Starting phenix.real_space_refine on Sun Mar 17 18:03:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wqn_21872/03_2024/6wqn_21872_trim_updated.pdb" } resolution = 2.9 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= 0.001 sd= 0.012 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: 6 Type Number sf(0) Gaussians P 2793 5.49 5 S 53 5.16 5 C 39728 2.51 5 N 14987 2.21 5 O 23136 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 23": "NH1" <-> "NH2" Residue "A ARG 29": "NH1" <-> "NH2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 84": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "B GLU 30": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G GLU 77": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "K GLU 15": "OE1" <-> "OE2" Residue "K GLU 23": "OE1" <-> "OE2" Residue "K GLU 24": "OE1" <-> "OE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "L GLU 32": "OE1" <-> "OE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L GLU 54": "OE1" <-> "OE2" Residue "L TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "L GLU 184": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M GLU 24": "OE1" <-> "OE2" Residue "M GLU 38": "OE1" <-> "OE2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "O GLU 28": "OE1" <-> "OE2" Residue "O GLU 39": "OE1" <-> "OE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "P ARG 4": "NH1" <-> "NH2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "P ARG 34": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 42": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "S GLU 18": "OE1" <-> "OE2" Residue "S GLU 27": "OE1" <-> "OE2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S ARG 107": "NH1" <-> "NH2" Residue "S GLU 120": "OE1" <-> "OE2" Residue "S GLU 147": "OE1" <-> "OE2" Residue "S GLU 157": "OE1" <-> "OE2" Residue "S ARG 168": "NH1" <-> "NH2" Residue "S GLU 196": "OE1" <-> "OE2" Residue "S GLU 203": "OE1" <-> "OE2" Residue "S GLU 204": "OE1" <-> "OE2" Residue "V ARG 2": "NH1" <-> "NH2" Residue "V ARG 14": "NH1" <-> "NH2" Residue "V GLU 22": "OE1" <-> "OE2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V GLU 64": "OE1" <-> "OE2" Residue "V GLU 92": "OE1" <-> "OE2" Residue "V GLU 117": "OE1" <-> "OE2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "W GLU 108": "OE1" <-> "OE2" Residue "W GLU 120": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "X GLU 15": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X GLU 86": "OE1" <-> "OE2" Residue "X GLU 105": "OE1" <-> "OE2" Residue "Y ARG 10": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Y ARG 56": "NH1" <-> "NH2" Residue "Y ARG 60": "NH1" <-> "NH2" Residue "Y GLU 80": "OE1" <-> "OE2" Residue "Y GLU 111": "OE1" <-> "OE2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y GLU 116": "OE1" <-> "OE2" Residue "Y GLU 135": "OE1" <-> "OE2" Residue "Z GLU 28": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z GLU 74": "OE1" <-> "OE2" Residue "Z GLU 76": "OE1" <-> "OE2" Residue "Z GLU 95": "OE1" <-> "OE2" Residue "a GLU 71": "OE1" <-> "OE2" Residue "a GLU 78": "OE1" <-> "OE2" Residue "a GLU 91": "OE1" <-> "OE2" Residue "a GLU 114": "OE1" <-> "OE2" Residue "a GLU 118": "OE1" <-> "OE2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I GLU 25": "OE1" <-> "OE2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I ARG 79": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 80700 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 907 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 4, 'TRANS': 107} Chain: "B" Number of atoms: 2094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2094 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 17, 'TRANS': 256} Chain: "C" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 943 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "D" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 785 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 97} Chain: "E" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 105} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 654 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain breaks: 1 Chain: "G" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 702 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain breaks: 1 Chain: "H" Number of atoms: 727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 727 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 463 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 1, 'TRANS': 57} Chain: "K" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 436 Classifications: {'peptide': 53} Link IDs: {'TRANS': 52} Chain: "L" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1621 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 206} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 432 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "N" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 397 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "O" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 390 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 1, 'TRANS': 45} Chain: "P" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 372 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "Q" Number of atoms: 521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 521 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "R" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 296 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "S" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1472 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 9, 'TRANS': 182} Chain: "V" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1138 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "X" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1082 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain: "Y" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1089 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "Z" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 951 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "1" Number of atoms: 57631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2687, 57631 Inner-chain residues flagged as termini: ['pdbres=" A 1 318 "', 'pdbres=" A 11459 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2687} Modifications used: {'5*END': 4, 'rna2p_pur': 269, 'rna2p_pyr': 127, 'rna3p_pur': 1283, 'rna3p_pyr': 1008} Link IDs: {'rna2p': 396, 'rna3p': 2290} Chain breaks: 8 Chain: "2" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 2358 Classifications: {'RNA': 111} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 50, 'rna3p_pyr': 49} Link IDs: {'rna2p': 12, 'rna3p': 98} Chain: "I" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 597 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "1" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'ZC0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.55, per 1000 atoms: 0.39 Number of scatterers: 80700 At special positions: 0 Unit cell: (210.325, 236.28, 184.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 53 16.00 P 2793 15.00 F 3 9.00 O 23136 8.00 N 14987 7.00 C 39728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 30 " - pdb=" SG CYS N 33 " distance=2.87 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.02 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.05 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: 29.52 Conformation dependent library (CDL) restraints added in 3.5 seconds 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4812 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 42 sheets defined 22.1% alpha, 17.4% beta 531 base pairs and 1502 stacking pairs defined. Time for finding SS restraints: 33.90 Creating SS restraints... Processing helix chain 'A' and resid 5 through 8 No H-bonds generated for 'chain 'A' and resid 5 through 8' Processing helix chain 'A' and resid 12 through 14 No H-bonds generated for 'chain 'A' and resid 12 through 14' Processing helix chain 'A' and resid 100 through 102 No H-bonds generated for 'chain 'A' and resid 100 through 102' Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'B' and resid 265 through 269 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.639A pdb=" N LYS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 Processing helix chain 'C' and resid 32 through 72 removed outlier: 3.665A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA C 67 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N HIS C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 92 through 101 removed outlier: 3.505A pdb=" N GLU C 97 " --> pdb=" O LYS C 93 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 101 " --> pdb=" O GLU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 3.639A pdb=" N LEU C 109 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 110 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR C 111 " --> pdb=" O ALA C 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 removed outlier: 3.824A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 38 Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.542A pdb=" N SER E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 68 No H-bonds generated for 'chain 'E' and resid 66 through 68' Processing helix chain 'F' and resid 35 through 46 removed outlier: 3.593A pdb=" N LYS F 39 " --> pdb=" O LYS F 35 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 67 No H-bonds generated for 'chain 'G' and resid 65 through 67' Processing helix chain 'H' and resid 15 through 24 Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.505A pdb=" N VAL H 51 " --> pdb=" O GLU H 47 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG H 53 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 