Starting phenix.real_space_refine on Mon Feb 19 19:55:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/02_2024/6wrs_21887_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/02_2024/6wrs_21887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/02_2024/6wrs_21887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/02_2024/6wrs_21887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/02_2024/6wrs_21887_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wrs_21887/02_2024/6wrs_21887_trim_updated.pdb" } resolution = 3.2 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= 0.000 sd= 0.011 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 2803 5.49 5 S 56 5.16 5 C 39947 2.51 5 N 15057 2.21 5 O 23251 1.98 5 F 1 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 ARG 41": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 168": "OE1" <-> "OE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "C ARG 3": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "D GLU 6": "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 73": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "F GLU 14": "OE1" <-> "OE2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 52": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "L ARG 86": "NH1" <-> "NH2" Residue "L ARG 92": "NH1" <-> "NH2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "N ARG 6": "NH1" <-> "NH2" Residue "N ARG 7": "NH1" <-> "NH2" Residue "N GLU 29": "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 57": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "S GLU 35": "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 132": "OE1" <-> "OE2" Residue "S ARG 168": "NH1" <-> "NH2" Residue "S GLU 196": "OE1" <-> "OE2" Residue "V ARG 2": "NH1" <-> "NH2" Residue "V GLU 9": "OE1" <-> "OE2" Residue "V ARG 14": "NH1" <-> "NH2" Residue "V TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 22": "OE1" <-> "OE2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V GLU 130": "OE1" <-> "OE2" Residue "V ARG 144": "NH1" <-> "NH2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X GLU 73": "OE1" <-> "OE2" Residue "X GLU 90": "OE1" <-> "OE2" Residue "X GLU 98": "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 PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y GLU 136": "OE1" <-> "OE2" Residue "Z GLU 34": "OE1" <-> "OE2" Residue "Z GLU 39": "OE1" <-> "OE2" Residue "Z ARG 67": "NH1" <-> "NH2" Residue "Z GLU 70": "OE1" <-> "OE2" Residue "Z GLU 88": "OE1" <-> "OE2" Residue "Z GLU 115": "OE1" <-> "OE2" Residue "a GLU 71": "OE1" <-> "OE2" Residue "I ARG 22": "NH1" <-> "NH2" 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-5238/modules/chem_data/mon_lib" Total number of atoms: 81115 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 915 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} 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: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 853 Classifications: {'peptide': 111} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 106} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 711 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "G" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 770 Classifications: {'peptide': 100} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 481 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "L" Number of atoms: 1628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1628 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 8, 'TRANS': 206} 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: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 955 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain: "a" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'TRANS': 108} Chain breaks: 1 Chain: "1" Number of atoms: 57851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2698, 57851 Inner-chain residues flagged as termini: ['pdbres=" A 1 318 "', 'pdbres=" A 11459 "', 'pdbres=" U 11540 "', 'pdbres=" G 11556 "'] Classifications: {'RNA': 2698} Modifications used: {'5*END': 5, 'rna2p_pur': 268, 'rna2p_pyr': 139, 'rna3p_pur': 1285, 'rna3p_pyr': 1006} Link IDs: {'rna2p': 407, 'rna3p': 2290} Chain breaks: 6 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': 6, 'rna2p_pyr': 6, 'rna3p_pur': 51, 'rna3p_pyr': 48} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'U7V': 1} Classifications: {'undetermined': 1} Time building chain proxies: 31.35, per 1000 atoms: 0.39 Number of scatterers: 81115 At special positions: 0 Unit cell: (207.48, 237.12, 186.96, 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 56 16.00 P 2803 15.00 F 1 9.00 O 23251 8.00 N 15057 7.00 C 39947 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 33 " - pdb=" SG CYS N 43 " distance=2.04 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 27 " distance=2.04 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: 27.59 Conformation dependent library (CDL) restraints added in 3.5 seconds 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 41 sheets defined 19.4% alpha, 16.4% beta 513 base pairs and 1562 stacking pairs defined. Time for finding SS restraints: 33.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 13 removed outlier: 3.776A pdb=" N LYS A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N SER A 13 " --> pdb=" O ALA A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 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 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.579A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) 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 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'C' and resid 11 through 19 removed outlier: 4.092A pdb=" N LYS C 16 " --> pdb=" O ALA C 12 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N THR C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 29 removed outlier: 3.901A pdb=" N HIS C 29 " --> pdb=" O GLY C 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 26 through 29' Processing helix chain 'C' and resid 32 through 72 removed outlier: 3.827A pdb=" N GLN C 37 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN C 44 " --> pdb=" O MET C 40 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ARG C 51 " --> pdb=" O PHE C 47 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LYS C 54 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG C 55 " --> pdb=" O ARG C 51 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE C 57 " --> pdb=" O ARG C 53 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ARG C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N THR C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 86 removed outlier: 3.514A pdb=" N LYS C 85 " --> pdb=" O ASN C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 101 Processing helix chain 'C' and resid 103 through 116 removed outlier: 4.022A