Starting phenix.real_space_refine on Tue Feb 20 16:24:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc8_4383/02_2024/6gc8_4383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc8_4383/02_2024/6gc8_4383.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/6gc8_4383/02_2024/6gc8_4383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc8_4383/02_2024/6gc8_4383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc8_4383/02_2024/6gc8_4383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gc8_4383/02_2024/6gc8_4383.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= 0.070 sd= 0.537 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3015 5.49 5 Mg 5 5.21 5 S 70 5.16 5 C 43984 2.51 5 N 16558 2.21 5 O 25251 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 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 "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 114": "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-5238/modules/chem_data/mon_lib" Total number of atoms: 88884 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 62195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 276, 'rna2p_pyr': 148, 'rna3p_pur': 1396, 'rna3p_pyr': 1077} Link IDs: {'rna2p': 424, 'rna3p': 2472} Chain breaks: 3 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: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 417 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} 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: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} 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} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 34.44, per 1000 atoms: 0.39 Number of scatterers: 88884 At special positions: 0 Unit cell: (213.28, 209.56, 219.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 70 16.00 P 3015 15.00 Mg 5 11.99 O 25251 8.00 N 16558 7.00 C 43984 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: 39.31 Conformation dependent library (CDL) restraints added in 3.8 seconds 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5628 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 45 sheets defined 28.3% alpha, 20.5% beta 812 base pairs and 1766 stacking pairs defined. Time for finding SS restraints: 32.39 Creating SS restraints... Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.353A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG C 202 " --> pdb=" O HIS C 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.978A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.410A 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 removed outlier: 3.812A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 39 removed outlier: 3.517A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.778A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 removed outlier: 3.567A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 160 Processing helix chain 'E' and resid 178 through 183 removed outlier: 3.957A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 3.751A 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: 3.795A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE F 19 " --> pdb=" O LEU F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.581A pdb=" N VAL F 27 " --> pdb=" O VAL F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 60 removed outlier: 3.647A pdb=" N ASP F 50 " --> pdb=" O LYS F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 removed outlier: 3.539A pdb=" N ILE F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE F 105 " --> pdb=" O ARG F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.516A pdb=" N LEU F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU F 169 " --> pdb=" O GLY F 165 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE F 172 " --> pdb=" O LEU F 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 80 removed outlier: 3.504A pdb=" N ALA G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL G 78 " --> pdb=" O MET G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.736A pdb=" N GLY G 141 " --> pdb=" O LYS G 137 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN G 142 " --> pdb=" O GLN G 138 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 54 removed outlier: 4.027A pdb=" N GLU H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.806A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG J 37 " --> pdb=" O ALA J 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 removed outlier: 3.576A pdb=" N VAL J 62 " --> pdb=" O ALA J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 removed outlier: 3.582A pdb=" N ALA J 94 " --> pdb=" O GLU J 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 107 removed outlier: 4.390A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 3.626A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 removed outlier: 3.599A 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: 3.545A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.842A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 72 removed outlier: 3.673A pdb=" N ALA L 72 " --> pdb=" O ARG L 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 69 through 72' Processing helix chain 'L' and resid 128 through 136 removed outlier: 3.758A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) Processing helix chain 'L' and resid 137 through 139 No H-bonds generated for 'chain 'L' and resid 137 through 139' Processing helix chain 'M' and resid 43 through 55 removed outlier: 3.721A pdb=" N ARG M 55 " --> pdb=" O ARG M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 122 removed outlier: 3.541A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.726A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.508A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 69 removed outlier: 3.583A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 removed outlier: 3.790A pdb=" N VAL N 76 " --> pdb=" O ASP N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 removed outlier: 3.525A pdb=" N ARG N 86 " --> pdb=" O GLU N 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 3.758A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU O 18 " --> pdb=" O ALA O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.547A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 55 through 60' Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.681A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 10 removed outlier: 3.818A pdb=" N GLN P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 101 removed outlier: 3.606A pdb=" N ARG P 100 " --> pdb=" O TYR P 97 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 108 removed outlier: 3.984A pdb=" N ARG P 108 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 20 removed outlier: 3.556A pdb=" N ALA Q 9 " --> pdb=" O ARG Q 5 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE Q 16 " --> pdb=" O ARG Q 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.008A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE Q 39 " --> pdb=" O PHE Q 35 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS Q 40 " --> pdb=" O GLN Q 36 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG Q 57 " --> pdb=" O LYS Q 53 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA Q 62 " --> pdb=" O GLN Q 58 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.555A pdb=" N ALA Q 98 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.822A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.830A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 removed outlier: 3.680A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.552A pdb=" N ALA S 56 " --> pdb=" O GLU S 52 " (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 Processing helix chain 'T' and resid 17 through 26 removed outlier: 3.647A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.544A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 22 removed outlier: 4.319A pdb=" N ALA V 16 " --> pdb=" O GLN V 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 51 removed outlier: 