55 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 18 removed outlier: 3.575A pdb=" N GLN K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 23 through 34 Processing helix chain 'K' and resid 40 through 60 removed outlier: 4.384A pdb=" N ARG K 44 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR K 45 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS K 48 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE K 50 " --> pdb=" O ARG K 47 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS K 54 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL K 56 " --> pdb=" O LEU K 53 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA K 57 " --> pdb=" O LYS K 54 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG K 58 " --> pdb=" O THR K 55 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG K 60 " --> pdb=" O ALA K 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 80 removed outlier: 3.870A pdb=" N HIS L 76 " --> pdb=" O PRO L 72 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA L 77 " --> pdb=" O ALA L 73 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ALA L 80 " --> pdb=" O HIS L 76 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 109 No H-bonds generated for 'chain 'L' and resid 107 through 109' Processing helix chain 'L' and resid 130 through 133 No H-bonds generated for 'chain 'L' and resid 130 through 133' Processing helix chain 'M' and resid 17 through 26 removed outlier: 3.647A pdb=" N THR M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU M 24 " --> pdb=" O ARG M 20 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 26 " --> pdb=" O THR M 22 " (cutoff:3.500A) Processing helix chain 'M' and resid 41 through 49 removed outlier: 3.677A pdb=" N GLY M 45 " --> pdb=" O PRO M 41 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS M 49 " --> pdb=" O GLY M 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 18 removed outlier: 3.518A pdb=" N LYS N 15 " --> pdb=" O THR N 11 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 17 removed outlier: 3.584A pdb=" N SER P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 19 through 22 No H-bonds generated for 'chain 'P' and resid 19 through 22' Processing helix chain 'P' and resid 26 through 38 removed outlier: 3.556A pdb=" N LEU P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) Processing helix chain 'Q' and resid 8 through 11 No H-bonds generated for 'chain 'Q' and resid 8 through 11' Processing helix chain 'Q' and resid 33 through 35 No H-bonds generated for 'chain 'Q' and resid 33 through 35' Processing helix chain 'Q' and resid 38 through 45 removed outlier: 3.526A pdb=" N LEU Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG Q 45 " --> pdb=" O LYS Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 52 through 55 No H-bonds generated for 'chain 'Q' and resid 52 through 55' Processing helix chain 'Q' and resid 60 through 62 No H-bonds generated for 'chain 'Q' and resid 60 through 62' Processing helix chain 'R' and resid 30 through 32 No H-bonds generated for 'chain 'R' and resid 30 through 32' Processing helix chain 'S' and resid 30 through 42 removed outlier: 3.933A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 120 removed outlier: 3.551A pdb=" N ALA S 113 " --> pdb=" O ALA S 109 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL S 118 " --> pdb=" O LEU S 114 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU S 120 " --> pdb=" O PHE S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 146 Processing helix chain 'S' and resid 161 through 168 removed outlier: 3.854A pdb=" N ALA S 167 " --> pdb=" O VAL S 163 " (cutoff:3.500A) Processing helix chain 'S' and resid 178 through 180 No H-bonds generated for 'chain 'S' and resid 178 through 180' Processing helix chain 'S' and resid 183 through 188 Processing helix chain 'S' and resid 196 through 205 removed outlier: 3.625A pdb=" N LYS S 200 " --> pdb=" O GLU S 196 " (cutoff:3.500A) Processing helix chain 'V' and resid 26 through 38 removed outlier: 4.332A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N SER V 35 " --> pdb=" O SER V 31 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 62 No H-bonds generated for 'chain 'V' and resid 60 through 62' Processing helix chain 'V' and resid 69 through 72 No H-bonds generated for 'chain 'V' and resid 69 through 72' Processing helix chain 'V' and resid 90 through 94 Processing helix chain 'V' and resid 98 through 109 removed outlier: 3.586A pdb=" N ILE V 102 " --> pdb=" O PRO V 98 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N MET V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 114 through 121 removed outlier: 3.811A pdb=" N LYS V 118 " --> pdb=" O ARG V 114 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS V 121 " --> pdb=" O GLU V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 134 through 136 No H-bonds generated for 'chain 'V' and resid 134 through 136' Processing helix chain 'W' and resid 104 through 109 Processing helix chain 'W' and resid 112 through 117 removed outlier: 3.524A pdb=" N SER W 116 " --> pdb=" O MET W 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 60 No H-bonds generated for 'chain 'X' and resid 57 through 60' Processing helix chain 'X' and resid 93 through 99 removed outlier: 3.892A pdb=" N GLU X 98 " --> pdb=" O ALA X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 132 through 136 Processing helix chain 'Y' and resid 44 through 58 removed outlier: 3.627A pdb=" N ALA Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N MET Y 54 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) Processing helix chain 'Y' and resid 113 through 117 Processing helix chain 'Y' and resid 119 through 122 No H-bonds generated for 'chain 'Y' and resid 119 through 122' Processing helix chain 'Z' and resid 10 through 27 removed outlier: 3.617A pdb=" N LYS Z 14 " --> pdb=" O SER Z 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA Z 15 " --> pdb=" O ASP Z 11 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU Z 17 " --> pdb=" O ARG Z 13 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 51 removed outlier: 4.008A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU Z 47 " --> pdb=" O VAL Z 43 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE Z 48 " --> pdb=" O VAL Z 44 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR Z 49 " --> pdb=" O GLU Z 45 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 64 removed outlier: 3.675A pdb=" N ALA Z 63 " --> pdb=" O ARG Z 59 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS Z 64 " --> pdb=" O ARG Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 84 No H-bonds generated for 'chain 'Z' and resid 81 through 84' Processing helix chain 'a' and resid 7 through 20 removed outlier: 4.010A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR a 20 " --> pdb=" O ALA a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 70 through 86 removed outlier: 3.717A pdb=" N GLU a 78 " --> pdb=" O THR a 74 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA a 79 " --> pdb=" O LYS a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 113 Processing sheet with id= A, first strand: chain 'A' and resid 85 through 90 removed outlier: 3.880A pdb=" N LYS A 85 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 87 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR A 27 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR A 60 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 3 through 5 Processing sheet with id= C, first strand: chain 'B' and resid 34 through 36 Processing sheet with id= D, first strand: chain 'B' and resid 114 through 116 removed outlier: 6.576A pdb=" N LEU B 93 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ILE B 81 " --> pdb=" O ILE B 91 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 129 through 131 Processing sheet with id= F, first strand: chain 'B' and resid 171 through 175 Processing sheet with id= G, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.753A pdb=" N PHE D 2 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE D 40 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N GLU D 6 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N VAL D 38 " --> pdb=" O GLU D 6 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 19 through 22 removed outlier: 3.608A pdb=" N ILE D 20 " --> pdb=" O LEU D 95 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY D 66 " --> pdb=" O TYR D 92 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS D 64 " --> pdb=" O LYS D 94 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 32 through 35 removed outlier: 3.653A pdb=" N VAL D 58 " --> pdb=" O PHE D 35 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.465A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 3 through 7 removed outlier: 6.367A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N VAL E 71 " --> pdb=" O SER E 108 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 82 through 87 Processing sheet with id= M, first strand: chain 'F' and resid 52 through 57 removed outlier: 3.554A pdb=" N LYS F 77 " --> pdb=" O MET F 56 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG F 9 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 9 through 11 Processing sheet with id= O, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.538A pdb=" N LYS G 43 " --> pdb=" O LEU G 57 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 81 through 83 Processing sheet with id= Q, first strand: chain 'G' and resid 23 through 27 removed outlier: 6.714A pdb=" N VAL G 34 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N THR G 26 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG G 32 " --> pdb=" O THR G 26 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 