pdb=" N LYS C 112 " --> pdb=" O GLN C 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 24 removed outlier: 4.651A pdb=" N LEU E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL E 20 " --> pdb=" O LYS E 16 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP E 22 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 24 " --> pdb=" O VAL E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 38 removed outlier: 3.710A pdb=" N LYS E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 52 removed outlier: 4.326A pdb=" N LYS E 49 " --> pdb=" O PRO E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'F' and resid 35 through 46 removed outlier: 4.265A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (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 removed outlier: 3.627A pdb=" N LYS H 19 " --> pdb=" O ARG H 15 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU H 21 " --> pdb=" O ASP H 17 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG H 22 " --> pdb=" O LEU H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.694A pdb=" N GLU H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 23 removed outlier: 3.794A pdb=" N ILE K 18 " --> pdb=" O ILE K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 60 removed outlier: 3.784A pdb=" N ARG K 44 " --> pdb=" O ALA K 41 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR K 45 " --> pdb=" O ARG K 42 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS K 48 " --> pdb=" O THR K 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE K 50 " --> pdb=" O ARG K 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS K 54 " --> pdb=" O ALA K 51 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR K 55 " --> pdb=" O ARG K 52 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG K 58 " --> pdb=" O THR K 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 71 through 74 No H-bonds generated for 'chain 'L' and resid 71 through 74' Processing helix chain 'L' and resid 130 through 134 Processing helix chain 'M' and resid 17 through 25 removed outlier: 3.544A pdb=" N LYS M 21 " --> pdb=" O GLU M 17 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR M 22 " --> pdb=" O THR M 18 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA M 25 " --> pdb=" O LYS M 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 19 removed outlier: 3.694A pdb=" N ARG N 16 " --> pdb=" O ARG N 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG N 17 " --> pdb=" O LYS N 13 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR N 18 " --> pdb=" O ASN N 14 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N HIS N 19 " --> pdb=" O LYS N 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 14 removed outlier: 3.580A pdb=" N SER P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 10 through 14' 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 28 through 38 Processing helix chain 'Q' and resid 38 through 41 No H-bonds generated for 'chain 'Q' and resid 38 through 41' Processing helix chain 'Q' and resid 52 through 57 removed outlier: 3.645A pdb=" N LYS Q 56 " --> pdb=" O LYS Q 52 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG Q 57 " --> pdb=" O SER Q 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 52 through 57' 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 41 removed outlier: 3.907A pdb=" N GLU S 35 " --> pdb=" O SER S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 107 removed outlier: 3.615A pdb=" N ARG S 107 " --> pdb=" O LYS S 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 103 through 107' Processing helix chain 'S' and resid 110 through 120 removed outlier: 3.555A pdb=" N SER S 115 " --> pdb=" O ARG S 111 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN S 119 " --> pdb=" O SER S 115 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU S 120 " --> pdb=" O PHE S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 136 through 145 removed outlier: 4.092A pdb=" N ASN S 141 " --> pdb=" O LYS S 137 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU S 143 " --> pdb=" O PHE S 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER S 144 " --> pdb=" O LYS S 140 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 165 Processing helix chain 'S' and resid 183 through 188 Processing helix chain 'S' and resid 196 through 205 Processing helix chain 'V' and resid 26 through 33 removed outlier: 3.810A pdb=" N SER V 31 " --> pdb=" O GLY V 27 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU V 32 " --> pdb=" O ARG V 28 " (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 90 through 96 Processing helix chain 'V' and resid 98 through 109 removed outlier: 3.596A pdb=" N ILE V 102 " --> pdb=" O PRO V 98 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS V 107 " --> pdb=" O GLU V 103 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY V 108 " --> pdb=" O ASN V 104 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N MET V 109 " --> pdb=" O SER V 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 119 No H-bonds generated for 'chain 'V' and resid 116 through 119' Processing helix chain 'W' and resid 104 through 106 No H-bonds generated for 'chain 'W' and resid 104 through 106' Processing helix chain 'W' and resid 114 through 117 No H-bonds generated for 'chain 'W' and resid 114 through 117' 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 79 through 84 removed outlier: 4.473A pdb=" N LYS X 84 " --> pdb=" O ASP X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 93 through 99 Processing helix chain 'X' and resid 130 through 138 removed outlier: 3.679A pdb=" N GLU X 134 " --> pdb=" O ALA X 130 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 57 removed outlier: 4.305A pdb=" N TYR Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 114 through 122 removed outlier: 3.562A pdb=" N SER Y 122 " --> pdb=" O LEU Y 118 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 13 No H-bonds generated for 'chain 'Z' and resid 10 through 13' Processing helix chain 'Z' and resid 20 through 26 removed outlier: 3.949A pdb=" N ILE Z 25 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 34 through 52 removed outlier: 3.738A pdb=" N GLU Z 39 " --> pdb=" O ALA Z 35 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N SER Z 42 " --> pdb=" O LYS Z 38 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL Z 43 " --> pdb=" O GLU Z 39 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL Z 44 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU Z 45 " --> pdb=" O ARG Z 41 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS Z 46 " --> pdb=" O SER Z 42 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR Z 49 " --> pdb=" O GLU Z 45 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU Z 50 " --> pdb=" O LYS Z 46 " (cutoff:3.500A) Processing helix chain 'Z' and resid 56 through 64 removed