3.546A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 removed outlier: 3.522A pdb=" N TYR V 57 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 62 removed outlier: 3.922A pdb=" N ARG X 56 " --> pdb=" O ALA X 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 73 Processing helix chain 'Y' and resid 2 through 6 removed outlier: 3.603A pdb=" N GLU Y 5 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU Y 6 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 2 through 6' Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.520A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 23 through 34 removed outlier: 3.514A pdb=" N ASN Y 27 " --> pdb=" O ARG Y 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU Y 28 " --> pdb=" O GLU Y 24 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 45 removed outlier: 3.898A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 46 through 56 removed outlier: 3.670A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.594A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 16 Processing helix chain '2' and resid 8 through 17 removed outlier: 3.720A pdb=" N ARG 2 14 " --> pdb=" O LEU 2 10 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER 2 15 " --> pdb=" O LYS 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 23 removed outlier: 3.704A pdb=" N ARG 2 21 " --> pdb=" O GLY 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.566A pdb=" N VAL 2 30 " --> pdb=" O ASN 2 26 " (cutoff:3.500A) Processing helix chain '3' and resid 6 through 11 Processing helix chain '3' and resid 36 through 42 removed outlier: 3.863A pdb=" N HIS 3 42 " --> pdb=" O LYS 3 38 " (cutoff:3.500A) Processing helix chain '3' and resid 50 through 52 No H-bonds generated for 'chain '3' and resid 50 through 52' Processing helix chain '3' and resid 53 through 61 removed outlier: 3.564A pdb=" N VAL 3 57 " --> pdb=" O ASP 3 53 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE 3 58 " --> pdb=" O LEU 3 54 " (cutoff:3.500A) removed outlier: 3.958A 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: 3.589A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 104 removed outlier: 3.632A pdb=" N ARG C 101 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (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: 5.776A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG C 181 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 6.785A 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 15 removed outlier: 5.917A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL D 189 " --> pdb=" O THR D 25 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP D 176 " --> pdb=" O LYS D 190 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL D 107 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.747A pdb=" N ALA D 47 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL D 37 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 118 through 119 removed outlier: 3.597A pdb=" N GLY D 163 " --> pdb=" O ALA D 119 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 3 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.421A pdb=" N ILE E 119 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR E 189 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.690A pdb=" N LEU F 65 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 87 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY F 85 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR F 156 " --> pdb=" O GLU F 31 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE F 33 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR F 154 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 17 through 18 removed outlier: 3.805A pdb=" N ILE G 23 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG G 34 " --> pdb=" O ILE G 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 43 removed outlier: 3.603A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 120 through 126 removed outlier: 7.294A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY G 134 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE G 82 " --> pdb=" O GLY G 134 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL G 89 " --> pdb=" O GLY G 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 94 through 98 Processing sheet with id=AB7, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AB8, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.645A pdb=" N ILE J 54 " --> pdb=" O LYS J 123 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC1, first strand: chain 'K' and resid 7 through 10 removed outlier: 3.740A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU K 45 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL K 19 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE K 43 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N CYS K 21 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE K 41 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N LYS K 23 " --> pdb=" O ILE K 39 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE K 39 " --> pdb=" O LYS K 23 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU K 58 " --> pdb=" O ILE K 41 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL K 63 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 77 through 79 removed outlier: 6.681A pdb=" N ALA P 57 " --> pdb=" O ILE P 49 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE P 49 " --> pdb=" O ALA P 57 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N THR P 59 " --> pdb=" O ILE P 47 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ILE P 63 " --> pdb=" O GLU P 43 " (cutoff:3.500A) removed outlier: 9.290A pdb=" N GLU P 43 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 74 through 76 removed outlier: 3.929A pdb=" N LYS L 109 " --> pdb=" O ALA L 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 89 through 90 removed outlier: 5.919A pdb=" N VAL L 90 " --> pdb=" O ARG L 123 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N VAL L 122 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'M' and resid 62 through 65 removed outlier: 6.506A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU M 104 " --> pdb=" O PHE M 31 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE M 31 " --> pdb=" O GLU M 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 39 through 42 removed outlier: 3.583A pdb=" N GLY M 39 " --> pdb=" O ILE M 96 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL M 89 " --> pdb=" O GLU M 75 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU M 75 " --> pdb=" O VAL M 89 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR M 91 " --> pdb=" O ILE M 73 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 33 through 37 removed outlier: 3.501A pdb=" N THR N 36 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 47 through 50 removed outlier: 6.625A pdb=" N VAL O 39 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ALA O 50 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ALA O 37 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 89 through 90 removed outlier: 4.328A pdb=" N LYS P 110 " --> pdb=" O ALA P 90 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.774A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N TYR R 2 " --> pdb=" O ILE R 41 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE R 41 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL R 4 " --> pdb=" O LEU R 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 19 through 23 removed outlier: 7.025A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE R 101 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL R 58 " --> pdb=" O ILE R 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'R' and resid 72 through 74 Processing sheet with id=AD4, first strand: chain 'R' and resid 77 through 78 removed outlier: 3.540A pdb=" N ARG R 78 " --> pdb=" O TYR R 83 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'S' and resid 2 through 10 removed outlier: 5.792A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ASP S 94 " --> pdb=" O