVERT: Z 46 MET cc_start: 0.7382 (mtp) cc_final: 0.7075 (mtm) REVERT: 2 8 SER cc_start: 0.7954 (t) cc_final: 0.7612 (m) REVERT: 2 35 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7164 (mtm-85) REVERT: 3 48 MET cc_start: 0.8035 (mmm) cc_final: 0.7752 (mmt) outliers start: 212 outliers final: 149 residues processed: 753 average time/residue: 0.8422 time to fit residues: 1074.7529 Evaluate side-chains 751 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 590 time to evaluate : 3.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 43 ILE Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 105 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 13 ARG Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain V residue 51 GLN Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 45 PHE Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 184 optimal weight: 20.0000 chunk 494 optimal weight: 5.9990 chunk 108 optimal weight: 50.0000 chunk 322 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 549 optimal weight: 0.9990 chunk 456 optimal weight: 0.9990 chunk 254 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 288 optimal weight: 10.0000 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN H 11 ASN J 135 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN O 19 GLN O 61 GLN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 9 GLN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 98 ASN V 24 ASN ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 HIS Y 15 ASN Y 58 ASN 0 18 HIS 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 91786 Z= 0.294 Angle : 0.682 13.926 138070 Z= 0.350 Chirality : 0.038 0.299 17737 Planarity : 0.005 0.100 6884 Dihedral : 23.485 178.406 47637 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.39 % Favored : 90.55 % Rotamer: Outliers : 8.12 % Allowed : 22.13 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2898 helix: -1.00 (0.19), residues: 706 sheet: -0.99 (0.21), residues: 558 loop : -1.96 (0.14), residues: 1634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP F 96 HIS 0.009 0.002 HIS C 199 PHE 0.027 0.002 PHE W 22 TYR 0.031 0.002 TYR S 38 ARG 0.011 0.001 ARG N 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 634 time to evaluate : 3.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 ASN cc_start: 0.7949 (OUTLIER) cc_final: 0.7605 (p0) REVERT: C 220 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6822 (ptp-170) REVERT: D 13 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.5939 (ptp90) REVERT: D 165 MET cc_start: 0.7415 (OUTLIER) cc_final: 0.6602 (tpp) REVERT: F 36 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.5237 (t0) REVERT: F 47 LYS cc_start: 0.6557 (OUTLIER) cc_final: 0.5708 (ttpp) REVERT: F 70 ARG cc_start: 0.3543 (OUTLIER) cc_final: 0.2665 (ttp-170) REVERT: J 131 ASN cc_start: 0.7799 (p0) cc_final: 0.7330 (p0) REVERT: K 1 MET cc_start: 0.7776 (mtt) cc_final: 0.7444 (mtt) REVERT: K 3 GLN cc_start: 0.6477 (OUTLIER) cc_final: 0.5805 (pt0) REVERT: L 42 SER cc_start: 0.8088 (t) cc_final: 0.7404 (p) REVERT: N 2 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7155 (mtp85) REVERT: N 8 ARG cc_start: 0.6890 (ptp-170) cc_final: 0.6515 (ptp-170) REVERT: O 17 LYS cc_start: 0.6740 (tptp) cc_final: 0.6141 (tptp) REVERT: P 55 HIS cc_start: 0.6222 (OUTLIER) cc_final: 0.5507 (m90) REVERT: T 5 GLU cc_start: 0.8169 (mp0) cc_final: 0.7828 (tm-30) REVERT: U 25 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.6240 (mttt) REVERT: V 21 ARG cc_start: 0.6823 (mtt90) cc_final: 0.6598 (ttm110) REVERT: Y 5 GLU cc_start: 0.6007 (mp0) cc_final: 0.5389 (mp0) REVERT: Z 46 MET cc_start: 0.7394 (mtp) cc_final: 0.7159 (mtm) REVERT: 2 8 SER cc_start: 0.7805 (t) cc_final: 0.7486 (m) REVERT: 2 35 ARG cc_start: 0.7633 (mtm-85) cc_final: 0.7242 (mtm-85) REVERT: 3 48 MET cc_start: 0.8114 (mmm) cc_final: 0.7798 (mmt) REVERT: 3 61 LEU cc_start: 0.8806 (mp) cc_final: 0.8456 (tt) outliers start: 194 outliers final: 149 residues processed: 739 average time/residue: 0.8063 time to fit residues: 1010.3175 Evaluate side-chains 764 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 604 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 ASN Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 2 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 27 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 25 LYS Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 529 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 313 optimal weight: 10.0000 chunk 401 optimal weight: 3.9990 chunk 310 optimal weight: 5.9990 chunk 462 optimal weight: 20.0000 chunk 306 optimal weight: 40.0000 chunk 547 optimal weight: 5.9990 chunk 342 optimal weight: 6.9990 chunk 333 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN H 11 ASN J 135 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6971 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 91786 Z= 0.297 Angle : 0.690 14.774 138070 Z= 0.353 Chirality : 0.038 0.296 17737 Planarity : 0.005 0.099 6884 Dihedral : 23.502 175.609 47637 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.28 % Favored : 89.61 % Rotamer: Outliers : 8.20 % Allowed : 23.31 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.15), residues: 2898 helix: -0.92 (0.19), residues: 699 sheet: -1.06 (0.22), residues: 