outlier: 3.822A pdb=" N ASN Z 61 " --> pdb=" O ALA Z 57 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N LYS Z 64 " --> pdb=" O ARG Z 60 " (cutoff:3.500A) Processing helix chain 'Z' and resid 81 through 86 Processing helix chain 'Z' and resid 89 through 92 No H-bonds generated for 'chain 'Z' and resid 89 through 92' Processing helix chain 'a' and resid 7 through 14 removed outlier: 4.247A pdb=" N LYS a 13 " --> pdb=" O LYS a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 87 removed outlier: 3.751A pdb=" N LYS a 82 " --> pdb=" O GLU a 78 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS a 83 " --> pdb=" O ALA a 79 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA a 85 " --> pdb=" O ALA a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 114 removed outlier: 3.519A pdb=" N ALA a 111 " --> pdb=" O ALA a 107 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA a 112 " --> pdb=" O LEU a 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG a 113 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU a 114 " --> pdb=" O GLU a 110 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 86 through 88 removed outlier: 9.177A pdb=" N GLU A 46 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE A 66 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 62 " --> pdb=" O ILE A 50 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG A 52 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 7.107A 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 91 through 95 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: 4.026A pdb=" N PHE D 2 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE D 40 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N GLU D 6 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 6.562A 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 23 removed outlier: 3.515A pdb=" N TYR D 92 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.797A 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: 3.619A pdb=" N ALA D 60 " --> pdb=" O PHE D 33 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 99 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR D 61 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ILE D 97 " --> pdb=" O THR D 61 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 71 through 77 removed outlier: 4.591A pdb=" N SER D 82 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 2 through 7 removed outlier: 6.846A pdb=" N SER E 108 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.623A 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: 3.632A pdb=" N SER F 52 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG F 76 " --> pdb=" O VAL F 29 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 9 " --> pdb=" O ASP F 28 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 20 through 22 Processing sheet with id= O, first strand: chain 'G' and resid 41 through 43 removed outlier: 3.591A pdb=" N LYS G 43 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 57 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 23 through 27 removed outlier: 6.822A pdb=" N VAL G 34 " --> pdb=" O ILE G 24 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR G 26 " --> pdb=" O ARG G 32 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG G 32 " --> pdb=" O THR G 26 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 63 through 65 removed outlier: 6.509A pdb=" N LEU H 4 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LYS H 5 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP H 44 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL H 30 " --> pdb=" O ILE H 89 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 77 through 80 removed outlier: 4.457A pdb=" N HIS H 88 " --> pdb=" O GLN H 78 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ASP H 80 " --> pdb=" O ILE H 86 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE H 86 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'J' and resid 13 through 16 Processing sheet with id= T, first strand: chain 'J' and resid 33 through 39 removed outlier: 4.077A pdb=" N ILE J 38 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS J 45 " --> pdb=" O ILE J 38 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 177 through 180 removed outlier: 4.780A pdb=" N VAL L 121 " --> pdb=" O LEU L 208 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU L 208 " --> pdb=" O VAL L 121 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL L 27 " --> pdb=" O ILE L 10 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N MET L 12 " --> pdb=" O VAL L 25 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL L 25 " --> pdb=" O MET L 12 " (cutoff:3.500A) removed outlier: 4.642A 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) Processing sheet with id= V, first strand: chain 'L' and resid 88 through 91 removed outlier: 3.713A pdb=" N ARG L 89 " --> pdb=" O VAL L 51 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN L 37 " --> pdb=" O GLN L 50 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY L 52 " --> pdb=" O VAL L 35 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N VAL L 35 " --> pdb=" O GLY L 52 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 34 through 37 Processing sheet with id= X, first strand: chain 'N' and resid 27 through 29 Processing sheet with id= Y, first strand: chain 'O' and resid 2 through 7 Processing sheet with id= Z, first strand: chain 'O' and resid 32 through 36 removed outlier: 3.535A pdb=" N LYS O 41 " --> pdb=" O CYS O 36 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 15 through 18 Processing sheet with id= AB, first strand: chain 'S' and resid 123 through 126 removed outlier: 6.248A pdb=" N LEU S 192 " --> pdb=" O THR S 124 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL S 126 " --> pdb=" O LEU S 192 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE S 194 " --> pdb=" O VAL S 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'S' and resid 152 through 156 removed outlier: 3.757A pdb=" N GLN S 174 " --> pdb=" O VAL S 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR S 156 " --> pdb=" O THR S 176 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'V' and resid 16 through 20 removed outlier: 6.640A pdb=" N TYR V 54 " --> pdb=" O TYR V 17 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE V 19 " --> pdb=" O TYR V 54 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ILE V 56 " --> pdb=" O ILE V 19 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'V' and resid 74 through 78 Processing sheet with id= AF, first strand: chain 'W' and resid 7 through 9 removed outlier: 3.615A pdb=" N LEU W 8 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL W 40 " --> pdb=" O ILE W 22 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N VAL W 24 " --> pdb=" O VAL W 38 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL W 38 " --> pdb=" O VAL W 24 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LYS W 59 " --> pdb=" O ILE W 87 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL W 63 " --> pdb=" O ALA W 83 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA W 83 " --> pdb=" O VAL W 63 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'W' and resid 69 through 71 removed outlier: 3.804A pdb=" N SER W 75 " --> pdb=" O ARG W 71 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'X' and resid 75 through 77 Processing sheet with id= AI, first strand: chain 'Y' and resid 32 through 34 removed outlier: 4.084A pdb=" N VAL Y 132 " --> pdb=" O GLY Y 33 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'Y' and resid 40 through 43 removed outlier: 3.589A pdb=" N ILE Y 42 " --> pdb=" O ALA Y 95 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA Y 89 " --> pdb=" O LYS Y 76 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N TYR Y 74 " --> pdb=" O GLU Y 91 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP Y 93 " --> pdb=" O THR Y 72 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THR Y 72 " --> pdb=" O TRP Y 93 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'Y' and resid 63 through 66 Processing sheet with id= AL, first strand: chain 'Z' and resid 29 through 33 removed outlier: 4.036A pdb=" N GLY Z 107 " --> pdb=" O SER Z 116 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ILE Z 118 " --> pdb=" O LYS Z 105 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N LYS Z 105 " --> pdb=" O ILE Z 118 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N GLU Z 120 " --> pdb=" O ILE Z 103 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ILE Z 103 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'a' and resid 30 through 35 removed outlier: 3.650A pdb=" N TYR a 34 " --> pdb=" O TYR a 41 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE a 44 " --> pdb=" O ALA a 54 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ALA a 54 " --> pdb=" O ILE a 44 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'I' and resid 59 through 61 removed outlier: 3.851A pdb=" N PHE I 68 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'I' and resid 74 through 77 404 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1204 hydrogen bonds 1954 hydrogen bond angles 0 basepair planarities 513 basepair parallelities 1562 stacking parallelities Total time for adding SS restraints: 105.96 Time building geometry restraints manager: 30.26 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: 7583 1.31 - 1.44: 39951 1.44 - 1.56: 35366 1.56 - 1.69: 5600 1.69 - 1.82: 98 Bond restraints: 88598 Sorted by residual: bond pdb=" C23 U7V 13001 " pdb=" O22 U7V 13001 " ideal model delta sigma weight residual 1.334 1.434 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C23 U7V 13001 " pdb=" N19 U7V 13001 " ideal model delta sigma weight residual 1.368 1.456 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" C PHE C 57 " pdb=" N ARG C 58 " ideal model delta sigma weight residual 1.334 1.391 -0.057 1.43e-02 4.89e+03 1.56e+01 bond pdb=" CG ASN K 8 " pdb=" ND2 ASN K 8 " ideal model delta sigma weight residual 1.328 1.247 0.081 2.10e-02 2.27e+03 1.47e+01 bond pdb=" N05 U7V 13001 " pdb=" N06 U7V 13001 " ideal model delta sigma weight residual 1.292 1.362 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 88593 not shown) Histogram of bond angle deviations from ideal: 95.01 - 102.82: 4805 102.82 - 110.62: 46329 110.62 - 118.43: 36060 118.43 - 126.24: 37138 126.24 - 134.05: 9125 Bond angle restraints: 133457 Sorted by residual: angle pdb=" N ARG L 86 " pdb=" CA ARG L 86 " pdb=" C ARG L 86 " ideal model delta sigma weight residual 111.36 123.23 -11.87 1.09e+00 8.42e-01 1.19e+02 angle pdb=" O2' C 1 674 " pdb=" C2' C 1 674 " pdb=" C1' C 1 674 " ideal model delta sigma weight residual 108.40 95.01 13.39 1.50e+00 4.44e-01 7.97e+01 angle pdb=" N GLU Z 74 " pdb=" CA GLU Z 74 " pdb=" C GLU Z 74 " ideal model delta sigma weight residual 110.50 98.11 12.39 1.41e+00 5.03e-01 7.72e+01 angle pdb=" O3' A 1 224 " pdb=" C3' A 1 224 " pdb=" C2' A 1 224 " ideal model delta sigma weight residual 109.50 97.37 12.13 1.50e+00 4.44e-01 6.54e+01 angle pdb=" N VAL J 7 " pdb=" CA VAL J 7 " pdb=" C VAL J 7 " ideal model delta sigma weight residual 110.72 118.77 -8.05 1.01e+00 9.80e-01 6.36e+01 ... (remaining 133452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 49571 35.79 - 71.57: 6299 71.57 - 107.36: 703 107.36 - 143.14: 16 143.14 - 178.93: 33 Dihedral angle restraints: 56622 sinusoidal: 49069 harmonic: 7553 Sorted by residual: 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 -170.52 84.52 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" O4' U 12655 " pdb=" C1' U 12655 " pdb=" N1 U 12655 " pdb=" C2 U 12655 " ideal model delta sinusoidal sigma weight residual 200.00 28.46 171.54 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C 1 402 " pdb=" C1' C 1 402 " pdb=" N1 C 1 402 " pdb=" C2 C 1 402 " ideal model delta sinusoidal sigma weight residual 200.00 28.47 171.53 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 56619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.170: 16801 0.170 - 0.339: 355 0.339 - 0.509: 37 0.509 - 0.678: 5 0.678 - 0.848: 2 Chirality restraints: 17200 Sorted by residual: chirality pdb=" CA ARG L 86 " pdb=" N ARG L 86 " pdb=" C ARG L 86 " pdb=" CB ARG L 86 " both_signs ideal model delta sigma weight residual False 2.51 1.66 0.85 2.00e-01 2.50e+01 1.80e+01 chirality pdb=" CA PHE X 50 " pdb=" N PHE X 50 " pdb=" C PHE X 50 " pdb=" CB PHE X 50 " both_signs ideal model delta sigma weight residual False 2.51 1.68 0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb=" C3' G 11761 " pdb=" C4' G 11761 " pdb=" O3' G 11761 " pdb=" C2' G 11761 " both_signs ideal model delta sigma weight residual False -2.48 -1.87 -0.61 2.00e-01 2.50e+01 9.24e+00 ... (remaining 17197 not shown) Planarity restraints: 6443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A 1 518 " -0.051 2.00e-02 2.50e+03 2.60e-02 1.86e+01 pdb=" N9 A 1 518 " 0.068 2.00e-02 2.50e+03 pdb=" C8 A 1 518 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A 1 518 " -0.007 2.00e-02 2.50e+03 pdb=" C5 A 1 518 " -0.005 2.00e-02 2.50e+03 pdb=" C6 A 1 518 " -0.008 2.00e-02 2.50e+03 pdb=" N6 A 1 518 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A 1 518 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A 1 518 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A 1 518 " 0.005 2.00e-02 2.50e+03 pdb=" C4 A 1 518 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 257 " -0.039 2.00e-02 2.50e+03 2.16e-02 1.40e+01 pdb=" N9 G 1 257 " 0.062 2.00e-02 2.50e+03 pdb=" C8 G 1 257 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G 1 257 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G 1 257 