39 through 44 removed outlier: 3.765A pdb=" N VAL H 39 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL H 31 " --> pdb=" O VAL H 39 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL H 43 " --> pdb=" O VAL H 27 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS H 88 " --> pdb=" O GLN H 78 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASP H 76 " --> pdb=" O ASP H 90 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU H 92 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N VAL H 74 " --> pdb=" O LEU H 92 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 63 through 65 Processing sheet with id= T, first strand: chain 'J' and resid 13 through 18 Processing sheet with id= U, first strand: chain 'J' and resid 33 through 38 Processing sheet with id= V, first strand: chain 'L' and resid 177 through 180 removed outlier: 4.765A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N MET L 12 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N VAL L 25 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLN L 14 " --> pdb=" O ILE L 23 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE L 23 " --> pdb=" O GLN L 14 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL L 194 " --> pdb=" O ASP L 189 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP L 189 " --> pdb=" O VAL L 194 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLN L 187 " --> pdb=" O LEU L 196 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LYS L 198 " --> pdb=" O VAL L 185 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL L 185 " --> pdb=" O LYS L 198 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.630A pdb=" N ILE L 49 " --> pdb=" O PHE L 91 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLN L 37 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY L 52 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL L 35 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 126 through 128 Processing sheet with id= Y, first strand: chain 'M' and resid 34 through 37 removed outlier: 3.563A pdb=" N THR M 7 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'N' and resid 27 through 29 Processing sheet with id= AA, first strand: chain 'O' and resid 2 through 7 Processing sheet with id= AB, first strand: chain 'O' and resid 33 through 36 removed outlier: 3.599A pdb=" N LYS O 41 " --> pdb=" O CYS O 36 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 14 through 16 Processing sheet with id= AD, first strand: chain 'R' and resid 15 through 18 Processing sheet with id= AE, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.713A pdb=" N LEU S 192 " --> pdb=" O THR S 124 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N VAL S 126 " --> pdb=" O LEU S 192 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ILE S 194 " --> pdb=" O VAL S 126 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR S 195 " --> pdb=" O VAL S 155 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'V' and resid 16 through 20 removed outlier: 6.529A pdb=" N TYR V 54 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ILE V 19 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ILE V 56 " --> pdb=" O ILE V 19 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'V' and resid 74 through 78 removed outlier: 3.565A pdb=" N ARG V 77 " --> pdb=" O LYS V 86 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'W' and resid 7 through 9 removed outlier: 6.568A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'X' and resid 75 through 77 Processing sheet with id= AJ, first strand: chain 'X' and resid 90 through 92 removed outlier: 6.673A pdb=" N THR X 122 " --> pdb=" O VAL X 91 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'Y' and resid 129 through 133 removed outlier: 4.148A pdb=" N PHE Y 104 " --> pdb=" O LEU Y 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA Y 36 " --> pdb=" O ILE Y 102 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ILE Y 102 " --> pdb=" O ALA Y 36 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'Y' and resid 40 through 43 removed outlier: 3.541A pdb=" N SER Y 40 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL Y 97 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TYR Y 74 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N TRP Y 93 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N THR Y 72 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'Z' and resid 29 through 33 removed outlier: 3.842A pdb=" N GLY Z 107 " --> pdb=" O SER Z 116 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE Z 118 " --> pdb=" O LYS Z 105 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS Z 105 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU Z 120 " --> pdb=" O ILE Z 103 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE Z 103 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'a' and resid 92 through 94 removed outlier: 3.751A pdb=" N ALA a 56 " --> pdb=" O ALA a 42 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA a 54 " --> pdb=" O ILE a 44 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP a 46 " --> pdb=" O THR a 52 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N THR a 52 " --> pdb=" O ASP a 46 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 59 through 61 Processing sheet with id= AP, first strand: chain 'I' and resid 74 through 79 476 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1253 hydrogen bonds 1928 hydrogen bond angles 0 basepair planarities 531 basepair parallelities 1502 stacking parallelities Total time for adding SS restraints: 102.11 Time building geometry restraints manager: 32.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6939 1.31 - 1.44: 40598 1.44 - 1.56: 34946 1.56 - 1.69: 5578 1.69 - 1.81: 92 Bond restraints: 88153 Sorted by residual: bond pdb=" C LYS N 5 " pdb=" N ARG N 6 " ideal model delta sigma weight residual 1.330 1.453 -0.123 1.45e-02 4.76e+03 7.19e+01 bond pdb=" C ARG X 71 " pdb=" N LYS X 72 " ideal model delta sigma weight residual 1.330 1.417 -0.088 1.32e-02 5.74e+03 4.40e+01 bond pdb=" C ARG N 6 " pdb=" N ARG N 7 " ideal model delta sigma weight residual 1.330 1.416 -0.086 1.31e-02 5.83e+03 4.33e+01 bond pdb=" C ASN X 70 " pdb=" N ARG X 71 " ideal model delta sigma weight residual 1.331 1.415 -0.084 1.44e-02 4.82e+03 3.43e+01 bond pdb=" N ILE G 24 " pdb=" CA ILE G 24 " ideal model delta sigma weight residual 1.457 1.493 -0.037 9.30e-03 1.16e+04 1.55e+01 ... (remaining 88148 not shown) Histogram of bond angle deviations from ideal: 96.84 - 104.32: 11641 104.32 - 111.81: 48663 111.81 - 119.29: 30358 119.29 - 126.77: 34174 126.77 - 134.25: 7971 Bond angle restraints: 132807 Sorted by residual: angle pdb=" C4' A 1 254 " pdb=" C3' A 1 254 " pdb=" O3' A 1 254 " ideal model delta sigma weight residual 113.00 128.88 -15.88 1.50e+00 4.44e-01 1.12e+02 angle pdb=" N ASP L 159 " pdb=" CA ASP L 159 " pdb=" C ASP L 159 " ideal model delta sigma weight residual 111.07 99.78 11.29 1.07e+00 8.73e-01 1.11e+02 angle pdb=" C4' A 12078 " pdb=" C3' A 12078 " pdb=" O3' A 12078 " ideal model delta sigma weight residual 109.40 96.84 12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" C4' G 11405 " pdb=" C3' G 11405 " pdb=" O3' G 11405 " ideal model delta sigma weight residual 113.00 124.51 -11.51 1.50e+00 4.44e-01 5.89e+01 angle pdb=" C4' G 12850 " pdb=" C3' G 12850 " pdb=" O3' G 12850 " ideal model delta sigma weight residual 113.00 124.48 -11.48 1.50e+00 4.44e-01 5.86e+01 ... (remaining 132802 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 49486 36.00 - 72.00: 6118 72.00 - 108.00: 686 108.00 - 144.00: 14 144.00 - 180.00: 12 Dihedral angle restraints: 56316 sinusoidal: 48829 harmonic: 7487 Sorted by residual: dihedral pdb=" O4' U 1 556 " pdb=" C1' U 1 556 " pdb=" N1 U 1 556 " pdb=" C2 U 1 556 " ideal model delta sinusoidal sigma weight residual -160.00 12.76 -172.76 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 1 895 " pdb=" C1' U 1 895 " pdb=" N1 U 1 895 " pdb=" C2 U 1 895 " ideal model delta sinusoidal sigma weight residual -160.00 9.56 -169.56 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" CB CYS N 33 " pdb=" SG CYS N 33 " pdb=" SG CYS N 43 " pdb=" CB CYS N 43 " ideal model delta sinusoidal sigma weight residual -86.00 -168.85 82.85 1 1.00e+01 1.00e-02 8.41e+01 ... (remaining 56313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 16590 0.095 - 0.189: 420 0.189 - 0.284: 92 0.284 - 0.379: 13 0.379 - 0.473: 8 Chirality restraints: 17123 Sorted by residual: chirality pdb=" C3' G 11466 " pdb=" C4' G 11466 " pdb=" O3' G 11466 " pdb=" C2' G 11466 " both_signs ideal model delta sigma weight residual False -2.48 -2.00 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" C3' U 12557 " pdb=" C4' U 12557 " pdb=" O3' U 12557 " pdb=" C2' U 12557 " both_signs ideal model delta sigma weight residual False -2.48 -2.05 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" C3' A 1 254 " pdb=" C4' A 1 254 " pdb=" O3' A 1 254 " pdb=" C2' A 1 254 " both_signs ideal model delta sigma weight residual False -2.48 -2.06 -0.42 2.00e-01 2.50e+01 4.39e+00 ... (remaining 17120 not shown) Planarity restraints: 6394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 102 " 0.023 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C LEU A 102 " -0.081 2.00e-02 2.50e+03 pdb=" O LEU A 102 " 0.030 2.00e-02 2.50e+03 pdb=" N ARG A 103 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A 1 254 " -0.038 2.00e-02 2.50e+03 2.29e-02 1.44e+01 pdb=" N9 A 1 254 " 0.064 2.00e-02 2.50e+03 pdb=" C8 A 1 254 " -0.011 2.00e-02 2.50e+03 pdb=" N7 A 1 254 " -0.004 2.00e-02 2.50e+03 pdb=" C5 A 1 254 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 1 254 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A 