515 loop : -1.96 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.004 TRP F 96 HIS 0.026 0.002 HIS X 19 PHE 0.019 0.002 PHE D 118 TYR 0.025 0.002 TYR S 38 ARG 0.008 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 630 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7678 (p0) REVERT: C 220 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6821 (ptp-170) REVERT: D 13 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.5807 (ptp90) REVERT: D 83 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.6429 (mmt90) REVERT: D 165 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.6620 (tpp) REVERT: E 197 GLU cc_start: 0.5916 (tm-30) cc_final: 0.5597 (tm-30) REVERT: F 47 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.5703 (ttpp) REVERT: F 70 ARG cc_start: 0.3658 (OUTLIER) cc_final: 0.2694 (ttp-170) REVERT: J 131 ASN cc_start: 0.7843 (p0) cc_final: 0.7386 (p0) REVERT: K 3 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.5886 (pt0) REVERT: N 2 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.7168 (mtp85) REVERT: N 8 ARG cc_start: 0.6887 (ptp-170) cc_final: 0.6564 (ptp-170) REVERT: P 55 HIS cc_start: 0.6245 (OUTLIER) cc_final: 0.5501 (m90) REVERT: S 82 MET cc_start: 0.5718 (OUTLIER) cc_final: 0.5146 (mtt) REVERT: X 45 PHE cc_start: 0.7191 (OUTLIER) cc_final: 0.6627 (m-10) REVERT: Y 39 GLN cc_start: 0.7406 (pm20) cc_final: 0.7189 (pm20) REVERT: Z 44 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7479 (tpp-160) REVERT: Z 46 MET cc_start: 0.7249 (mtp) cc_final: 0.7033 (mtm) REVERT: 2 8 SER cc_start: 0.7899 (t) cc_final: 0.7547 (m) REVERT: 2 35 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: 3 48 MET cc_start: 0.8107 (mmm) cc_final: 0.7797 (mmt) outliers start: 196 outliers final: 154 residues processed: 732 average time/residue: 0.8169 time to fit residues: 1012.6309 Evaluate side-chains 772 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 605 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 21 LEU Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain Q residue 108 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain S residue 2 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 27 LYS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 98 ASN Chi-restraints excluded: chain U residue 101 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 6 VAL Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 45 PHE Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain 3 residue 60 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 338 optimal weight: 4.9990 chunk 218 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 107 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 348 optimal weight: 9.9990 chunk 372 optimal weight: 30.0000 chunk 270 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 430 optimal weight: 3.9990 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN J 138 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN S 102 HIS ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 91786 Z= 0.400 Angle : 0.793 14.959 138070 Z= 0.400 Chirality : 0.042 0.301 17737 Planarity : 0.006 0.099 6884 Dihedral : 23.650 176.877 47637 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.32 % Favored : 88.61 % Rotamer: Outliers : 8.28 % Allowed : 23.56 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 2898 helix: -1.11 (0.19), residues: 695 sheet: -1.19 (0.22), residues: 533 loop : -2.13 (0.14), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP F 96 HIS 0.008 0.002 HIS C 199 PHE 0.028 0.003 PHE D 118 TYR 0.034 0.003 TYR S 38 ARG 0.008 0.001 ARG V 9 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 614 time to evaluate : 3.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 44 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7682 (p0) REVERT: C 220 ARG cc_start: 0.7119 (OUTLIER) cc_final: 0.6677 (ptp-170) REVERT: D 13 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6149 (ptp90) REVERT: D 83 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.6424 (mmt90) REVERT: D 165 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6734 (tpp) REVERT: F 6 TYR cc_start: 0.3875 (OUTLIER) cc_final: 0.3504 (t80) REVERT: F 47 LYS cc_start: 0.6525 (OUTLIER) cc_final: 0.5688 (ttpp) REVERT: F 70 ARG cc_start: 0.3462 (OUTLIER) cc_final: 0.2436 (ttp-170) REVERT: J 131 ASN cc_start: 0.7787 (p0) cc_final: 0.7350 (p0) REVERT: K 3 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.6269 (pt0) REVERT: K 105 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6452 (tmm-80) REVERT: L 82 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7606 (tt) REVERT: N 2 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7420 (mtp85) REVERT: P 55 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.5792 (m90) REVERT: R 68 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.8032 (mtp180) REVERT: S 82 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.5152 (mtt) REVERT: T 5 GLU cc_start: 0.8235 (mp0) cc_final: 0.7924 (tm-30) REVERT: X 19 HIS cc_start: 0.6600 (m90) cc_final: 0.6336 (m170) REVERT: X 45 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6650 (m-10) REVERT: Z 44 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7563 (tpp-160) REVERT: Z 46 MET cc_start: 0.7303 (mtp) cc_final: 0.7066 (mtm) REVERT: 0 