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G 1 257 " -0.007 2.00e-02 2.50e+03 pdb=" O6 G 1 257 " -0.001 2.00e-02 2.50e+03 pdb=" N1 G 1 257 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G 1 257 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G 1 257 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G 1 257 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G 1 257 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 1 515 " -0.038 2.00e-02 2.50e+03 2.10e-02 1.32e+01 pdb=" N9 G 1 515 " 0.061 2.00e-02 2.50e+03 pdb=" C8 G 1 515 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G 1 515 " -0.006 2.00e-02 2.50e+03 pdb=" C5 G 1 515 " -0.004 2.00e-02 2.50e+03 pdb=" C6 G 1 515 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G 1 515 " -0.005 2.00e-02 2.50e+03 pdb=" N1 G 1 515 " 0.000 2.00e-02 2.50e+03 pdb=" C2 G 1 515 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G 1 515 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G 1 515 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G 1 515 " -0.006 2.00e-02 2.50e+03 ... (remaining 6440 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 4523 2.66 - 3.22: 61875 3.22 - 3.78: 141454 3.78 - 4.34: 210166 4.34 - 4.90: 279639 Nonbonded interactions: 697657 Sorted by model distance: nonbonded pdb=" O2' U 1 661 " pdb=" OP2 G 1 662 " model vdw 2.100 2.440 nonbonded pdb=" O2' G 12432 " pdb=" OP2 C 12433 " model vdw 2.121 2.440 nonbonded pdb=" O2' G 11631 " pdb=" O5' A 11632 " model vdw 2.148 2.440 nonbonded pdb=" O2 C 11895 " pdb=" N2 G 11900 " model vdw 2.149 2.520 nonbonded pdb=" O2' A 1 10 " pdb=" OP1 U 1 11 " model vdw 2.161 2.440 ... (remaining 697652 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: 3.090 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: 0.080 Extract box with map and model: 12.240 Check model and map are aligned: 0.890 Set scattering table: 0.540 Process input model: 247.500 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 268.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.008 0.100 88598 Z= 0.460 Angle : 0.916 13.391 133457 Z= 0.599 Chirality : 0.059 0.848 17200 Planarity : 0.005 0.068 6443 Dihedral : 24.021 178.929 51764 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.63 % Allowed : 8.79 % Favored : 87.58 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 3.37 % 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: -3.55 (0.14), residues: 2617 helix: -2.60 (0.19), residues: 575 sheet: -1.77 (0.21), residues: 523 loop : -2.53 (0.13), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 213 HIS 0.008 0.001 HIS S 49 PHE 0.018 0.002 PHE X 50 TYR 0.028 0.002 TYR H 77 ARG 0.006 0.001 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 497 time to evaluate : 3.183 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8639 (pttt) cc_final: 0.8345 (ptmt) REVERT: A 65 LYS cc_start: 0.8077 (ptmm) cc_final: 0.7799 (ptmt) REVERT: A 85 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7820 (ptmt) REVERT: A 111 ARG cc_start: 0.6494 (ptt180) cc_final: 0.6260 (mtm110) REVERT: B 5 LYS cc_start: 0.7546 (tttt) cc_final: 0.7333 (mptt) REVERT: B 74 ILE cc_start: 0.7713 (mm) cc_final: 0.7506 (mt) REVERT: B 139 THR cc_start: 0.7988 (m) cc_final: 0.7498 (t) REVERT: B 147 LYS cc_start: 0.7272 (mttt) cc_final: 0.7034 (mttp) REVERT: B 167 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.5819 (ptmt) REVERT: C 11 ARG cc_start: 0.8107 (tpt170) cc_final: 0.7481 (ttp-110) REVERT: C 80 MET cc_start: 0.8140 (OUTLIER) cc_final: 0.7544 (mmm) REVERT: C 104 LYS cc_start: 0.6362 (tttt) cc_final: 0.5688 (mttt) REVERT: D 37 LYS cc_start: 0.8146 (mtpt) cc_final: 0.7708 (mmtt) REVERT: D 67 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7516 (mtm180) REVERT: E 4 LYS cc_start: 0.8766 (ptmt) cc_final: 0.8071 (ptpp) REVERT: E 37 LYS cc_start: 0.8147 (ttmm) cc_final: 0.7836 (mttm) REVERT: E 72 LYS cc_start: 0.7405 (tttt) cc_final: 0.7143 (tttm) REVERT: F 49 LYS cc_start: 0.8016 (mmtm) cc_final: 0.6719 (tttt) REVERT: F 90 PHE cc_start: 0.3940 (OUTLIER) cc_final: 0.2299 (p90) REVERT: G 58 GLU cc_start: 0.5971 (pt0) cc_final: 0.5499 (tt0) REVERT: G 69 GLN cc_start: 0.8494 (mt0) cc_final: 0.8278 (mt0) REVERT: J 3 LYS cc_start: 0.7215 (OUTLIER) cc_final: 0.6302 (mtpt) REVERT: J 28 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7226 (mtp180) REVERT: J 35 LYS cc_start: 0.8240 (tppt) cc_final: 0.7741 (tttt) REVERT: J 41 ASP cc_start: 0.3413 (OUTLIER) cc_final: 0.2824 (m-30) REVERT: L 3 LYS cc_start: 0.7099 (ptpp) cc_final: 0.6351 (ptpt) REVERT: L 14 GLN cc_start: 0.8649 (pt0) cc_final: 0.8332 (pt0) REVERT: L 55 ASP cc_start: 0.6040 (OUTLIER) cc_final: 0.5728 (t0) REVERT: L 71 LYS cc_start: 0.8092 (mttp) cc_final: 0.7794 (mttt) REVERT: M 24 GLU cc_start: 0.7787 (pp20) cc_final: 0.6407 (mm-30) REVERT: M 34 SER cc_start: 0.8023 (m) cc_final: 0.7753 (m) REVERT: N 27 MET cc_start: 0.7983 (pmm) cc_final: 0.7613 (pmm) REVERT: O 28 GLU cc_start: 0.4939 (pt0) cc_final: 0.4303 (mm-30) REVERT: O 38 ARG cc_start: 0.6226 (ptp-170) cc_final: 0.5854 (ptm-80) REVERT: P 37 ARG cc_start: 0.8083 (ttp-170) cc_final: 0.7847 (ttp-170) REVERT: R 18 LYS cc_start: 0.7831 (tttt) cc_final: 0.7554 (tttt) REVERT: R 24 MET cc_start: 0.8123 (ptm) cc_final: 0.7809 (ptp) REVERT: S 100 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7868 (mmtt) REVERT: V 15 LYS cc_start: 0.8283 (mttm) cc_final: 0.7993 (mttt) REVERT: V 38 ARG cc_start: 0.8257 (ttt180) cc_final: 0.7839 (ttt180) REVERT: V 76 TYR cc_start: 0.8637 (m-80) cc_final: 0.8179 (m-80) REVERT: V 121 LYS cc_start: 0.8300 (mttm) cc_final: 0.7911 (mmtp) REVERT: V 126 TYR cc_start: 0.7682 (m-80) cc_final: 0.7272 (m-80) REVERT: V 139 GLU cc_start: 0.7529 (mt-10) cc_final: 0.6882 (tt0) REVERT: V 142 GLU cc_start: 0.6982 (tp30) cc_final: 0.6623 (mt-10) REVERT: W 17 ARG cc_start: 0.7623 (mmm-85) cc_final: 0.7407 (mpt180) REVERT: W 66 LYS cc_start: 0.7801 (mtpt) cc_final: 0.7395 (mtpt) REVERT: W 76 TYR cc_start: 0.8994 (m-80) cc_final: 0.8378 (m-80) REVERT: X 10 GLU cc_start: 0.7034 (tp30) cc_final: 0.6773 (tp30) REVERT: X 16 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7864 (ptp-170) REVERT: X 98 GLU cc_start: 0.4949 (mt-10) cc_final: 0.4438 (tp30) REVERT: X 136 ILE cc_start: 0.7394 (mm) cc_final: 0.7163 (mp) REVERT: Y 59 LYS cc_start: 0.7083 (mmmt) cc_final: 0.6814 (mmmt) REVERT: Y 76 LYS cc_start: 0.8134 (tttp) cc_final: 0.7567 (mttp) REVERT: Y 136 GLU cc_start: 0.2976 (OUTLIER) cc_final: 0.2298 (mt-10) REVERT: Z 64 LYS cc_start: 0.8104 (mttt) cc_final: 0.7728 (mttt) REVERT: Z 101 THR cc_start: 0.8281 (m) cc_final: 0.7937 (p) REVERT: Z 106 GLN cc_start: 0.8269 (mm110) cc_final: 0.7689 (mt0) REVERT: a 22 LEU cc_start: 0.7031 (OUTLIER) cc_final: 0.6785 (tt) outliers start: 81 outliers final: 18 residues processed: 555 average time/residue: 0.8853 time to fit residues: 787.8669 Evaluate side-chains 445 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 418 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 167 LYS Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 90 PHE Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain J residue 3 LYS Chi-restraints excluded: chain J residue 28 ARG Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 20 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 28 LYS Chi-restraints excluded: chain a residue 102 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 453 optimal weight: 6.9990 chunk 407 optimal weight: 4.9990 chunk 225 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 274 optimal weight: 5.9990 chunk 217 optimal weight: 0.0770 chunk 420 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 255 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 487 optimal weight: 6.