ILE S 85 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE S 85 " --> pdb=" O ASP S 94 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE S 96 " --> pdb=" O LYS S 83 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS S 83 " --> pdb=" O ILE S 96 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.694A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N VAL T 31 " --> pdb=" O PRO T 14 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL T 57 " --> pdb=" O THR T 86 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.913A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'U' and resid 40 through 45 removed outlier: 4.252A pdb=" N GLY U 56 " --> pdb=" O GLN U 45 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.682A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 2 through 8 removed outlier: 8.132A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN V 87 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'W' and resid 18 through 19 removed outlier: 7.306A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'W' and resid 26 through 27 removed outlier: 6.740A pdb=" N HIS W 42 " --> pdb=" O ILE W 76 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N ILE W 78 " --> pdb=" O HIS W 42 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.623A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.900A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Z' and resid 34 through 38 Processing sheet with id=AE7, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain '1' and resid 19 through 24 removed outlier: 3.542A pdb=" N LYS 1 24 " --> pdb=" O GLU 1 6 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU 1 6 " --> pdb=" O LYS 1 24 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS 1 37 " --> pdb=" O VAL 1 46 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU 1 35 " --> pdb=" O TYR 1 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '3' and resid 14 through 15 removed outlier: 3.508A pdb=" N HIS 3 23 " --> pdb=" O ALA 3 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA 3 47 " --> pdb=" O HIS 3 23 " (cutoff:3.500A) 721 hydrogen bonds defined for protein. 2028 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1961 hydrogen bonds 3064 hydrogen bond angles 0 basepair planarities 812 basepair parallelities 1766 stacking parallelities Total time for adding SS restraints: 153.04 Time building geometry restraints manager: 42.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13791 1.33 - 1.45: 40883 1.45 - 1.57: 36097 1.57 - 1.69: 6026 1.69 - 1.81: 130 Bond restraints: 96927 Sorted by residual: bond pdb=" C GLN U 53 " pdb=" N PRO U 54 " ideal model delta sigma weight residual 1.336 1.395 -0.060 1.23e-02 6.61e+03 2.35e+01 bond pdb=" C VAL F 107 " pdb=" N PRO F 108 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.25e-02 6.40e+03 1.47e+01 bond pdb=" C LEU N 38 " pdb=" N PRO N 39 " ideal model delta sigma weight residual 1.336 1.382 -0.046 1.23e-02 6.61e+03 1.40e+01 bond pdb=" C LYS D 62 " pdb=" N PRO D 63 " ideal model delta sigma weight residual 1.335 1.383 -0.047 1.36e-02 5.41e+03 1.21e+01 bond pdb=" CB ASN U 98 " pdb=" CG ASN U 98 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.50e-02 1.60e+03 3.86e+00 ... (remaining 96922 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.89: 18389 106.89 - 114.30: 61587 114.30 - 121.71: 42482 121.71 - 129.11: 21423 129.11 - 136.52: 1954 Bond angle restraints: 145835 Sorted by residual: angle pdb=" C SER U 97 " pdb=" N ASN U 98 " pdb=" CA ASN U 98 " ideal model delta sigma weight residual 121.54 136.52 -14.98 1.91e+00 2.74e-01 6.15e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 133.71 -12.01 1.80e+00 3.09e-01 4.45e+01 angle pdb=" N GLN H 33 " pdb=" CA GLN H 33 " pdb=" C GLN H 33 " ideal model delta sigma weight residual 113.02 103.18 9.84 1.49e+00 4.50e-01 4.36e+01 angle pdb=" C GLN Y 45 " pdb=" N VAL Y 46 " pdb=" CA VAL Y 46 " ideal model delta sigma weight residual 121.97 132.43 -10.46 1.80e+00 3.09e-01 3.38e+01 angle pdb=" C3' A A1378 " pdb=" O3' A A1378 " pdb=" P U A1379 " ideal model delta sigma weight residual 120.20 127.77 -7.57 1.50e+00 4.44e-01 2.55e+01 ... (remaining 145830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.69: 54597 35.69 - 71.38: 6724 71.38 - 107.07: 781 107.07 - 142.75: 5 142.75 - 178.44: 12 Dihedral angle restraints: 62119 sinusoidal: 53371 harmonic: 8748 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 -113.20 -66.80 0 5.00e+00 4.00e-02 1.78e+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 -121.62 -58.38 0 5.00e+00 4.00e-02 1.36e+02 dihedral pdb=" CA PHE F 174 " pdb=" C PHE F 174 " pdb=" N PRO F 175 " pdb=" CA PRO F 175 " ideal model delta harmonic sigma weight residual -180.00 -128.98 -51.02 0 5.00e+00 4.00e-02 1.04e+02 ... (remaining 62116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 17929 0.064 - 0.128: 721 0.128 - 0.193: 70 0.193 - 0.257: 13 0.257 - 0.321: 8 Chirality restraints: 18741 Sorted by residual: chirality pdb=" C3' G A2304 " pdb=" C4' G A2304 " pdb=" O3' G A2304 " pdb=" C2' G A2304 " both_signs ideal model delta sigma weight residual False -2.48 -2.16 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB ILE J 84 " pdb=" CA ILE J 84 " pdb=" CG1 ILE J 84 " pdb=" CG2 ILE J 84 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" C3' C A2326 " pdb=" C4' C A2326 " pdb=" O3' C A2326 " pdb=" C2' C A2326 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 18738 not shown) Planarity restraints: 7243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 151 " 0.063 5.00e-02 4.00e+02 9.60e-02 1.48e+01 pdb=" N PRO D 152 " -0.166 5.00e-02 4.00e+02 pdb=" CA PRO D 152 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO D 152 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 11 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C GLY C 11 " 0.049 2.00e-02 2.50e+03 pdb=" O GLY C 11 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 12 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 149 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C ASN D 149 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN D 149 " -0.017 2.00e-02 2.50e+03 pdb=" N GLN D 150 " -0.016 2.00e-02 2.50e+03 ... (remaining 7240 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 4589 2.68 - 3.24: 70835 3.24 - 3.79: 180952 3.79 - 4.35: 239794 4.35 - 4.90: 313190 Nonbonded interactions: 809360 Sorted by model distance: nonbonded pdb=" O4 U B 95 " pdb="MG MG B 202 " model vdw 2.129 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 313 " model vdw 2.145 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 314 " model vdw 2.146 2.170 nonbonded pdb="MG MG B 201 " pdb=" O HOH B 306 " model vdw 2.155 2.170 nonbonded pdb="MG MG B 202 " pdb=" O HOH B 304 " model vdw 2.157 2.170 ... (remaining 809355 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=1.00 max=1.00 mean=1.00 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 8.000 Check model and map are aligned: 0.960 Set scattering table: 0.640 Process input model: 323.760 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.240 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 339.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5829 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 0.060 96927 Z= 0.141 Angle : 0.569 14.975 145835 Z= 0.324 Chirality : 0.029 0.321 18741 Planarity : 0.005 0.096 7243 Dihedral : 22.480 178.444 56491 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.29 % Favored : 93.51 % Rotamer: Outliers : 0.16 % Allowed : 3.60 % Favored : 96.