1 254 " -0.002 2.00e-02 2.50e+03 pdb=" N1 A 1 254 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A 1 254 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A 1 254 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A 1 254 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 12850 " -0.036 2.00e-02 2.50e+03 1.83e-02 1.00e+01 pdb=" N9 G 12850 " 0.050 2.00e-02 2.50e+03 pdb=" C8 G 12850 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 12850 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 12850 " -0.005 2.00e-02 2.50e+03 pdb=" C6 G 12850 " -0.005 2.00e-02 2.50e+03 pdb=" O6 G 12850 " -0.002 2.00e-02 2.50e+03 pdb=" N1 G 12850 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G 12850 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 12850 " -0.002 2.00e-02 2.50e+03 pdb=" N3 G 12850 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G 12850 " 0.004 2.00e-02 2.50e+03 ... (remaining 6391 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 325 2.54 - 3.13: 54839 3.13 - 3.72: 136386 3.72 - 4.31: 217033 4.31 - 4.90: 289833 Nonbonded interactions: 698416 Sorted by model distance: nonbonded pdb=" OG1 THR a 68 " pdb=" OP2 A 2 48 " model vdw 1.951 2.440 nonbonded pdb=" O2' A 2 46 " pdb=" O4' C 2 47 " model vdw 1.962 2.440 nonbonded pdb=" OP1 C 11865 " pdb=" O2' A 11954 " model vdw 1.996 2.440 nonbonded pdb=" O2' G 1 101 " pdb=" OP2 A 1 102 " model vdw 2.013 2.440 nonbonded pdb=" O2' A 1 229 " pdb=" OP1 A 1 230 " model vdw 2.035 2.440 ... (remaining 698411 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 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: 0.100 Extract box with map and model: 16.940 Check model and map are aligned: 0.910 Set scattering table: 0.550 Process input model: 247.460 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 284.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 88153 Z= 0.188 Angle : 0.496 17.499 132807 Z= 0.356 Chirality : 0.034 0.473 17123 Planarity : 0.003 0.047 6394 Dihedral : 23.060 179.997 51495 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.31 % Allowed : 25.63 % Favored : 72.06 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.14), residues: 2590 helix: -2.86 (0.17), residues: 596 sheet: -1.39 (0.21), residues: 546 loop : -2.35 (0.13), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 213 HIS 0.004 0.001 HIS V 133 PHE 0.012 0.001 PHE A 76 TYR 0.007 0.001 TYR F 71 ARG 0.004 0.000 ARG O 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 460 time to evaluate : 3.142 Fit side-chains revert: symmetry clash REVERT: A 12 LYS cc_start: 0.7808 (ttpt) cc_final: 0.7459 (ttpt) REVERT: A 14 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7659 (mt0) REVERT: C 41 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8723 (tttt) REVERT: D 6 GLU cc_start: 0.6425 (tt0) cc_final: 0.6035 (tp30) REVERT: D 71 ILE cc_start: 0.8046 (mt) cc_final: 0.7767 (mp) REVERT: F 4 ARG cc_start: 0.6831 (ttp-170) cc_final: 0.6414 (ttm170) REVERT: G 4 LYS cc_start: 0.6312 (mttt) cc_final: 0.5693 (pptt) REVERT: G 7 ASP cc_start: 0.6802 (p0) cc_final: 0.6481 (p0) REVERT: J 14 THR cc_start: 0.7940 (m) cc_final: 0.7696 (p) REVERT: J 20 HIS cc_start: 0.7328 (t-90) cc_final: 0.7084 (t70) REVERT: M 5 GLN cc_start: 0.7561 (tt0) cc_final: 0.7235 (tp40) REVERT: M 29 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5709 (mptt) REVERT: P 10 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8547 (ttmm) REVERT: V 9 GLU cc_start: 0.6373 (tt0) cc_final: 0.6158 (tp30) REVERT: V 80 ASN cc_start: 0.7706 (m-40) cc_final: 0.7305 (m-40) REVERT: W 30 ARG cc_start: 0.8308 (ttt180) cc_final: 0.8072 (ttt180) REVERT: Y 45 ARG cc_start: 0.7104 (mtp85) cc_final: 0.6735 (mtt90) REVERT: Y 63 LYS cc_start: 0.6704 (mmmm) cc_final: 0.6432 (mtpp) REVERT: Y 116 GLU cc_start: 0.6999 (tp30) cc_final: 0.6796 (tp30) REVERT: Z 89 ILE cc_start: 0.8098 (mm) cc_final: 0.7482 (mt) outliers start: 51 outliers final: 14 residues processed: 499 average time/residue: 1.7709 time to fit residues: 1150.6639 Evaluate side-chains 386 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 368 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLN Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 451 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 273 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 419 optimal weight: 10.0000 chunk 162 optimal weight: 0.3980 chunk 254 optimal weight: 10.0000 chunk 312 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 overall best weight: 6.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 ASN G 45 GLN L 50 GLN N 45 ASN P 27 ASN V 97 ASN V 131 HIS W 110 ASN X 78 ASN X 81 GLN Z 12 GLN I 86 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 88153 Z= 0.442 Angle : 0.913 9.932 132807 Z= 0.455 Chirality : 0.050 0.373 17123 Planarity : 0.007 0.055 6394 Dihedral : 23.465 176.623 46198 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 8.61 % Allowed : 23.19 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.14), residues: 2590 helix: -2.26 (0.17), residues: 630 sheet: -1.00 (0.21), residues: 571 loop : -2.20 (0.13), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 213 HIS 0.011 0.002 HIS R 32 PHE 0.019 0.003 PHE K 30 TYR 0.020 0.003 TYR E 62 ARG 0.010 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 332 time to evaluate : 3.194 Fit side-chains revert: symmetry clash REVERT: A 115 ILE cc_start: 0.6336 (OUTLIER) cc_final: 0.5899 (pp) REVERT: B 13 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7752 (tpt170) REVERT: B 268 LYS cc_start: 0.7473 (OUTLIER) cc_final: 0.6937 (tttm) REVERT: C 97 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6352 (mp0) REVERT: C 101 SER cc_start: 0.7301 (OUTLIER) cc_final: 0.7007 (m) REVERT: D 69 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7600 (tttp) REVERT: D 77 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7787 (mttt) REVERT: D 78 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.7911 (ptp-170) REVERT: E 27 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: E 86 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.8118 (tpp-160) REVERT: G 4 LYS cc_start: 0.6692 (mttt) cc_final: 0.5803 (pptt) REVERT: H 17 ASP cc_start: 0.6289 (m-30) cc_final: 0.6057 (m-30) REVERT: H 19 LYS cc_start: 0.6639 (mtpp) cc_final: 0.6411 (mtpp) REVERT: H 70 ILE cc_start: 0.6531 (OUTLIER) cc_final: 0.6146 (pp) REVERT: K 48 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7213 (mtpp) REVERT: L 123 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7496 (mttp) REVERT: L 168 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8171 (mmtp) REVERT: L 198 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7485 (ttmt) REVERT: P 12 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8294 (tttm) REVERT: V 63 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7667 (pp) REVERT: V 107 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8095 (mptm) REVERT: V 143 LEU cc_start: 0.7280 (mt) cc_final: 0.7053 (mt) REVERT: W 1 MET cc_start: 0.6638 (tmm) cc_final: 0.6304 (tmm) REVERT: W 4 GLN cc_start: 0.6649 (OUTLIER) cc_final: 0.6400 (tm-30) REVERT: W 105 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6086 (mm-30) REVERT: X 5 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7289 (mt-10) REVERT: Y 5 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7802 (mppt) REVERT: Y 63 LYS cc_start: 0.6904 (mmmm) cc_final: 0.6606 (mtpp) REVERT: Y 111 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7106 (tm-30) REVERT: Z 89 ILE cc_start: 0.8080 (mm) cc_final: 0.7808 (mt) outliers start: 190 outliers final: 94 residues processed: 477 average time/residue: 1.6997 time to fit residues: 1069.4668 Evaluate side-chains 441 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 325 time to evaluate : 4.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 94 VAL Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 9 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 73 ASP Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 37 ASN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 71 GLU Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 43 SER Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 270 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 404 optimal weight: 7.9990 chunk 330 optimal weight: 6.9990 chunk 134 optimal weight: 0.0470 chunk 486 optimal weight: 8.9990 chunk 525 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 482 optimal weight: 7.9990 chunk 165 optimal weight: 0.6980 chunk 390 optimal weight: 9.9990 overall best weight: 3.