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN B 53 HIS B 54 HIS D 63 ASN D 90 GLN E 61 ASN F 54 ASN G 67 ASN J 30 ASN J 34 GLN L 143 HIS N 50 ASN O 40 ASN Q 35 ASN Q 43 GLN R 36 GLN S 119 GLN S 148 GLN S 158 ASN S 174 GLN V 11 ASN V 59 ASN V 78 HIS X 54 GLN a 15 HIS a 43 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 88598 Z= 0.319 Angle : 0.745 11.592 133457 Z= 0.378 Chirality : 0.044 0.333 17200 Planarity : 0.006 0.056 6443 Dihedral : 23.757 179.942 46431 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.81 % Favored : 94.15 % Rotamer: Outliers : 4.21 % Allowed : 14.21 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.25 (0.14), residues: 2617 helix: -2.59 (0.18), residues: 580 sheet: -1.37 (0.21), residues: 551 loop : -2.33 (0.13), residues: 1486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 213 HIS 0.009 0.002 HIS V 48 PHE 0.027 0.002 PHE X 50 TYR 0.027 0.002 TYR F 68 ARG 0.008 0.001 ARG Z 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 395 time to evaluate : 4.540 Fit side-chains REVERT: A 51 LYS cc_start: 0.8531 (pttt) cc_final: 0.8310 (ptpt) REVERT: A 65 LYS cc_start: 0.8052 (ptmm) cc_final: 0.7777 (ptmt) REVERT: B 5 LYS cc_start: 0.7612 (tttt) cc_final: 0.7331 (mptt) REVERT: B 102 ARG cc_start: 0.7883 (mtt180) cc_final: 0.7648 (mtt90) REVERT: B 108 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7951 (ttpp) REVERT: C 11 ARG cc_start: 0.7849 (tpt170) cc_final: 0.7477 (ttp-110) REVERT: C 84 LYS cc_start: 0.7596 (ttpt) cc_final: 0.7307 (ttpp) REVERT: D 37 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7894 (mmtt) REVERT: D 67 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7249 (mtm180) REVERT: E 4 LYS cc_start: 0.8744 (ptmt) cc_final: 0.8115 (ptpp) REVERT: E 40 ASN cc_start: 0.6757 (p0) cc_final: 0.6510 (t0) REVERT: E 52 MET cc_start: 0.7175 (mmm) cc_final: 0.6613 (mmt) REVERT: F 69 GLN cc_start: 0.6761 (mm110) cc_final: 0.6334 (mm-40) REVERT: G 58 GLU cc_start: 0.5742 (pt0) cc_final: 0.5331 (tt0) REVERT: J 3 LYS cc_start: 0.7133 (pttm) cc_final: 0.6004 (mtpt) REVERT: J 35 LYS cc_start: 0.8615 (tppt) cc_final: 0.7736 (tttp) REVERT: J 41 ASP cc_start: 0.3850 (OUTLIER) cc_final: 0.2513 (m-30) REVERT: L 71 LYS cc_start: 0.8097 (mttp) cc_final: 0.7880 (mttt) REVERT: M 5 GLN cc_start: 0.7519 (tt0) cc_final: 0.7291 (tt0) REVERT: M 24 GLU cc_start: 0.7599 (pp20) cc_final: 0.6446 (mm-30) REVERT: N 27 MET cc_start: 0.8119 (pmm) cc_final: 0.7596 (pmm) REVERT: O 1 MET cc_start: 0.4983 (ptm) cc_final: 0.4588 (ptp) REVERT: O 4 ASN cc_start: 0.7084 (m-40) cc_final: 0.6784 (m-40) REVERT: O 38 ARG cc_start: 0.6219 (ptp-170) cc_final: 0.5802 (ptm-80) REVERT: Q 15 LYS cc_start: 0.8062 (ptmt) cc_final: 0.7328 (ptpp) REVERT: R 24 MET cc_start: 0.7916 (ptm) cc_final: 0.7584 (ptp) REVERT: R 36 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7985 (tm-30) REVERT: S 31 SER cc_start: 0.8696 (m) cc_final: 0.8264 (p) REVERT: S 201 LYS cc_start: 0.6136 (mmmt) cc_final: 0.5480 (mptt) REVERT: V 15 LYS cc_start: 0.8052 (mttm) cc_final: 0.7831 (mttt) REVERT: V 100 ARG cc_start: 0.7135 (ttp-170) cc_final: 0.6852 (ttp-170) REVERT: V 103 GLU cc_start: 0.7579 (tt0) cc_final: 0.7375 (tt0) REVERT: W 17 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7003 (mtm-85) REVERT: W 53 LYS cc_start: 0.7256 (OUTLIER) cc_final: 0.6777 (mttt) REVERT: X 85 PHE cc_start: 0.6327 (OUTLIER) cc_final: 0.6018 (m-10) REVERT: X 109 ILE cc_start: 0.8897 (mm) cc_final: 0.8586 (mt) REVERT: Y 59 LYS cc_start: 0.7140 (mmmt) cc_final: 0.6911 (mmmt) REVERT: Y 76 LYS cc_start: 0.8242 (tttp) cc_final: 0.7571 (mttp) REVERT: Y 136 GLU cc_start: 0.2787 (OUTLIER) cc_final: 0.2307 (pt0) REVERT: Z 29 ARG cc_start: 0.7428 (ttm110) cc_final: 0.7076 (ttt180) REVERT: Z 61 ASN cc_start: 0.8147 (m-40) cc_final: 0.7827 (m-40) REVERT: Z 64 LYS cc_start: 0.8121 (mttt) cc_final: 0.7751 (mttt) REVERT: Z 106 GLN cc_start: 0.8251 (mm110) cc_final: 0.7697 (mt0) REVERT: a 102 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6409 (p90) outliers start: 94 outliers final: 63 residues processed: 449 average time/residue: 0.9001 time to fit residues: 673.6464 Evaluate side-chains 439 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 370 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 55 ASP Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain V residue 11 ASN Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 85 PHE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 271 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 405 optimal weight: 7.9990 chunk 332 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 488 optimal weight: 7.9990 chunk 527 optimal weight: 8.9990 chunk 435 optimal weight: 7.9990 chunk 484 optimal weight: 7.9990 chunk 166 optimal weight: 6.9990 chunk 391 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN H 38 ASN L 182 ASN N 45 ASN R 36 GLN V 48 HIS W 4 GLN Y 25 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 88598 Z= 0.482 Angle : 0.888 10.493 133457 Z= 0.438 Chirality : 0.049 0.390 17200 Planarity : 0.007 0.068 6443 Dihedral : 23.944 178.038 46400 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 6.01 % Allowed : 16.54 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.28 (0.14), residues: 2617 helix: -2.66 (0.18), residues: 571 sheet: -1.24 (0.21), residues: 556 loop : -2.41 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 213 HIS 0.009 0.002 HIS X 126 PHE 0.025 0.003 PHE X 50 TYR 0.025 0.003 TYR V 76 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 378 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6593 (pm20) REVERT: A 51 LYS cc_start: 0.8532 (pttt) cc_final: 0.8263 (ptpt) REVERT: A 65 LYS cc_start: 0.8042 (ptmm) cc_final: 0.7746 (ptmt) REVERT: B 5 LYS cc_start: 0.7694 (tttt) cc_final: 0.7425 (mptt) REVERT: B 108 LYS cc_start: 0.8157 (ttpt) cc_final: 0.7952 (ttpp) REVERT: B 111 GLU cc_start: 0.3507 (OUTLIER) cc_final: 0.1711 (tm-30) REVERT: B 175 