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 4.12 % Twisted General : 0.30 % 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: -4.04 (0.12), residues: 3036 helix: -4.28 (0.08), residues: 730 sheet: -1.55 (0.20), residues: 568 loop : -2.38 (0.12), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 212 HIS 0.005 0.001 HIS 3 30 PHE 0.019 0.002 PHE U 94 TYR 0.017 0.002 TYR M 103 ARG 0.009 0.001 ARG W 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1305 time to evaluate : 3.577 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: 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 123 ILE cc_start: 0.7076 (mm) cc_final: 0.6860 (mm) REVERT: E 199 MET cc_start: 0.6679 (ttt) cc_final: 0.6375 (ttp) REVERT: Q 87 VAL cc_start: 0.7512 (t) cc_final: 0.7234 (t) REVERT: V 2 PHE cc_start: 0.5237 (m-80) cc_final: 0.4950 (m-80) REVERT: X 73 ARG cc_start: 0.5989 (ptt180) cc_final: 0.5772 (ptt180) REVERT: 1 12 SER cc_start: 0.6355 (t) cc_final: 0.6068 (m) REVERT: 1 33 LEU cc_start: 0.5938 (tp) cc_final: 0.5649 (tp) outliers start: 4 outliers final: 1 residues processed: 1308 average time/residue: 1.0093 time to fit residues: 2102.0753 Evaluate side-chains 787 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 786 time to evaluate : 3.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 51 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 504 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 251 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 305 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 468 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 285 optimal weight: 20.0000 chunk 348 optimal weight: 30.0000 chunk 543 optimal weight: 4.9990 overall best weight: 10.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 HIS ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN D 49 GLN D 67 HIS ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 94 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 HIS F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN G 142 GLN H 20 ASN ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 ASN J 128 ASN J 136 GLN K 29 HIS L 54 GLN ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 11 GLN P 76 HIS Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS S 102 HIS T 28 ASN U 65 GLN V 24 ASN ** W 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 33 HIS Y 39 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 42 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 96927 Z= 0.498 Angle : 0.982 15.499 145835 Z= 0.491 Chirality : 0.048 0.325 18741 Planarity : 0.008 0.115 7243 Dihedral : 23.863 178.762 50443 Min Nonbonded Distance : 1.681 Molprobity Statistics. All-atom Clashscore : 38.75 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.83 % Favored : 90.65 % Rotamer: Outliers : 7.95 % Allowed : 19.90 % Favored : 72.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 3.09 % Twisted General : 0.27 % 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: -2.98 (0.13), residues: 3036 helix: -1.94 (0.15), residues: 786 sheet: -1.46 (0.19), residues: 587 loop : -2.21 (0.13), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.005 TRP Q 60 HIS 0.017 0.003 HIS G 114 PHE 0.033 0.004 PHE D 118 TYR 0.028 0.003 TYR S 38 ARG 0.015 0.001 ARG G 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 846 time to evaluate : 3.617 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: C 59 GLN cc_start: 0.6651 (mt0) cc_final: 0.6272 (mt0) REVERT: C 113 ASP cc_start: 0.4412 (OUTLIER) cc_final: 0.4072 (m-30) REVERT: D 208 LYS cc_start: 0.6917 (mttm) cc_final: 0.6544 (mttm) REVERT: E 51 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5423 (mp0) REVERT: F 127 TYR cc_start: 0.4180 (t80) cc_final: 0.3468 (t80) REVERT: G 44 HIS cc_start: 0.5387 (t70) cc_final: 0.4862 (t-170) REVERT: M 80 VAL cc_start: 0.8128 (OUTLIER) cc_final: 0.7906 (t) REVERT: O 31 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7347 (m) REVERT: Q 14 LYS cc_start: 0.6920 (tttt) cc_final: 0.6607 (mtpt) REVERT: Q 48 ASP cc_start: 0.5964 (m-30) cc_final: 0.5709 (m-30) REVERT: R 2 TYR cc_start: 0.6621 (OUTLIER) cc_final: 0.6181 (p90) REVERT: S 9 HIS cc_start: 0.8377 (OUTLIER) cc_final: 0.7316 (m-70) REVERT: T 5 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7757 (tm-30) REVERT: V 24 ASN cc_start: 0.5362 (t0) cc_final: 0.5074 (t0) REVERT: V 85 LYS cc_start: 0.6333 (mtpp) cc_final: 0.5108 (mtpp) REVERT: X 10 ARG cc_start: 0.6901 (tpp80) cc_final: 0.6669 (tpp80) REVERT: Y 17 GLU cc_start: 0.6451 (tm-30) cc_final: 0.6219 (tm-30) REVERT: Y 38 GLN cc_start: 0.7783 (pm20) cc_final: 0.6599 (pm20) outliers start: 199 outliers final: 129 residues processed: 953 average time/residue: 0.9362 time to fit residues: 1494.2012 Evaluate side-chains 862 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 727 time to evaluate : 3.610 ------------------------------------------------------------------------------- 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 90 ILE Chi-restraints excluded: chain C residue 113 ASP Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 96 TRP Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 ASP Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 66 LYS Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 99 VAL Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 9 HIS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 43 LYS Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 301 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 451 optimal weight: 0.0030 chunk 369 optimal weight: 5.9990 chunk 149 optimal weight: 10.0000 chunk 544 optimal weight: 9.9990 chunk 587 optimal weight: 8.9990 chunk 484 optimal weight: 8.9990 chunk 539 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 436 optimal weight: 7.9990 overall best weight: 6.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 136 GLN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 13 HIS O 29 HIS O 98 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS S 102 HIS ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 45 GLN 0 3 GLN 0 4 GLN ** 2 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 96927 Z= 0.304 Angle : 0.711 12.003 145835 Z= 0.361 Chirality : 0.039 0.281 18741 Planarity : 0.006 0.102 7243 Dihedral : 23.706 179.990 50443 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 25.92 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.73 % Favored : 91.04 % Rotamer: Outliers : 7.95 % Allowed : 24.22 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.20 % 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: -2.60 (0.14), residues: 3036 helix: -1.17 (0.17), residues: 808 sheet: -1.32 (0.21), residues: 535 loop : -2.18 (0.13), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 60 HIS 0.021 0.002 HIS S 9 PHE 0.019 0.002 PHE 3 13 TYR 0.021 0.002 TYR S 38 ARG 0.017 0.001 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 792 time to evaluate : 3.917 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: symmetry clash REVERT: D 88 GLU cc_start: 0.3943 (tp30) cc_final: 0.3493 (tp30) REVERT: D 208 LYS cc_start: 0.7012 (mttm) cc_final: 0.6552 (mttm) REVERT: F 47 LYS cc_start: 0.7663 (mmmm) cc_final: 0.7223 (mmmt) REVERT: F 163 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7605 (mm-30) REVERT: G 44 HIS cc_start: 0.5230 (t70) cc_final: 0.4716 (t-170) REVERT: H 1 MET cc_start: 0.3001 (pmm) cc_final: 0.1990 (pmm) REVERT: K 13 ASN cc_start: 0.6694 (p0) cc_final: 0.6133 (p0) REVERT: L 3 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5876 (mp) REVERT: M 58 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6848 (mtmm) REVERT: O 17 LYS cc_start: 0.5420 (OUTLIER) cc_final: 0.4841 (tptp) REVERT: O 21 LEU cc_start: 0.6173 (mm) cc_final: 0.5868 (mm) REVERT: R 40 MET cc_start: 0.5202 (tpt) cc_final: 0.4632 (tpt) REVERT: R 79 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6507 (ptt-90) REVERT: S 29 VAL cc_start: 0.7216 (t) cc_final: 0.6900 (t) REVERT: X 10 ARG cc_start: 0.6935 (tpp80) cc_final: 0.6632 (tpp80) REVERT: X 71 ARG cc_start: 0.7400 (mmp80) cc_final: 0.6624 (mtm-85) REVERT: 0 24 VAL cc_start: 0.5728 (OUTLIER) cc_final: 0.5524 (p) REVERT: 1 7 LYS cc_start: 0.5453 (mttt) cc_final: 0.5241 (mttp) REVERT: 3 30 HIS cc_start: 0.6087 (OUTLIER) cc_final: 0.5409 (p90) REVERT: 3 51 LYS cc_start: 0.7264 (ttpp) cc_final: 0.6715 (tptm) outliers start: 199 outliers final: 145 residues processed: 892 average