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN F 73 ASN G 44 HIS G 45 GLN L 134 HIS N 32 ASN S 46 GLN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 88153 Z= 0.285 Angle : 0.705 9.896 132807 Z= 0.362 Chirality : 0.041 0.333 17123 Planarity : 0.005 0.053 6394 Dihedral : 23.247 176.630 46175 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.97 % Allowed : 24.46 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.14), residues: 2590 helix: -1.81 (0.19), residues: 629 sheet: -0.74 (0.21), residues: 562 loop : -2.02 (0.13), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 213 HIS 0.006 0.002 HIS R 32 PHE 0.016 0.002 PHE K 30 TYR 0.015 0.002 TYR E 62 ARG 0.005 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 343 time to evaluate : 3.228 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.6008 (OUTLIER) cc_final: 0.5704 (tt0) REVERT: A 115 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5887 (pp) REVERT: B 13 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7802 (tpt170) REVERT: B 163 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7885 (mt0) REVERT: B 247 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7848 (mmp) REVERT: B 268 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7019 (tttm) REVERT: C 97 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: C 101 SER cc_start: 0.7128 (OUTLIER) cc_final: 0.6919 (m) REVERT: C 103 GLU cc_start: 0.5975 (OUTLIER) cc_final: 0.5724 (mt-10) REVERT: D 77 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7708 (mttt) REVERT: F 4 ARG cc_start: 0.6810 (ttp-170) cc_final: 0.6379 (ttm170) REVERT: G 4 LYS cc_start: 0.6567 (mttt) cc_final: 0.5716 (pptt) REVERT: H 17 ASP cc_start: 0.6324 (m-30) cc_final: 0.6110 (m-30) REVERT: H 19 LYS cc_start: 0.6621 (mtpp) cc_final: 0.6410 (mtpp) REVERT: H 26 LYS cc_start: 0.7291 (pttt) cc_final: 0.7085 (ptpt) REVERT: S 27 GLU cc_start: 0.6194 (tt0) cc_final: 0.5981 (tt0) REVERT: S 157 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.6312 (mt-10) REVERT: V 63 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7655 (pp) REVERT: V 143 LEU cc_start: 0.7246 (mt) cc_final: 0.7005 (mt) REVERT: W 4 GLN cc_start: 0.6680 (OUTLIER) cc_final: 0.6469 (tm-30) REVERT: W 80 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7064 (m-30) REVERT: W 105 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.6049 (mm-30) REVERT: X 5 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: X 10 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6610 (tp30) REVERT: Y 63 LYS cc_start: 0.6770 (mmmm) cc_final: 0.6541 (mtpp) REVERT: Y 111 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7162 (tm-30) REVERT: Y 112 GLU cc_start: 0.7157 (mm-30) cc_final: 0.6919 (tp30) REVERT: Z 34 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7114 (tp30) REVERT: Z 55 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.7113 (p0) REVERT: Z 89 ILE cc_start: 0.8100 (mm) cc_final: 0.7590 (mt) REVERT: I 19 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7309 (tptp) outliers start: 176 outliers final: 89 residues processed: 475 average time/residue: 1.7365 time to fit residues: 1085.0778 Evaluate side-chains 446 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 336 time to evaluate : 3.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 123 LEU Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 28 SER Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain W residue 120 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 55 ASP Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 480 optimal weight: 10.0000 chunk 365 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 232 optimal weight: 0.0980 chunk 326 optimal weight: 8.9990 chunk 488 optimal weight: 8.9990 chunk 517 optimal weight: 9.9990 chunk 255 optimal weight: 9.9990 chunk 462 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN N 32 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 88153 Z= 0.372 Angle : 0.833 10.441 132807 Z= 0.420 Chirality : 0.046 0.374 17123 Planarity : 0.006 0.057 6394 Dihedral : 23.491 176.299 46169 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 9.19 % Allowed : 24.32 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.14), residues: 2590 helix: -1.86 (0.18), residues: 630 sheet: -0.71 (0.22), residues: 545 loop : -2.00 (0.13), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.007 0.002 HIS X 4 PHE 0.016 0.002 PHE K 30 TYR 0.021 0.003 TYR Y 57 ARG 0.007 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 334 time to evaluate : 3.240 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5985 (OUTLIER) cc_final: 0.5698 (tt0) REVERT: A 115 ILE cc_start: 0.6261 (OUTLIER) cc_final: 0.5884 (pp) REVERT: B 268 LYS cc_start: 0.7462 (OUTLIER) cc_final: 0.6975 (tttm) REVERT: C 97 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6321 (mp0) REVERT: C 101 SER cc_start: 0.7197 (OUTLIER) cc_final: 0.6987 (m) REVERT: C 103 GLU cc_start: 0.6021 (OUTLIER) cc_final: 0.5776 (mt-10) REVERT: D 69 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7438 (tttp) REVERT: D 77 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7759 (mttt) REVERT: D 78 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7885 (ptp-170) REVERT: E 27 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8247 (mmtt) REVERT: F 18 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.4637 (mm-30) REVERT: F 77 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.7610 (pttm) REVERT: G 4 LYS cc_start: 0.6607 (mttt) cc_final: 0.5741 (pptt) REVERT: H 17 ASP cc_start: 0.6361 (m-30) cc_final: 0.6143 (m-30) REVERT: H 37 LYS cc_start: 0.5418 (OUTLIER) cc_final: 0.4929 (mtmt) REVERT: K 48 LYS cc_start: 0.7490 (OUTLIER) cc_final: 0.7113 (mtpp) REVERT: L 123 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7414 (mtpp) REVERT: L 198 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7499 (ttmt) REVERT: N 21 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7552 (ttmt) REVERT: O 47 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6025 (tt0) REVERT: Q 43 GLN cc_start: 0.8995 (OUTLIER) cc_final: 0.8578 (mt0) REVERT: S 157 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6329 (mt-10) REVERT: V 32 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6619 (tt0) REVERT: V 63 ILE cc_start: 0.8318 (OUTLIER) cc_final: 0.7680 (pp) REVERT: W 4 GLN cc_start: 0.6696 (OUTLIER) cc_final: 0.6463 (tm-30) REVERT: W 80 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7059 (m-30) REVERT: W 105 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6073 (mm-30) REVERT: X 5 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: X 10 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6545 (tp30) REVERT: Y 63 LYS cc_start: 0.6859 (mmmm) cc_final: 0.6615 (mtpp) REVERT: Y 116 GLU cc_start: 0.7278 (tp30) cc_final: 0.6977 (mm-30) REVERT: Z 34 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7115 (tp30) REVERT: Z 66 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7458 (tp) REVERT: Z 89 ILE cc_start: 0.8070 (mm) cc_final: 0.7775 (mt) REVERT: I 19 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7335 (tptp) outliers start: 203 outliers final: 120 residues processed: 483 average time/residue: 1.6972 time to fit residues: 1088.1212 Evaluate side-chains 473 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 323 time to evaluate : 3.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 4 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 430 optimal weight: 10.0000 chunk 293 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 385 optimal weight: 7.9990 chunk 213 optimal weight: 2.9990 chunk 441 optimal weight: 7.9990 chunk 357 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 464 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN L 182 ASN N 32 ASN R 32 HIS V 97 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 88153 Z= 0.356 Angle : 0.803 10.629 132807 Z= 0.406 Chirality : 0.045 0.370 17123 Planarity : 0.006 0.058 6394 Dihedral : 23.426 176.194 46169 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 9.78 % Allowed : 24.41 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.14), residues: 2590 helix: -1.83 (0.18), residues: 638 sheet: -0.64 (0.22), residues: 549 loop : -1.96 (0.13), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.007 0.002 HIS R 32 PHE 0.017 0.002 PHE K 30 TYR 0.019 0.002 TYR H 77 ARG 0.007 0.001 ARG X 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 324 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5998 (OUTLIER) cc_final: 0.5719 (tt0) REVERT: A 115 ILE cc_start: 0.6303 (OUTLIER) cc_final: 0.5929 (pp) REVERT: B 114 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6219 (mp10) REVERT: B 163 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7992 (tt0) REVERT: B 268 LYS cc_start: 0.7465 (OUTLIER) cc_final: 0.6986 (tttm) REVERT: C 84 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7503 (tttp) REVERT: C 97 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6312 (mp0) REVERT: C 103 GLU cc_start: 0.6004 (OUTLIER) cc_final: 0.5764 (mt-10) REVERT: D 69 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7450 (tttp) REVERT: D 77 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.7760 (mttt) REVERT: D 78 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7862 (ptp-170) REVERT: E 27 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8241 (mmtt) REVERT: F 9 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7000 (mtm-85) REVERT: F 18 GLU cc_start: 0.5051 (OUTLIER) cc_final: 0.4797 (mm-30) REVERT: F 77 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.7574 (pttm) REVERT: G 4 LYS cc_start: 0.6602 (mttt) cc_final: 0.5717 (pptt) REVERT: G 17 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7358 (ttmt) REVERT: H 17 ASP cc_start: 0.6433 (m-30) cc_final: 0.6188 (m-30) REVERT: H 37 LYS cc_start: 0.5420 (OUTLIER) cc_final: 0.4959 (mtmt) REVERT: K 48 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7109 (mtpp) REVERT: L 123 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7488 (mtpp) REVERT: L 198 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7512 (ttmt) REVERT: M 5 GLN cc_start: 0.7701 (tt0) cc_final: 0.7325 (tp40) REVERT: O 47 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.5952 (tt0) REVERT: Q 43 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: S 150 LYS cc_start: 0.7224 (tmtt) cc_final: 0.6933 (tptt) REVERT: S 157 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6324 (mt-10) REVERT: V 63 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7659 (pp) REVERT: W 80 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.7008 (m-30) REVERT: W 105 GLU cc_start: 0.6759 (OUTLIER) cc_final: 0.6046 (mm-30) REVERT: X 5 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: X 10 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6567 (tp30) REVERT: Y 63 LYS cc_start: 0.6806 (mmmm) cc_final: 0.6572 (mtpp) REVERT: Y 111 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: Z 34 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7135 (tp30) REVERT: Z 66 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7466 (tp) REVERT: Z 89 ILE cc_start: 0.8103 (mm) cc_final: 0.7586 (mt) REVERT: I 19 LYS cc_start: 0.7863 (OUTLIER) cc_final: 0.7353 (tptp) outliers start: 216 outliers final: 137 residues processed: 489 average time/residue: 1.6962 time to fit residues: 1099.1162 Evaluate side-chains 494 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 325 time to evaluate : 3.