6 LYS cc_start: 0.8060 (tttt) cc_final: 0.7707 (pttt) REVERT: 2 8 SER cc_start: 0.8003 (t) cc_final: 0.7632 (m) REVERT: 2 35 ARG cc_start: 0.7678 (mtm-85) cc_final: 0.7230 (mtm-85) outliers start: 198 outliers final: 160 residues processed: 722 average time/residue: 0.8184 time to fit residues: 999.6380 Evaluate side-chains 767 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 590 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 44 ASN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 163 ILE Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 212 TRP Chi-restraints excluded: chain C residue 215 VAL Chi-restraints excluded: chain C residue 220 ARG Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 83 ARG Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 165 MET Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 6 TYR Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 55 ASP Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 56 ASP Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 105 ARG Chi-restraints excluded: chain L residue 27 LEU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 19 PHE Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 73 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain S residue 2 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 9 GLU Chi-restraints excluded: chain U residue 17 ASP Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 71 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 45 PHE Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 16 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 44 ARG Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 2 residue 45 SER Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 58 ILE Chi-restraints excluded: chain 3 residue 60 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 498 optimal weight: 0.6980 chunk 524 optimal weight: 3.9990 chunk 478 optimal weight: 8.9990 chunk 510 optimal weight: 20.0000 chunk 307 optimal weight: 30.0000 chunk 222 optimal weight: 10.0000 chunk 400 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 461 optimal weight: 0.9990 chunk 482 optimal weight: 0.9990 chunk 508 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 HIS ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN H 11 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN S 102 HIS ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 42 HIS Y 15 ASN Z 19 HIS 0 3 GLN 1 25 ASN ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 91786 Z= 0.145 Angle : 0.569 14.564 138070 Z= 0.294 Chirality : 0.032 0.286 17737 Planarity : 0.005 0.095 6884 Dihedral : 23.376 178.913 47637 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.11 % Favored : 91.82 % Rotamer: Outliers : 5.10 % Allowed : 27.28 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.15), residues: 2898 helix: -0.51 (0.20), residues: 690 sheet: -0.89 (0.22), residues: 517 loop : -1.74 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP F 96 HIS 0.009 0.001 HIS V 44 PHE 0.022 0.002 PHE Q 78 TYR 0.023 0.002 TYR H 25 ARG 0.011 0.001 ARG U 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 648 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 116 GLN cc_start: 0.7832 (tp40) cc_final: 0.7626 (mm-40) REVERT: D 13 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.5865 (ptp90) REVERT: E 101 TYR cc_start: 0.7516 (t80) cc_final: 0.7014 (t80) REVERT: F 47 LYS cc_start: 0.6269 (OUTLIER) cc_final: 0.5482 (ttpp) REVERT: F 70 ARG cc_start: 0.3121 (OUTLIER) cc_final: 0.2520 (ttp-170) REVERT: J 131 ASN cc_start: 0.7674 (p0) cc_final: 0.7247 (p0) REVERT: K 3 GLN cc_start: 0.6024 (OUTLIER) cc_final: 0.5779 (pt0) REVERT: N 2 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6612 (mtp85) REVERT: P 55 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5441 (m90) REVERT: S 82 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.5056 (mtt) REVERT: V 21 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6417 (ttm110) REVERT: X 43 LYS cc_start: 0.6622 (OUTLIER) cc_final: 0.6247 (tptp) REVERT: X 45 PHE cc_start: 0.7181 (OUTLIER) cc_final: 0.6583 (m-10) REVERT: 0 49 ARG cc_start: 0.7205 (ttm110) cc_final: 0.6981 (tpp80) REVERT: 2 8 SER cc_start: 0.7641 (t) cc_final: 0.7337 (m) REVERT: 3 48 MET cc_start: 0.7945 (mmm) cc_final: 0.7584 (mmt) outliers start: 122 outliers final: 87 residues processed: 715 average time/residue: 0.8639 time to fit residues: 1054.6985 Evaluate side-chains 702 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 606 time to evaluate : 3.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 70 ARG Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 11 ASN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 45 PHE Chi-restraints excluded: chain X residue 58 ILE Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 335 optimal weight: 8.9990 chunk 539 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 375 optimal weight: 2.9990 chunk 565 optimal weight: 2.9990 chunk 520 optimal weight: 8.9990 chunk 450 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 348 optimal weight: 7.9990 chunk 276 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS 1 25 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 91786 Z= 0.297 Angle : 0.686 15.572 138070 Z= 0.349 Chirality : 0.037 0.280 17737 Planarity : 0.005 0.092 6884 Dihedral : 23.454 176.678 47637 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.49 % Favored : 89.44 % Rotamer: Outliers : 4.81 % Allowed : 27.78 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.15), residues: 2898 helix: -0.78 (0.19), residues: 699 sheet: -1.01 (0.22), residues: 540 loop : -1.88 (0.14), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.004 TRP F 96 HIS 0.010 0.002 HIS C 52 PHE 0.046 0.002 PHE C 29 TYR 0.029 0.002 TYR S 38 ARG 0.011 0.001 ARG K 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5796 Ramachandran restraints generated. 