time/residue: 0.9082 time to fit residues: 1359.8731 Evaluate side-chains 869 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 717 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 72 ASN Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 94 TYR Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 17 LYS Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 79 ILE Chi-restraints excluded: chain Q residue 87 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 1 residue 11 VAL Chi-restraints excluded: chain 1 residue 23 THR Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 60 CYS Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 537 optimal weight: 4.9990 chunk 409 optimal weight: 7.9990 chunk 282 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 259 optimal weight: 20.0000 chunk 365 optimal weight: 10.0000 chunk 545 optimal weight: 7.9990 chunk 578 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 517 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN D 149 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 ASN H 33 GLN J 136 GLN L 99 ASN ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 29 HIS ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 65 ASN Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 58 GLN R 18 GLN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 15 ASN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 6 GLN 2 26 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6480 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 96927 Z= 0.242 Angle : 0.645 11.354 145835 Z= 0.331 Chirality : 0.036 0.263 18741 Planarity : 0.005 0.101 7243 Dihedral : 23.638 178.331 50443 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 23.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.39 % Favored : 90.42 % Rotamer: Outliers : 8.27 % Allowed : 25.50 % Favored : 66.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.27 % 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: -2.35 (0.14), residues: 3036 helix: -0.87 (0.17), residues: 799 sheet: -1.21 (0.22), residues: 520 loop : -2.06 (0.13), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 60 HIS 0.008 0.002 HIS R 82 PHE 0.025 0.002 PHE H 47 TYR 0.018 0.002 TYR S 38 ARG 0.009 0.001 ARG S 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 980 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 773 time to evaluate : 3.709 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: D 28 GLU cc_start: 0.3908 (tp30) cc_final: 0.3443 (tp30) REVERT: D 208 LYS cc_start: 0.7035 (mttm) cc_final: 0.6555 (mttm) REVERT: F 37 MET cc_start: 0.4945 (ttm) cc_final: 0.4540 (ttm) REVERT: F 47 LYS cc_start: 0.7674 (mmmm) cc_final: 0.7296 (mmmt) REVERT: F 141 ASP cc_start: 0.4026 (t0) cc_final: 0.3778 (t0) REVERT: H 1 MET cc_start: 0.3362 (pmm) cc_final: 0.1800 (pmm) REVERT: K 13 ASN cc_start: 0.6340 (p0) cc_final: 0.5982 (p0) REVERT: K 88 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6754 (m-40) REVERT: L 3 LEU cc_start: 0.5951 (mp) cc_final: 0.5690 (mp) REVERT: L 55 MET cc_start: 0.7152 (tpp) cc_final: 0.6901 (tpp) REVERT: M 1 MET cc_start: 0.4212 (OUTLIER) cc_final: 0.3657 (mmm) REVERT: P 80 VAL cc_start: 0.4688 (OUTLIER) cc_final: 0.4277 (p) REVERT: P 92 ARG cc_start: 0.6006 (mpp-170) cc_final: 0.5787 (mpp-170) REVERT: R 2 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5983 (p90) REVERT: T 43 ILE cc_start: 0.8286 (mp) cc_final: 0.8079 (mp) REVERT: T 63 VAL cc_start: 0.7311 (OUTLIER) cc_final: 0.7016 (t) REVERT: T 79 ASP cc_start: 0.4600 (OUTLIER) cc_final: 0.4399 (m-30) REVERT: U 66 VAL cc_start: 0.5169 (OUTLIER) cc_final: 0.4930 (t) REVERT: X 10 ARG cc_start: 0.6862 (tpp80) cc_final: 0.6574 (tpp80) REVERT: X 73 ARG cc_start: 0.7688 (ptt180) cc_final: 0.6615 (ttp80) REVERT: 3 51 LYS cc_start: 0.7382 (ttpp) cc_final: 0.6995 (tptm) outliers start: 207 outliers final: 153 residues processed: 878 average time/residue: 0.9273 time to fit residues: 1383.9121 Evaluate side-chains 872 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 712 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 33 GLN Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 115 ILE Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 17 LYS Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 86 SER Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 8 ASN Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 33 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 481 optimal weight: 1.9990 chunk 328 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 430 optimal weight: 3.9990 chunk 238 optimal weight: 10.0000 chunk 493 optimal weight: 10.0000 chunk 399 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 518 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS D 149 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 76 HIS J 128 ASN N 73 ASN O 29 HIS ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.5922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 96927 Z= 0.248 Angle : 0.648 14.199 145835 Z= 0.330 Chirality : 0.036 0.303 18741 Planarity : 0.005 0.101 7243 Dihedral : 23.659 178.867 50443 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.20 % Allowed : 9.78 % Favored : 90.02 % Rotamer: Outliers : 8.47 % Allowed : 26.98 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.20 % 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: -2.22 (0.14), residues: 3036 helix: -0.75 (0.18), residues: 791 sheet: -1.04 (0.22), residues: 505 loop : -2.02 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 80 HIS 0.014 0.002 HIS R 12 PHE 0.039 0.002 PHE 2 18 TYR 0.025 0.002 TYR E 101 ARG 0.007 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 746 time to evaluate : 3.646 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: symmetry clash revert: symmetry clash REVERT: C 145 MET cc_start: 0.5945 (tmm) cc_final: 0.5553 (tmm) REVERT: D 208 LYS cc_start: 0.6997 (mttm) cc_final: 0.6586 (mttm) REVERT: F 37 MET cc_start: 0.4555 (ttm) cc_final: 0.4156 (ttm) REVERT: F 153 ILE cc_start: 0.7322 (pt) cc_final: 0.7074 (pt) REVERT: G 25 ILE cc_start: 0.6660 (tt) cc_final: 0.6446 (mt) REVERT: H 1 MET cc_start: 0.4014 (pmm) cc_final: 0.2315 (pmm) REVERT: H 2 GLN cc_start: 0.6378 (tp-100) cc_final: 0.6140 (tp40) REVERT: K 13 ASN cc_start: 0.6358 (p0) cc_final: 0.5861 (p0) REVERT: K 88 ASN cc_start: 0.6895 (OUTLIER) cc_final: 0.6442 (m-40) REVERT: L 55 MET cc_start: 0.7131 (tpp) cc_final: 0.6387 (tpp) REVERT: L 60 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4661 (mtt180) REVERT: M 1 MET cc_start: 0.4083 (OUTLIER) cc_final: 0.3352 (mmm) REVERT: N 24 MET cc_start: 0.6025 (mmt) cc_final: 0.5371 (mmm) REVERT: P 80 VAL cc_start: 0.4818 (OUTLIER) cc_final: 0.4447 (p) REVERT: P 92 ARG cc_start: 0.6089 (mpp-170) cc_final: 0.5821 (mpp-170) REVERT: Q 110 GLU cc_start: 0.5599 (tp30) cc_final: 0.5306 (tp30) REVERT: R 79 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6493 (ptt-90) REVERT: T 1 MET cc_start: 0.5376 (pmm) cc_final: 0.5171 (pmm) REVERT: T 63 VAL cc_start: 0.7596 (OUTLIER) cc_final: 0.7242 (t) REVERT: T 79 ASP cc_start: 0.4775 (OUTLIER) cc_final: 0.4498 (m-30) REVERT: U 66 VAL cc_start: 0.5920 (t) cc_final: 0.5639 (t) REVERT: U 86 PHE cc_start: 0.6173 (OUTLIER) cc_final: 0.5911 (t80) REVERT: V 24 ASN cc_start: 0.5178 (t0) cc_final: 0.4926 (t0) REVERT: X 10 ARG cc_start: 0.6938 (tpp80) cc_final: 0.6558 (tpp80) REVERT: X 71 ARG cc_start: 0.7726 (mmp80) cc_final: 0.6438 (mtm-85) REVERT: Z 10 ARG cc_start: 0.7263 (mtm-85) cc_final: 0.6880 (mtm-85) REVERT: 3 51 LYS cc_start: 0.7433 (ttpp) cc_final: 0.6938 (tptm) outliers start: 212 outliers final: 172 residues processed: 855 average time/residue: 0.9465 time to fit residues: 1378.8822 Evaluate side-chains 893 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 713 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE 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 90 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 123 LYS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 71 LYS Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 1 residue 11 VAL 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 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 194 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 339 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 480 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 191 optimal weight: 30.0000 chunk 303 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 149 ASN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 136 GLN N 9 GLN N 62 ASN N 73 ASN O 29 HIS ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 51 GLN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.6518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 96927 Z= 0.350 Angle : 0.765 13.113 145835 Z= 0.387 Chirality : 0.041 0.403 18741 Planarity : 0.006 0.109 7243 Dihedral : 23.872 179.897 50443 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 30.