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 17 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 31 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 157 GLU Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 89 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 21 SER Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 94 ILE Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 34 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 173 optimal weight: 2.9990 chunk 465 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 303 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 517 optimal weight: 9.9990 chunk 429 optimal weight: 20.0000 chunk 239 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 171 optimal weight: 0.5980 chunk 271 optimal weight: 10.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN N 32 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 88153 Z= 0.175 Angle : 0.635 12.472 132807 Z= 0.335 Chirality : 0.038 0.318 17123 Planarity : 0.005 0.060 6394 Dihedral : 23.367 176.014 46169 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 7.93 % Allowed : 26.54 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.15), residues: 2590 helix: -1.52 (0.19), residues: 637 sheet: -0.52 (0.22), residues: 557 loop : -1.89 (0.14), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 213 HIS 0.006 0.001 HIS C 29 PHE 0.017 0.001 PHE K 30 TYR 0.022 0.002 TYR Y 57 ARG 0.007 0.000 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 337 time to evaluate : 3.203 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5935 (OUTLIER) cc_final: 0.5680 (tt0) REVERT: A 115 ILE cc_start: 0.6244 (OUTLIER) cc_final: 0.5866 (pp) REVERT: B 114 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6187 (mp10) REVERT: B 163 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7803 (mt0) REVERT: B 247 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7785 (mmt) REVERT: C 78 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7082 (mtt-85) REVERT: C 103 GLU cc_start: 0.5952 (OUTLIER) cc_final: 0.5746 (mt-10) REVERT: D 69 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7432 (tttp) REVERT: D 77 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7527 (mttt) REVERT: D 78 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7808 (ptp-170) REVERT: F 9 ARG cc_start: 0.7476 (OUTLIER) cc_final: 0.6929 (mtm-85) REVERT: F 77 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.8145 (pttm) REVERT: G 4 LYS cc_start: 0.6589 (mttt) cc_final: 0.5677 (pptt) REVERT: H 17 ASP cc_start: 0.6350 (m-30) cc_final: 0.6142 (m-30) REVERT: L 198 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7486 (ttmt) REVERT: M 5 GLN cc_start: 0.7713 (tt0) cc_final: 0.7297 (tp40) REVERT: O 47 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.5993 (tt0) REVERT: Q 43 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8601 (mt0) REVERT: S 150 LYS cc_start: 0.7208 (tmtt) cc_final: 0.6918 (tptt) REVERT: V 63 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7585 (pp) REVERT: W 80 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: X 5 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7179 (mt-10) REVERT: X 10 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6523 (tp30) REVERT: Y 111 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7546 (tm-30) REVERT: Y 116 GLU cc_start: 0.7334 (tp30) cc_final: 0.6973 (mm-30) REVERT: Z 66 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7423 (tp) REVERT: Z 89 ILE cc_start: 0.8094 (mm) cc_final: 0.7571 (mt) REVERT: I 19 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7321 (tptp) outliers start: 175 outliers final: 114 residues processed: 464 average time/residue: 1.6965 time to fit residues: 1039.6559 Evaluate side-chains 462 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 327 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 9 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 139 GLU Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 34 ASN Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 89 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Z residue 3 TYR Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain a residue 5 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 499 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 378 optimal weight: 10.9990 chunk 292 optimal weight: 10.0000 chunk 435 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 515 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN D 63 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 88153 Z= 0.498 Angle : 0.979 11.487 132807 Z= 0.484 Chirality : 0.052 0.403 17123 Planarity : 0.007 0.077 6394 Dihedral : 23.688 176.224 46169 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 9.60 % Allowed : 24.82 % Favored : 65.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.14), residues: 2590 helix: -1.90 (0.18), residues: 634 sheet: -0.72 (0.21), residues: 566 loop : -1.99 (0.14), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 213 HIS 0.009 0.002 HIS X 4 PHE 0.018 0.003 PHE K 30 TYR 0.025 0.003 TYR H 77 ARG 0.010 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 322 time to evaluate : 3.261 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7756 (mmtp) cc_final: 0.7519 (mmtm) REVERT: A 84 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5614 (tt0) REVERT: A 115 ILE cc_start: 0.6228 (OUTLIER) cc_final: 0.5862 (pp) REVERT: B 163 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: B 268 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.6985 (tttm) REVERT: C 78 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6633 (mmt-90) REVERT: C 103 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5716 (mt-10) REVERT: D 69 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7447 (tttp) REVERT: D 77 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.7824 (mttt) REVERT: D 78 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7896 (ptp-170) REVERT: E 27 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8263 (mmtt) REVERT: F 9 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7066 (mtm-85) REVERT: F 18 GLU cc_start: 0.4960 (OUTLIER) cc_final: 0.4682 (mm-30) REVERT: G 41 MET cc_start: 0.6894 (OUTLIER) cc_final: 0.6488 (pp-130) REVERT: H 17 ASP cc_start: 0.6433 (m-30) cc_final: 0.6176 (m-30) REVERT: H 26 LYS cc_start: 0.7076 (OUTLIER) cc_final: 0.6593 (pttt) REVERT: H 37 LYS cc_start: 0.5305 (OUTLIER) cc_final: 0.4827 (mtmt) REVERT: K 48 LYS cc_start: 0.7460 (OUTLIER) cc_final: 0.7143 (mtpp) REVERT: L 198 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7520 (ttmt) REVERT: O 47 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6004 (tt0) REVERT: Q 43 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: R 36 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: S 150 LYS cc_start: 0.7211 (tmtt) cc_final: 0.6920 (tptt) REVERT: V 32 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6652 (tt0) REVERT: V 63 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.7693 (pp) REVERT: W 80 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7021 (m-30) REVERT: X 5 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: X 10 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6569 (tp30) REVERT: Y 5 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7691 (mppt) REVERT: Y 6 ARG cc_start: 0.6894 (ptm-80) cc_final: 0.6392 (ptm-80) REVERT: Y 111 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7435 (tm-30) REVERT: Y 133 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7044 (mtmm) REVERT: Z 66 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7477 (tp) REVERT: Z 89 ILE cc_start: 0.8119 (mm) cc_final: 0.7594 (mt) REVERT: I 19 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7354 (tptp) outliers start: 212 outliers final: 139 residues processed: 483 average time/residue: 1.7138 time to fit residues: 1094.2870 Evaluate side-chains 488 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 319 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 108 LYS Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 117 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain V residue 139 GLU Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 4 GLN Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain X residue 89 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 133 LYS Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 319 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 307 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 327 optimal weight: 6.9990 chunk 351 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 48 optimal weight: 8.9990 chunk 405 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN B 70 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 88153 Z= 0.425 Angle : 0.897 12.176 132807 Z= 0.450 Chirality : 0.049 0.387 17123 Planarity : 0.007 0.069 6394 Dihedral : 23.654 176.414 46169 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 9.15 % Allowed : 25.68 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.14), residues: 2590 helix: -1.93 (0.18), residues: 633 sheet: -0.73 (0.21), residues: 557 loop : -1.98 (0.13), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.008 0.002 HIS X 4 PHE 0.017 0.003 PHE K 30 TYR 0.027 0.003 TYR Y 57 ARG 0.007 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 327 time to evaluate : 3.232 Fit side-chains revert: symmetry clash REVERT: A 5 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7512 (mmtm) REVERT: A 84 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5608 (tt0) REVERT: A 115 ILE cc_start: 0.6222 (OUTLIER) cc_final: 0.5870 (pp) REVERT: B 163 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7998 (tt0) REVERT: B 268 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6999 (tttm) REVERT: C 78 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6642 (mmt-90) REVERT: C 103 GLU cc_start: 0.5908 (OUTLIER) cc_final: 0.5693 (mt-10) REVERT: D 10 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7737 (mtpt) REVERT: D 69 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7433 (tttp) REVERT: D 77 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.7814 (mttt) REVERT: D 78 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.7860 (ptp-170) REVERT: F 9 ARG cc_start: 0.7574 (OUTLIER) cc_final: 0.7049 (mtm-85) REVERT: G 41 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6481 (pp-130) REVERT: H 17 ASP cc_start: 0.6452 (m-30) cc_final: 0.6201 (m-30) REVERT: H 26 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6573 (pttt) REVERT: H 37 LYS cc_start: 0.5297 (OUTLIER) cc_final: 0.4785 (mtmt) REVERT: K 48 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.7126 (mtpp) REVERT: L 198 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7532 (ttmt) REVERT: N 21 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7506 (ttmt) REVERT: O 47 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6004 (tt0) REVERT: P 12 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8369 (tttm) REVERT: Q 43 GLN cc_start: 0.8996 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: R 36 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7643 (tt0) REVERT: V 9 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6602 (mm-30) REVERT: V 63 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7644 (pp) REVERT: W 80 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7053 (m-30) REVERT: X 5 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: X 10 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6570 (tp30) REVERT: Y 5 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7670 (mppt) REVERT: Y 6 ARG cc_start: 0.6878 (ptm-80) cc_final: 0.6386 (ptm-80) REVERT: Y 111 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: Y 133 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7045 (mtmm) REVERT: Z 66 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7461 (tp) REVERT: Z 89 ILE cc_start: 0.8130 (mm) cc_final: 0.7593 (mt) REVERT: Z 91 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6393 (mm-30) REVERT: I 19 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7336 (tptp) outliers start: 202 outliers final: 145 residues processed: 481 average time/residue: 1.7556 time to fit residues: 1128.1365 Evaluate side-chains 498 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 321 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 51 ARG Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 5 LYS Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 26 LYS Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 117 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 9 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain X residue 89 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 133 LYS Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 91 GLU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 469 optimal weight: 8.9990 chunk 494 optimal weight: 10.0000 chunk 450 optimal weight: 10.0000 chunk 480 optimal weight: 7.9990 chunk 493 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 209 optimal weight: 8.9990 chunk 377 optimal weight: 7.9990 chunk 147 optimal weight: 2.9990 chunk 434 optimal weight: 7.9990 chunk 454 optimal weight: 8.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN B 128 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 32 ASN V 97 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 88153 Z= 0.499 Angle : 0.975 10.959 132807 Z= 0.482 Chirality : 0.052 0.405 17123 Planarity : 0.007 0.078 6394 Dihedral : 23.685 176.421 46169 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 9.51 % Allowed : 25.63 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.62 (0.14), residues: 2590 helix: -2.01 (0.18), residues: 631 sheet: -0.76 (0.22), residues: 558 loop : -2.03 (0.13), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP B 213 HIS 0.009 0.002 HIS X 4 PHE 0.017 0.003 PHE K 30 TYR 0.029 0.003 TYR Y 57 ARG 0.009 0.001 ARG X 47 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 325 time to evaluate : 3.204 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5894 (OUTLIER) cc_final: 0.5607 (tt0) REVERT: A 115 ILE cc_start: 0.6207 (OUTLIER) cc_final: 0.5851 (pp) REVERT: B 163 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.8033 (tt0) REVERT: B 268 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.6981 (tttm) REVERT: C 78 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.6640 (mmt-90) REVERT: C 84 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7502 (tttp) REVERT: C 103 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5693 (mt-10) REVERT: D 10 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7770 (mtpt) REVERT: D 69 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7460 (tttp) REVERT: D 77 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.7870 (mttt) REVERT: D 78 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7975 (ptp-170) REVERT: E 27 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8257 (mmtt) REVERT: F 9 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.7070 (mtm-85) REVERT: G 41 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6497 (pp-130) REVERT: H 17 ASP cc_start: 0.6434 (m-30) cc_final: 0.6191 (m-30) REVERT: H 37 LYS cc_start: 0.5311 (OUTLIER) cc_final: 0.4836 (mtmt) REVERT: K 48 LYS cc_start: 0.7489 (OUTLIER) cc_final: 0.7166 (mtpp) REVERT: L 168 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.7659 (mmtt) REVERT: L 198 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7523 (ttmt) REVERT: N 21 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7520 (ttmt) REVERT: N 35 GLU cc_start: 0.6176 (mm-30) cc_final: 0.5957 (mm-30) REVERT: O 47 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6021 (tt0) REVERT: P 12 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8372 (tttm) REVERT: Q 43 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: R 36 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7617 (tt0) REVERT: V 9 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6740 (mm-30) REVERT: V 32 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6655 (tt0) REVERT: V 63 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.7689 (pp) REVERT: W 80 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: W 105 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6122 (mm-30) REVERT: X 5 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7306 (mt-10) REVERT: X 10 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6592 (tp30) REVERT: Y 5 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7678 (mppt) REVERT: Y 6 ARG cc_start: 0.6826 (ptm-80) cc_final: 0.6308 (ptm-80) REVERT: Y 111 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: Y 133 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7054 (mtmm) REVERT: Z 66 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7474 (tp) REVERT: Z 89 ILE cc_start: 0.8117 (mm) cc_final: 0.7579 (mt) REVERT: I 19 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7341 (tptp) outliers start: 210 outliers final: 141 residues processed: 483 average time/residue: 1.6694 time to fit residues: 1070.2820 Evaluate side-chains 496 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 320 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 27 LYS Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 20 SER Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 117 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 9 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 89 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 133 LYS Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 478 optimal weight: 7.9990 chunk 315 optimal weight: 7.9990 chunk 508 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 353 optimal weight: 9.9990 chunk 532 optimal weight: 7.9990 chunk 490 optimal weight: 5.9990 chunk 424 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 327 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 ASN F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 97 ASN X 81 GLN Z 12 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 88153 Z= 0.422 Angle : 0.898 11.487 132807 Z= 0.451 Chirality : 0.049 0.383 17123 Planarity : 0.007 0.072 6394 Dihedral : 23.665 176.405 46169 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 8.70 % Allowed : 26.13 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2590 helix: -1.99 (0.18), residues: 631 sheet: -0.75 (0.22), residues: 552 loop : -2.03 (0.13), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.007 0.002 HIS X 4 PHE 0.017 0.003 PHE K 30 TYR 0.033 0.003 TYR Y 57 ARG 0.007 0.001 ARG X 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5180 Ramachandran restraints generated. 