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7117 (ttp80) REVERT: B 186 SER cc_start: 0.8190 (m) cc_final: 0.7980 (t) REVERT: C 11 ARG cc_start: 0.7830 (tpt170) cc_final: 0.7439 (ttp-110) REVERT: C 84 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7475 (ttpp) REVERT: D 24 LYS cc_start: 0.7519 (tttt) cc_final: 0.6741 (ttmm) REVERT: D 37 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7807 (mmtt) REVERT: D 67 ARG cc_start: 0.7568 (mtp180) cc_final: 0.7110 (mtm180) REVERT: E 4 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8143 (ptpp) REVERT: E 40 ASN cc_start: 0.6698 (p0) cc_final: 0.6264 (t0) REVERT: E 52 MET cc_start: 0.7306 (mmm) cc_final: 0.6683 (mmt) REVERT: F 69 GLN cc_start: 0.6705 (mm110) cc_final: 0.6160 (mm110) REVERT: G 58 GLU cc_start: 0.5581 (pt0) cc_final: 0.5284 (tt0) REVERT: H 63 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7326 (tt) REVERT: J 35 LYS cc_start: 0.8663 (tppt) cc_final: 0.7694 (tttt) REVERT: J 41 ASP cc_start: 0.3535 (OUTLIER) cc_final: 0.2498 (m-30) REVERT: J 45 LYS cc_start: 0.5394 (pttp) cc_final: 0.4315 (ttpt) REVERT: J 46 LYS cc_start: 0.8285 (mmtp) cc_final: 0.7983 (mttt) REVERT: J 48 TRP cc_start: 0.8235 (m100) cc_final: 0.7409 (m100) REVERT: K 16 GLU cc_start: 0.5504 (mm-30) cc_final: 0.5215 (tp30) REVERT: M 24 GLU cc_start: 0.7833 (pp20) cc_final: 0.6516 (mm-30) REVERT: M 43 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.7916 (tp) REVERT: N 27 MET cc_start: 0.8070 (pmm) cc_final: 0.7678 (pmm) REVERT: O 1 MET cc_start: 0.5326 (ptm) cc_final: 0.5076 (pmm) REVERT: O 38 ARG cc_start: 0.6172 (ptp-170) cc_final: 0.5809 (ptm-80) REVERT: Q 15 LYS cc_start: 0.8247 (ptmt) cc_final: 0.7428 (ptpp) REVERT: R 24 MET cc_start: 0.7930 (ptm) cc_final: 0.7592 (ptp) REVERT: R 36 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: V 61 SER cc_start: 0.8521 (t) cc_final: 0.8239 (p) REVERT: V 100 ARG cc_start: 0.7025 (ttp-170) cc_final: 0.6765 (ttp-170) REVERT: V 103 GLU cc_start: 0.7621 (tt0) cc_final: 0.7348 (tt0) REVERT: V 137 GLN cc_start: 0.6609 (OUTLIER) cc_final: 0.4774 (mp10) REVERT: V 144 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5283 (ptp-170) REVERT: W 1 MET cc_start: 0.7445 (tmt) cc_final: 0.7227 (tmt) REVERT: W 17 ARG cc_start: 0.7601 (mmm-85) cc_final: 0.7021 (mtm-85) REVERT: W 53 LYS cc_start: 0.7029 (OUTLIER) cc_final: 0.6363 (mptt) REVERT: W 76 TYR cc_start: 0.9141 (m-80) cc_final: 0.8926 (m-80) REVERT: X 70 ASN cc_start: 0.8139 (m-40) cc_final: 0.7861 (m-40) REVERT: X 109 ILE cc_start: 0.8901 (mm) cc_final: 0.8543 (mt) REVERT: Y 76 LYS cc_start: 0.8304 (tttp) cc_final: 0.7596 (mttp) REVERT: Z 29 ARG cc_start: 0.7493 (ttm110) cc_final: 0.7089 (ttt180) REVERT: Z 61 ASN cc_start: 0.8173 (m-40) cc_final: 0.7856 (m-40) REVERT: Z 64 LYS cc_start: 0.8085 (mttt) cc_final: 0.7666 (mttt) REVERT: Z 91 GLU cc_start: 0.6247 (mt-10) cc_final: 0.5806 (mp0) REVERT: Z 106 GLN cc_start: 0.8252 (mm110) cc_final: 0.7643 (mt0) REVERT: a 102 HIS cc_start: 0.6950 (OUTLIER) cc_final: 0.6426 (p-80) outliers start: 134 outliers final: 101 residues processed: 464 average time/residue: 0.8783 time to fit residues: 677.5040 Evaluate side-chains 484 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 372 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 66 ILE Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 115 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 482 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 328 optimal weight: 5.9990 chunk 490 optimal weight: 5.9990 chunk 519 optimal weight: 9.9990 chunk 256 optimal weight: 8.9990 chunk 464 optimal weight: 10.0000 chunk 139 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 65 GLN a 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 88598 Z= 0.355 Angle : 0.751 10.064 133457 Z= 0.377 Chirality : 0.044 0.359 17200 Planarity : 0.006 0.057 6443 Dihedral : 23.762 178.564 46396 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.63 % Allowed : 17.48 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.09 (0.14), residues: 2617 helix: -2.53 (0.19), residues: 580 sheet: -1.06 (0.22), residues: 547 loop : -2.30 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 213 HIS 0.006 0.002 HIS X 126 PHE 0.027 0.002 PHE X 50 TYR 0.020 0.002 TYR F 68 ARG 0.008 0.001 ARG R 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 375 time to evaluate : 3.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8519 (pttt) cc_final: 0.8271 (ptpt) REVERT: A 65 LYS cc_start: 0.8048 (ptmm) cc_final: 0.7795 (ptmt) REVERT: B 5 LYS cc_start: 0.7558 (tttt) cc_final: 0.7309 (mptt) REVERT: B 111 GLU cc_start: 0.3383 (OUTLIER) cc_final: 0.1609 (tm-30) REVERT: B 175 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8397 (ttm170) REVERT: B 186 SER cc_start: 0.8339 (m) cc_final: 0.8084 (t) REVERT: C 11 ARG cc_start: 0.7786 (tpt170) cc_final: 0.7426 (ttp-110) REVERT: C 84 LYS cc_start: 0.7679 (ttpt) cc_final: 0.7431 (ttpp) REVERT: D 24 LYS cc_start: 0.7430 (tttt) cc_final: 0.6664 (ttmm) REVERT: D 37 LYS cc_start: 0.8240 (mtpt) cc_final: 0.7776 (mmtt) REVERT: D 67 ARG cc_start: 0.7591 (mtp180) cc_final: 0.7130 (mtm180) REVERT: E 4 LYS cc_start: 0.8720 (ptmt) cc_final: 0.8108 (ptpp) REVERT: E 40 ASN cc_start: 0.6940 (p0) cc_final: 0.6366 (t0) REVERT: E 52 MET cc_start: 0.7285 (mmm) cc_final: 0.6727 (mmt) REVERT: E 75 TYR cc_start: 0.8419 (p90) cc_final: 0.8135 (p90) REVERT: F 69 GLN cc_start: 0.6846 (mm110) cc_final: 0.6391 (mm-40) REVERT: G 58 GLU cc_start: 0.5538 (pt0) cc_final: 0.5167 (tt0) REVERT: H 43 VAL cc_start: 0.7011 (p) cc_final: 0.6477 (m) REVERT: H 63 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7235 (tt) REVERT: J 35 LYS cc_start: 0.8590 (tppt) cc_final: 0.7728 (tttt) REVERT: J 41 ASP cc_start: 0.3749 (OUTLIER) cc_final: 0.2542 (m-30) REVERT: J 45 LYS cc_start: 0.5437 (OUTLIER) cc_final: 0.4254 (ttpt) REVERT: J 46 LYS cc_start: 0.8367 (mmtp) cc_final: 0.8155 (mttt) REVERT: J 48 TRP cc_start: 0.8212 (m100) cc_final: 0.7360 (m100) REVERT: M 24 GLU cc_start: 0.7791 (pp20) cc_final: 0.6477 (mm-30) REVERT: M 43 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.7875 (tp) REVERT: N 27 MET cc_start: 0.8048 (pmm) cc_final: 0.7626 (pmm) REVERT: O 38 ARG cc_start: 0.6167 (ptp-170) cc_final: 0.5687 (ptm-80) REVERT: O 39 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6078 (mp0) REVERT: Q 55 MET cc_start: 0.6970 (mmm) cc_final: 0.6510 (mmt) REVERT: R 24 MET cc_start: 0.7863 (ptm) cc_final: 0.7535 (ptp) REVERT: R 36 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: V 100 ARG cc_start: 0.7059 (ttp-170) cc_final: 0.6853 (ttp-170) REVERT: V 103 GLU cc_start: 0.7610 (tt0) cc_final: 0.7349 (tt0) REVERT: W 1 MET cc_start: 0.7260 (tmt) cc_final: 0.7017 (tmt) REVERT: W 17 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7020 (mtm-85) REVERT: W 53 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6474 (mptt) REVERT: W 76 TYR cc_start: 0.9124 (m-80) cc_final: 0.8845 (m-80) REVERT: Y 55 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7285 (m) REVERT: Y 76 LYS cc_start: 0.8312 (tttp) cc_final: 0.7615 (mttp) REVERT: Y 136 GLU cc_start: 0.2645 (OUTLIER) cc_final: 0.2216 (pt0) REVERT: Z 29 ARG cc_start: 0.7483 (ttm110) cc_final: 0.7139 (ttt180) REVERT: Z 61 ASN cc_start: 0.8189 (m-40) cc_final: 0.7845 (m-40) REVERT: Z 64 LYS cc_start: 0.8114 (mttt) cc_final: 0.7696 (mttt) REVERT: Z 91 GLU cc_start: 0.6322 (mt-10) cc_final: 0.5752 (mp0) REVERT: Z 106 GLN cc_start: 0.8238 (mm110) cc_final: 0.7640 (mt0) REVERT: a 102 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6516 (p-80) outliers start: 148 outliers final: 108 residues processed: 481 average time/residue: 0.8100 time to fit residues: 653.6981 Evaluate side-chains 483 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 363 time to evaluate : 3.