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.23 % Favored : 88.54 % Rotamer: Outliers : 9.51 % Allowed : 27.74 % Favored : 62.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.27 % 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: -2.41 (0.14), residues: 3036 helix: -0.82 (0.17), residues: 782 sheet: -1.21 (0.22), residues: 516 loop : -2.16 (0.13), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 80 HIS 0.013 0.002 HIS R 12 PHE 0.030 0.003 PHE 2 18 TYR 0.019 0.002 TYR S 38 ARG 0.010 0.001 ARG U 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 734 time to evaluate : 3.624 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: C 90 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5896 (mt) REVERT: C 200 MET cc_start: 0.5337 (OUTLIER) cc_final: 0.3983 (tpp) REVERT: D 208 LYS cc_start: 0.6871 (mttm) cc_final: 0.6483 (mttm) REVERT: F 93 GLU cc_start: 0.5759 (mm-30) cc_final: 0.5407 (mp0) REVERT: F 127 TYR cc_start: 0.5155 (t80) cc_final: 0.4849 (t80) REVERT: G 25 ILE cc_start: 0.6780 (tt) cc_final: 0.6559 (mt) REVERT: H 1 MET cc_start: 0.4027 (pmm) cc_final: 0.2446 (pmm) REVERT: H 2 GLN cc_start: 0.6791 (tp-100) cc_final: 0.6543 (tp-100) REVERT: K 13 ASN cc_start: 0.6610 (p0) cc_final: 0.5953 (p0) REVERT: K 88 ASN cc_start: 0.7109 (OUTLIER) cc_final: 0.6661 (m-40) REVERT: K 92 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: L 55 MET cc_start: 0.7187 (tpp) cc_final: 0.6148 (tpp) REVERT: L 60 ARG cc_start: 0.5141 (OUTLIER) cc_final: 0.4601 (mtt180) REVERT: M 59 ARG cc_start: 0.7225 (mmp80) cc_final: 0.7007 (mpt180) REVERT: M 100 LYS cc_start: 0.6755 (tppt) cc_final: 0.6263 (tptt) REVERT: O 31 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.6978 (m) REVERT: P 80 VAL cc_start: 0.5179 (OUTLIER) cc_final: 0.4881 (p) REVERT: Q 56 PHE cc_start: 0.6896 (OUTLIER) cc_final: 0.5693 (m-10) REVERT: Q 60 TRP cc_start: 0.7549 (m-10) cc_final: 0.7232 (m-90) REVERT: Q 110 GLU cc_start: 0.5784 (tp30) cc_final: 0.5473 (tp30) REVERT: R 79 ARG cc_start: 0.7145 (OUTLIER) cc_final: 0.6531 (ptt-90) REVERT: S 102 HIS cc_start: 0.7378 (m-70) cc_final: 0.7081 (m-70) REVERT: T 1 MET cc_start: 0.5411 (pmm) cc_final: 0.5198 (pmm) REVERT: U 66 VAL cc_start: 0.5808 (t) cc_final: 0.5546 (t) REVERT: U 86 PHE cc_start: 0.6197 (OUTLIER) cc_final: 0.5979 (t80) REVERT: V 24 ASN cc_start: 0.5103 (t0) cc_final: 0.4789 (t0) REVERT: W 11 ASP cc_start: 0.6314 (t70) cc_final: 0.6056 (t70) REVERT: W 79 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6428 (mm-30) REVERT: Y 47 ARG cc_start: 0.6960 (tmm-80) cc_final: 0.6717 (tmm-80) REVERT: Z 53 MET cc_start: 0.5705 (ptm) cc_final: 0.5065 (ptp) REVERT: 3 51 LYS cc_start: 0.7652 (ttpp) cc_final: 0.7282 (tptm) outliers start: 238 outliers final: 191 residues processed: 861 average time/residue: 0.8753 time to fit residues: 1278.4633 Evaluate side-chains 912 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 710 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE 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 90 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 200 MET Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 152 ASP Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 92 GLU Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 60 ARG Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 54 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 14 LYS Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 79 ARG Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 108 SER 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 63 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 86 PHE Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain W residue 79 GLU Chi-restraints excluded: chain X residue 5 GLN Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 38 GLU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 9 ARG Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 11 VAL 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 26 ASN Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 54 LEU Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 557 optimal weight: 9.9990 chunk 65 optimal weight: 20.0000 chunk 329 optimal weight: 6.9990 chunk 422 optimal weight: 3.9990 chunk 327 optimal weight: 7.9990 chunk 487 optimal weight: 0.5980 chunk 323 optimal weight: 5.9990 chunk 576 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 351 optimal weight: 10.0000 chunk 266 optimal weight: 10.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 ASN E 29 HIS ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 136 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS V 51 GLN ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN 2 29 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 96927 Z= 0.179 Angle : 0.604 12.651 145835 Z= 0.308 Chirality : 0.034 0.424 18741 Planarity : 0.005 0.113 7243 Dihedral : 23.684 177.770 50443 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.99 % Favored : 90.91 % Rotamer: Outliers : 6.67 % Allowed : 31.25 % Favored : 62.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.20 % 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: -2.09 (0.14), residues: 3036 helix: -0.46 (0.18), residues: 792 sheet: -1.04 (0.22), residues: 519 loop : -2.00 (0.14), residues: 1725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 80 HIS 0.011 0.001 HIS R 12 PHE 0.032 0.002 PHE 2 18 TYR 0.021 0.001 TYR S 38 ARG 0.007 0.001 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 746 time to evaluate : 3.788 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: C 145 MET cc_start: 0.5570 (tmm) cc_final: 0.5302 (tmm) REVERT: D 208 LYS cc_start: 0.6873 (mttm) cc_final: 0.6524 (mttm) REVERT: H 1 MET cc_start: 0.3564 (pmm) cc_final: 0.2381 (pmm) REVERT: H 2 GLN cc_start: 0.6810 (tp-100) cc_final: 0.6581 (tp40) REVERT: K 13 ASN cc_start: 0.6419 (p0) cc_final: 0.5855 (p0) REVERT: L 55 MET cc_start: 0.7089 (tpp) cc_final: 0.6593 (tpp) REVERT: M 100 LYS cc_start: 0.6735 (tppt) cc_final: 0.6287 (tptt) REVERT: N 24 MET cc_start: 0.5961 (mmt) cc_final: 0.5413 (mmm) REVERT: O 31 THR cc_start: 0.7272 (OUTLIER) cc_final: 0.6837 (m) REVERT: P 92 ARG cc_start: 0.6242 (mpp-170) cc_final: 0.5973 (mpp-170) REVERT: Q 60 TRP cc_start: 0.7290 (m-10) cc_final: 0.7027 (m-90) REVERT: Q 110 GLU cc_start: 0.5558 (tp30) cc_final: 0.5266 (tp30) REVERT: S 109 ASP cc_start: 0.6258 (p0) cc_final: 0.5690 (t70) REVERT: T 1 MET cc_start: 0.5338 (pmm) cc_final: 0.5138 (pmm) REVERT: T 63 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7104 (t) REVERT: T 79 ASP cc_start: 0.4855 (OUTLIER) cc_final: 0.4588 (m-30) REVERT: V 24 ASN cc_start: 0.4982 (t0) cc_final: 0.4736 (t0) REVERT: W 11 ASP cc_start: 0.6153 (t70) cc_final: 0.5862 (t70) REVERT: Y 4 LYS cc_start: 0.6352 (mmtt) cc_final: 0.6104 (mmtm) REVERT: Z 53 MET cc_start: 0.5517 (ptm) cc_final: 0.4822 (ptp) REVERT: 1 7 LYS cc_start: 0.5515 (mttt) cc_final: 0.5182 (mttp) REVERT: 2 22 MET cc_start: 0.7850 (mmm) cc_final: 0.7571 (tpt) REVERT: 3 30 HIS cc_start: 0.6050 (OUTLIER) cc_final: 0.5668 (p90) REVERT: 3 51 LYS cc_start: 0.7487 (ttpp) cc_final: 0.6884 (tptm) outliers start: 167 outliers final: 134 residues processed: 840 average time/residue: 0.8810 time to fit residues: 1252.0446 Evaluate side-chains 850 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 712 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 41 LYS Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 52 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 70 ARG Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain P residue 1 SER Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain T residue 88 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 54 ILE 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 26 ASN Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 356 optimal weight: 10.0000 chunk 230 optimal weight: 30.0000 chunk 344 optimal weight: 4.9990 chunk 173 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 392 optimal weight: 20.0000 chunk 284 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 453 optimal weight: 9.