2898 Oldfield, 0 Emsley, 2898 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 596 time to evaluate : 3.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.5812 (ptp90) REVERT: F 47 LYS cc_start: 0.6438 (OUTLIER) cc_final: 0.5386 (ttpp) REVERT: J 55 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8630 (mt) REVERT: J 131 ASN cc_start: 0.7829 (p0) cc_final: 0.7396 (p0) REVERT: K 3 GLN cc_start: 0.6552 (OUTLIER) cc_final: 0.6088 (pt0) REVERT: N 2 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.7026 (mtp85) REVERT: O 62 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6353 (mm) REVERT: P 55 HIS cc_start: 0.6187 (OUTLIER) cc_final: 0.5466 (m90) REVERT: R 68 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7964 (mtp180) REVERT: S 82 MET cc_start: 0.5723 (OUTLIER) cc_final: 0.5147 (mtt) REVERT: X 45 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6684 (m-10) REVERT: 0 54 ILE cc_start: 0.6005 (mm) cc_final: 0.5626 (mm) REVERT: 2 8 SER cc_start: 0.7950 (t) cc_final: 0.7504 (m) REVERT: 3 30 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7056 (p90) REVERT: 3 48 MET cc_start: 0.8007 (mmm) cc_final: 0.7569 (mmt) outliers start: 115 outliers final: 96 residues processed: 665 average time/residue: 0.8000 time to fit residues: 908.7243 Evaluate side-chains 699 residues out of total 2392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 592 time to evaluate : 2.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain E residue 24 ASN Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 176 ASP Chi-restraints excluded: chain E residue 189 THR Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 76 PHE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 17 VAL Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 93 ILE Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain K residue 3 GLN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 84 CYS Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain N residue 2 ARG Chi-restraints excluded: chain N residue 10 LEU Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 74 GLU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 87 ILE Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 12 MET Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain Q residue 29 ARG Chi-restraints excluded: chain Q residue 40 LYS Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain Q residue 103 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 64 VAL Chi-restraints excluded: chain R residue 68 ARG Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 82 MET Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 54 THR Chi-restraints excluded: chain W residue 63 VAL Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 43 LYS Chi-restraints excluded: chain X residue 45 PHE Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 19 ASP Chi-restraints excluded: chain 0 residue 45 ASP Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 60 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 357 optimal weight: 0.0270 chunk 480 optimal weight: 8.9990 chunk 138 optimal weight: 10.0000 chunk 415 optimal weight: 8.9990 chunk 66 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 451 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 463 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 overall best weight: 7.6050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN ** J 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** 0 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.125679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.099386 restraints weight = 212976.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.101880 restraints weight = 74797.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.103364 restraints weight = 40605.498| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 91786 Z= 0.394 Angle : 0.796 16.347 138070 Z= 0.402 Chirality : 0.042 0.292 17737 Planarity : 0.006 0.095 6884 Dihedral : 23.685 177.661 47637 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 26.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.22 % Favored : 87.72 % Rotamer: Outliers : 5.27 % Allowed : 27.74 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.22 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.14), residues: 2898 helix: -1.13 (0.19), residues: 704 sheet: -1.22 (0.22), residues: 538 loop : -2.09 (0.14), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP F 96 HIS 0.012 0.002 HIS C 52 PHE 0.026 0.003 PHE D 127 TYR 0.033 0.003 TYR S 38 ARG 0.011 0.001 ARG P 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16776.71 seconds wall clock time: 298 minutes 51.24 seconds (17931.24 seconds total)