2590 Oldfield, 0 Emsley, 2590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 322 time to evaluate : 3.307 Fit side-chains revert: symmetry clash REVERT: A 84 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5600 (tt0) REVERT: A 115 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5876 (pp) REVERT: B 163 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8027 (tt0) REVERT: B 268 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.7022 (tttm) REVERT: C 78 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6634 (mmt-90) REVERT: C 84 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7488 (tttp) REVERT: C 103 GLU cc_start: 0.5939 (OUTLIER) cc_final: 0.5685 (mt-10) REVERT: D 10 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7787 (mtpt) REVERT: D 69 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7448 (tttp) REVERT: D 77 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7825 (mttt) REVERT: D 78 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7865 (ptp-170) REVERT: F 9 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7043 (mtm-85) REVERT: G 41 MET cc_start: 0.6900 (OUTLIER) cc_final: 0.6488 (pp-130) REVERT: H 17 ASP cc_start: 0.6450 (m-30) cc_final: 0.6216 (m-30) REVERT: H 37 LYS cc_start: 0.5299 (OUTLIER) cc_final: 0.4794 (mtmt) REVERT: K 48 LYS cc_start: 0.7464 (OUTLIER) cc_final: 0.7136 (mtpp) REVERT: L 123 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7438 (mtpp) REVERT: L 168 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7644 (mmtt) REVERT: L 198 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7521 (ttmt) REVERT: N 21 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7513 (ttmt) REVERT: O 47 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6014 (tt0) REVERT: P 12 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8366 (tttm) REVERT: Q 43 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: V 9 GLU cc_start: 0.6926 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: V 32 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.6633 (tt0) REVERT: V 63 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7662 (pp) REVERT: W 80 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7022 (m-30) REVERT: W 105 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6104 (mm-30) REVERT: X 5 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: X 10 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6594 (tp30) REVERT: Y 5 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7679 (mppt) REVERT: Y 6 ARG cc_start: 0.6828 (ptm-80) cc_final: 0.6323 (ptm-80) REVERT: Y 111 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7420 (tm-30) REVERT: Y 133 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.7052 (mtmm) REVERT: Z 66 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7468 (tp) REVERT: Z 89 ILE cc_start: 0.8115 (mm) cc_final: 0.7592 (mt) REVERT: I 19 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7337 (tptp) outliers start: 192 outliers final: 144 residues processed: 464 average time/residue: 1.7023 time to fit residues: 1047.0394 Evaluate side-chains 496 residues out of total 2211 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 318 time to evaluate : 3.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain B residue 23 GLU Chi-restraints excluded: chain B residue 32 SER Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 157 SER Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 204 ASN Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 247 MET Chi-restraints excluded: chain B residue 265 SER Chi-restraints excluded: chain B residue 268 LYS Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 74 MET Chi-restraints excluded: chain C residue 78 ARG Chi-restraints excluded: chain C residue 84 LYS Chi-restraints excluded: chain C residue 88 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 69 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 77 LYS Chi-restraints excluded: chain D residue 78 ARG Chi-restraints excluded: chain E residue 2 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 9 ARG Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 55 ILE Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 41 MET Chi-restraints excluded: chain G residue 42 LYS Chi-restraints excluded: chain G residue 43 LYS Chi-restraints excluded: chain G residue 56 ILE Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 89 LYS Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain H residue 14 THR Chi-restraints excluded: chain H residue 27 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 37 LYS Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 46 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 76 ASP Chi-restraints excluded: chain H residue 85 GLN Chi-restraints excluded: chain H residue 86 ILE Chi-restraints excluded: chain J residue 8 THR Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 16 GLU Chi-restraints excluded: chain K residue 30 PHE Chi-restraints excluded: chain K residue 48 LYS Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 3 LYS Chi-restraints excluded: chain L residue 19 ASN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 54 GLU Chi-restraints excluded: chain L residue 61 LYS Chi-restraints excluded: chain L residue 81 ASP Chi-restraints excluded: chain L residue 95 ASP Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 114 ASP Chi-restraints excluded: chain L residue 117 ASP Chi-restraints excluded: chain L residue 123 LYS Chi-restraints excluded: chain L residue 145 SER Chi-restraints excluded: chain L residue 168 LYS Chi-restraints excluded: chain L residue 189 ASP Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 198 LYS Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain N residue 21 LYS Chi-restraints excluded: chain N residue 33 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain O residue 47 GLU Chi-restraints excluded: chain P residue 12 LYS Chi-restraints excluded: chain Q residue 19 SER Chi-restraints excluded: chain Q residue 37 SER Chi-restraints excluded: chain Q residue 43 GLN Chi-restraints excluded: chain Q residue 53 SER Chi-restraints excluded: chain R residue 7 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 117 LYS Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 124 THR Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 152 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 9 GLU Chi-restraints excluded: chain V residue 18 VAL Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 35 SER Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 94 ARG Chi-restraints excluded: chain V residue 107 LYS Chi-restraints excluded: chain V residue 112 SER Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 12 ASP Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 104 ARG Chi-restraints excluded: chain W residue 105 GLU Chi-restraints excluded: chain X residue 5 GLU Chi-restraints excluded: chain X residue 10 GLU Chi-restraints excluded: chain X residue 69 ILE Chi-restraints excluded: chain X residue 73 GLU Chi-restraints excluded: chain X residue 76 ILE Chi-restraints excluded: chain X residue 89 THR Chi-restraints excluded: chain X residue 95 LEU Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 117 LEU Chi-restraints excluded: chain X residue 122 THR Chi-restraints excluded: chain X residue 144 GLU Chi-restraints excluded: chain Y residue 5 LYS Chi-restraints excluded: chain Y residue 28 THR Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 43 THR Chi-restraints excluded: chain Y residue 96 VAL Chi-restraints excluded: chain Y residue 111 GLU Chi-restraints excluded: chain Y residue 129 THR Chi-restraints excluded: chain Y residue 133 LYS Chi-restraints excluded: chain Z residue 11 ASP Chi-restraints excluded: chain Z residue 14 LYS Chi-restraints excluded: chain Z residue 32 THR Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 42 SER Chi-restraints excluded: chain Z residue 65 THR Chi-restraints excluded: chain Z residue 66 LEU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 71 ILE Chi-restraints excluded: chain Z residue 72 LEU Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain a residue 40 ILE Chi-restraints excluded: chain a residue 57 SER Chi-restraints excluded: chain a residue 68 THR Chi-restraints excluded: chain a residue 82 LYS Chi-restraints excluded: chain a residue 106 LYS Chi-restraints excluded: chain I residue 19 LYS Chi-restraints excluded: chain I residue 66 THR Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 535 random chunks: chunk 260 optimal weight: 8.9990 chunk 337 optimal weight: 7.9990 chunk 452 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 391 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 425 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 436 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 73 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 81 GLN Z 12 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.134936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.115378 restraints weight = 85202.257| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 0.64 r_work: 0.2920 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 88153 Z= 0.349 Angle : 0.834 11.429 132807 Z= 0.425 Chirality : 0.046 0.371 17123 Planarity : 0.006 0.065 6394 Dihedral : 23.640 176.419 46169 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 8.70 % Allowed : 26.13 % Favored : 65.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.14), residues: 2590 helix: -1.92 (0.18), residues: 631 sheet: -0.73 (0.22), residues: 553 loop : -2.00 (0.13), residues: 1406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 213 HIS 0.007 0.002 HIS a 15 PHE 0.017 0.002 PHE K 30 TYR 0.031 0.003 TYR Y 57 ARG 0.008 0.001 ARG C 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16819.86 seconds wall clock time: 297 minutes 44.61 seconds (17864.61 seconds total)