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 44 ASN ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 136 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 ASN O 100 HIS P 2 ASN Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 65 ASN R 43 ASN ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 HIS ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 96927 Z= 0.402 Angle : 0.809 12.767 145835 Z= 0.406 Chirality : 0.043 0.479 18741 Planarity : 0.006 0.116 7243 Dihedral : 23.940 179.776 50443 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 32.84 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.99 % Favored : 87.78 % Rotamer: Outliers : 8.35 % Allowed : 29.54 % Favored : 62.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.27 % 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: 3036 helix: -0.87 (0.17), residues: 792 sheet: -1.38 (0.22), residues: 533 loop : -2.19 (0.14), residues: 1711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 80 HIS 0.014 0.002 HIS R 12 PHE 0.037 0.003 PHE O 117 TYR 0.027 0.002 TYR S 38 ARG 0.020 0.001 ARG U 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 724 time to evaluate : 3.655 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: E 101 TYR cc_start: 0.4962 (t80) cc_final: 0.4742 (t80) REVERT: E 164 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6971 (mm) REVERT: H 1 MET cc_start: 0.4097 (pmm) cc_final: 0.2593 (pmm) REVERT: K 13 ASN cc_start: 0.6783 (p0) cc_final: 0.6082 (p0) REVERT: M 136 MET cc_start: 0.5396 (tmm) cc_final: 0.4921 (tmm) REVERT: Q 56 PHE cc_start: 0.6901 (OUTLIER) cc_final: 0.6219 (m-10) REVERT: Q 60 TRP cc_start: 0.7538 (m-10) cc_final: 0.7236 (m-90) REVERT: Q 110 GLU cc_start: 0.5867 (tp30) cc_final: 0.5566 (tp30) REVERT: R 2 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6620 (p90) REVERT: R 74 ILE cc_start: 0.7552 (mp) cc_final: 0.7343 (mp) REVERT: S 36 LEU cc_start: 0.7179 (mp) cc_final: 0.6938 (mt) REVERT: T 1 MET cc_start: 0.5620 (pmm) cc_final: 0.5402 (pmm) REVERT: T 63 VAL cc_start: 0.7620 (OUTLIER) cc_final: 0.7277 (t) REVERT: W 11 ASP cc_start: 0.6448 (t70) cc_final: 0.6215 (t70) REVERT: X 9 LYS cc_start: 0.5693 (mmmt) cc_final: 0.5475 (mmmt) REVERT: Z 53 MET cc_start: 0.5680 (ptm) cc_final: 0.4835 (ptp) REVERT: 3 51 LYS cc_start: 0.7446 (ttpp) cc_final: 0.7163 (tptm) outliers start: 209 outliers final: 169 residues processed: 842 average time/residue: 0.9491 time to fit residues: 1361.5082 Evaluate side-chains 878 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 705 time to evaluate : 3.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE 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 90 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 50 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain R residue 101 ILE Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 74 ILE 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 60 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain T residue 79 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 22 PHE Chi-restraints excluded: chain W residue 46 ASN Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 16 ASN Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 11 VAL 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 26 ASN Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 32 LEU Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 524 optimal weight: 8.9990 chunk 552 optimal weight: 8.9990 chunk 503 optimal weight: 9.9990 chunk 537 optimal weight: 8.9990 chunk 323 optimal weight: 0.9990 chunk 233 optimal weight: 20.0000 chunk 421 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 485 optimal weight: 6.9990 chunk 507 optimal weight: 4.9990 chunk 535 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN N 73 ASN P 55 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 96927 Z= 0.290 Angle : 0.711 14.306 145835 Z= 0.361 Chirality : 0.039 0.481 18741 Planarity : 0.005 0.119 7243 Dihedral : 23.887 178.760 50443 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 27.57 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.44 % Favored : 89.33 % Rotamer: Outliers : 7.07 % Allowed : 31.45 % Favored : 61.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.30 % 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: -2.47 (0.14), residues: 3036 helix: -0.84 (0.18), residues: 792 sheet: -1.41 (0.22), residues: 529 loop : -2.17 (0.14), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 61 HIS 0.013 0.002 HIS R 12 PHE 0.032 0.003 PHE E 158 TYR 0.028 0.002 TYR F 127 ARG 0.018 0.001 ARG U 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 718 time to evaluate : 4.351 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 145 MET cc_start: 0.5936 (tmm) cc_final: 0.5576 (tmm) REVERT: H 1 MET cc_start: 0.3665 (pmm) cc_final: 0.2279 (pmm) REVERT: K 7 MET cc_start: 0.6390 (tpt) cc_final: 0.6123 (tpt) REVERT: L 6 LEU cc_start: 0.6924 (tp) cc_final: 0.6713 (tp) REVERT: L 55 MET cc_start: 0.7307 (tpp) cc_final: 0.7051 (tpp) REVERT: M 100 LYS cc_start: 0.6738 (tppt) cc_final: 0.6211 (tptt) REVERT: M 136 MET cc_start: 0.5384 (tmm) cc_final: 0.4986 (tmm) REVERT: Q 56 PHE cc_start: 0.6817 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: Q 110 GLU cc_start: 0.5747 (tp30) cc_final: 0.5452 (tp30) REVERT: R 2 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6769 (p90) REVERT: R 74 ILE cc_start: 0.7563 (mp) cc_final: 0.7339 (mp) REVERT: S 36 LEU cc_start: 0.7150 (mp) cc_final: 0.6925 (mt) REVERT: X 69 GLU cc_start: 0.7076 (mm-30) cc_final: 0.6861 (mp0) REVERT: Z 53 MET cc_start: 0.5782 (ptm) cc_final: 0.4882 (ptp) REVERT: 0 45 ASP cc_start: 0.5892 (p0) cc_final: 0.5651 (p0) REVERT: 3 51 LYS cc_start: 0.7523 (ttpp) cc_final: 0.7099 (tptm) outliers start: 177 outliers final: 161 residues processed: 819 average time/residue: 0.9303 time to fit residues: 1305.2473 Evaluate side-chains 866 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 703 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE 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 90 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 124 CYS Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 120 ARG Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 38 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 74 ILE 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 79 ASP Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 47 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 25 GLN Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 22 THR Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 21 THR Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 352 optimal weight: 0.9990 chunk 567 optimal weight: 4.9990 chunk 346 optimal weight: 9.9990 chunk 269 optimal weight: 10.0000 chunk 394 optimal weight: 30.0000 chunk 595 optimal weight: 10.0000 chunk 548 optimal weight: 5.9990 chunk 474 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 290 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 136 GLN N 23 ASN N 62 ASN N 73 ASN P 55 HIS Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 29 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.7140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 96927 Z= 0.225 Angle : 0.654 14.561 145835 Z= 0.332 Chirality : 0.036 0.444 18741 Planarity : 0.005 0.119 7243 Dihedral : 23.791 177.869 50443 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.30 % Favored : 88.54 % Rotamer: Outliers : 6.75 % Allowed : 31.93 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.30 % 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: -2.38 (0.14), residues: 3036 helix: -0.69 (0.18), residues: 793 sheet: -1.27 (0.22), residues: 516 loop : -2.18 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 61 HIS 0.014 0.002 HIS P 55 PHE 0.035 0.002 PHE E 158 TYR 0.028 0.002 TYR F 127 ARG 0.016 0.001 ARG U 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6072 Ramachandran restraints generated. 3036 Oldfield, 0 Emsley, 3036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 721 time to evaluate : 3.767 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: C 145 MET cc_start: 0.5739 (tmm) cc_final: 0.5337 (tmm) REVERT: D 204 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5561 (ttmt) REVERT: F 84 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7972 (mm) REVERT: F 163 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6689 (mm-30) REVERT: H 1 MET cc_start: 0.3576 (pmm) cc_final: 0.2243 (pmm) REVERT: L 55 MET cc_start: 0.7554 (tpp) cc_final: 0.7155 (tpp) REVERT: M 136 MET cc_start: 0.5413 (tmm) cc_final: 0.5023 (tmm) REVERT: N 23 ASN cc_start: 0.7319 (OUTLIER) cc_final: 0.6678 (t0) REVERT: O 17 LYS cc_start: 0.5558 (tptp) cc_final: 0.5322 (tptp) REVERT: P 92 ARG cc_start: 0.6532 (mpp-170) cc_final: 0.6152 (mpp-170) REVERT: Q 32 ARG cc_start: 0.7023 (mtt180) cc_final: 0.6470 (mtp180) REVERT: Q 56 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6218 (m-10) REVERT: Q 110 GLU cc_start: 0.5634 (tp30) cc_final: 0.5351 (tp30) REVERT: R 2 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6698 (p90) REVERT: R 37 GLU cc_start: 0.6349 (pm20) cc_final: 0.6118 (pm20) REVERT: R 95 ASP cc_start: 0.3856 (t0) cc_final: 0.3438 (t70) REVERT: X 69 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6867 (mp0) REVERT: Y 24 GLU cc_start: 0.4413 (OUTLIER) cc_final: 0.3105 (mp0) REVERT: Z 53 MET cc_start: 0.5477 (ptm) cc_final: 0.4958 (ptp) REVERT: 3 35 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6953 (mmtm) REVERT: 3 51 LYS cc_start: 0.7451 (ttpp) cc_final: 0.7159 (tptm) outliers start: 169 outliers final: 156 residues processed: 819 average time/residue: 0.8810 time to fit residues: 1223.9210 Evaluate side-chains 860 residues out of total 2504 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 697 time to evaluate : 3.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 24 HIS Chi-restraints excluded: chain C residue 53 ILE 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 133 ASN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 173 LEU Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 260 LYS Chi-restraints excluded: chain C residue 263 ASP Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 12 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 32 ASN Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 127 PHE Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 84 ILE Chi-restraints excluded: chain F residue 87 LYS Chi-restraints excluded: chain F residue 155 ILE Chi-restraints excluded: chain F residue 163 GLU Chi-restraints excluded: chain F residue 176 PHE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 54 ARG Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 ASP Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 64 VAL Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 75 SER Chi-restraints excluded: chain K residue 95 ILE Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 10 GLU Chi-restraints excluded: chain L residue 35 HIS Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 42 THR Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 67 VAL Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain N residue 6 SER Chi-restraints excluded: chain N residue 23 ASN Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 73 ASN Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 LYS Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 5 SER Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain P residue 15 ASP Chi-restraints excluded: chain P residue 35 SER Chi-restraints excluded: chain P residue 52 ARG Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 72 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 81 ASP Chi-restraints excluded: chain Q residue 17 LEU Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 56 PHE Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 2 TYR Chi-restraints excluded: chain R residue 12 HIS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 12 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL 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 79 ASP Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 51 LEU Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 66 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 30 ILE Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 89 ILE Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain X residue 15 ASN Chi-restraints excluded: chain X residue 32 LEU Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 67 LEU Chi-restraints excluded: chain Y residue 24 GLU Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 54 VAL Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 3 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 37 HIS Chi-restraints excluded: chain 0 residue 54 ILE Chi-restraints excluded: chain 1 residue 11 VAL 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 26 ASN Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain 3 residue 3 ILE Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 30 HIS Chi-restraints excluded: chain 3 residue 61 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 376 optimal weight: 9.9990 chunk 505 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 437 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 475 optimal weight: 0.0670 chunk 198 optimal weight: 10.0000 chunk 487 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 overall best weight: 6.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 29 HIS ** H 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN J 136 GLN L 54 GLN N 23 ASN N 62 ASN N 73 ASN P 55 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** 0 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.104301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.085028 restraints weight = 294473.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.087487 restraints weight = 102331.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.088873 restraints weight = 52652.315| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 96927 Z= 0.294 Angle : 0.717 13.703 145835 Z= 0.362 Chirality : 0.039 0.418 18741 Planarity : 0.006 0.118 7243 Dihedral : 23.843 178.529 50443 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 28.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.73 % Favored : 88.08 % Rotamer: Outliers : 7.35 % Allowed : 31.41 % Favored : 61.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 2.06 % Twisted General : 0.27 % 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: 3036 helix: -0.83 (0.18), residues: 794 sheet: -1.34 (0.22), residues: 518 loop : -2.24 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 61 HIS 0.016 0.002 HIS Z 33 PHE 0.034 0.003 PHE E 158 TYR 0.023 0.002 TYR J 74 ARG 0.015 0.001 ARG J 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20284.24 seconds wall clock time: 359 minutes 49.43 seconds (21589.43 seconds total)