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 432 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 386 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 442 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 265 optimal weight: 10.0000 chunk 465 optimal weight: 7.9990 chunk 130 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 36 GLN V 11 ASN X 38 GLN a 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 88598 Z= 0.457 Angle : 0.864 10.087 133457 Z= 0.427 Chirality : 0.048 0.383 17200 Planarity : 0.007 0.063 6443 Dihedral : 23.939 179.563 46396 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 7.40 % Allowed : 18.74 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.18 (0.14), residues: 2617 helix: -2.58 (0.18), residues: 581 sheet: -1.08 (0.22), residues: 542 loop : -2.38 (0.13), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 213 HIS 0.008 0.002 HIS Q 31 PHE 0.028 0.003 PHE X 50 TYR 0.024 0.003 TYR S 99 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 371 time to evaluate : 3.194 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8539 (pttt) cc_final: 0.8225 (ptpt) REVERT: A 65 LYS cc_start: 0.8102 (ptmm) cc_final: 0.7813 (ptmt) REVERT: B 111 GLU cc_start: 0.3663 (OUTLIER) cc_final: 0.1828 (tm-30) REVERT: B 175 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8329 (ttm170) REVERT: B 186 SER cc_start: 0.8408 (m) cc_final: 0.8171 (t) REVERT: C 11 ARG cc_start: 0.7854 (tpt170) cc_final: 0.7420 (ttp-110) REVERT: C 71 GLN cc_start: 0.8501 (mt0) cc_final: 0.8195 (mt0) REVERT: C 84 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7415 (ttpp) REVERT: D 24 LYS cc_start: 0.7503 (tttt) cc_final: 0.6691 (ttmm) REVERT: D 37 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7819 (mmtt) REVERT: D 67 ARG cc_start: 0.7730 (mtp180) cc_final: 0.7230 (mtm180) REVERT: E 4 LYS cc_start: 0.8724 (ptmt) cc_final: 0.8144 (ptpp) REVERT: F 69 GLN cc_start: 0.6816 (mm110) cc_final: 0.6405 (mm110) REVERT: G 58 GLU cc_start: 0.5616 (pt0) cc_final: 0.5204 (tt0) REVERT: H 43 VAL cc_start: 0.7097 (p) cc_final: 0.6538 (m) REVERT: H 63 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7054 (tt) REVERT: J 3 LYS cc_start: 0.7140 (pttm) cc_final: 0.6430 (ptmt) REVERT: J 41 ASP cc_start: 0.4142 (OUTLIER) cc_final: 0.2842 (m-30) REVERT: J 45 LYS cc_start: 0.5467 (OUTLIER) cc_final: 0.4293 (ttpt) REVERT: M 43 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7922 (tp) REVERT: O 38 ARG cc_start: 0.6123 (ptp-170) cc_final: 0.5751 (ptm-80) REVERT: Q 55 MET cc_start: 0.6958 (mmm) cc_final: 0.6516 (mmt) REVERT: R 24 MET cc_start: 0.7886 (ptm) cc_final: 0.7561 (ptp) REVERT: R 36 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7964 (tm-30) REVERT: V 137 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.4899 (mp10) REVERT: V 144 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5600 (ptp-170) REVERT: W 17 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.6922 (mtm-85) REVERT: W 53 LYS cc_start: 0.7072 (OUTLIER) cc_final: 0.6363 (mptt) REVERT: W 54 LYS cc_start: 0.7592 (ttmt) cc_final: 0.7178 (ttpp) REVERT: W 76 TYR cc_start: 0.9189 (m-80) cc_final: 0.8944 (m-80) REVERT: W 113 LYS cc_start: 0.7946 (tptt) cc_final: 0.7129 (ttmm) REVERT: X 70 ASN cc_start: 0.8130 (m-40) cc_final: 0.7882 (m-40) REVERT: X 109 ILE cc_start: 0.8879 (mm) cc_final: 0.8538 (mt) REVERT: Y 76 LYS cc_start: 0.8311 (tttp) cc_final: 0.7608 (mttp) REVERT: Y 136 GLU cc_start: 0.2547 (OUTLIER) cc_final: 0.2073 (mt-10) REVERT: Z 10 SER cc_start: 0.8540 (t) cc_final: 0.8195 (m) REVERT: Z 29 ARG cc_start: 0.7487 (ttm110) cc_final: 0.7103 (ttt180) REVERT: Z 61 ASN cc_start: 0.8210 (m-40) cc_final: 0.7895 (m-40) REVERT: Z 64 LYS cc_start: 0.8073 (mttt) cc_final: 0.7670 (mttt) outliers start: 165 outliers final: 142 residues processed: 488 average time/residue: 0.8186 time to fit residues: 670.7762 Evaluate side-chains 527 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 374 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain B residue 16 MET Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 77 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 12 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain R residue 26 ILE Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 11 ASN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 43 VAL Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 86 GLU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 174 optimal weight: 0.9980 chunk 467 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 304 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 519 optimal weight: 10.0000 chunk 431 optimal weight: 9.9990 chunk 240 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 171 optimal weight: 0.3980 chunk 272 optimal weight: 8.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 88598 Z= 0.216 Angle : 0.660 9.853 133457 Z= 0.339 Chirality : 0.040 0.334 17200 Planarity : 0.005 0.052 6443 Dihedral : 23.748 176.775 46394 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 6.23 % Allowed : 20.08 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.84 (0.15), residues: 2617 helix: -2.28 (0.19), residues: 575 sheet: -0.96 (0.22), residues: 563 loop : -2.14 (0.14), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 213 HIS 0.006 0.001 HIS Q 31 PHE 0.032 0.002 PHE X 50 TYR 0.014 0.002 TYR S 99 ARG 0.009 0.000 ARG R 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 380 time to evaluate : 3.160 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8522 (pttt) cc_final: 0.8267 (ptpt) REVERT: A 65 LYS cc_start: 0.8035 (ptmm) cc_final: 0.7808 (ptmt) REVERT: A 111 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.5849 (ptt-90) REVERT: B 111 GLU cc_start: 0.3557 (OUTLIER) cc_final: 0.1766 (tm-30) REVERT: B 175 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8379 (ttm170) REVERT: B 186 SER cc_start: 0.8408 (m) cc_final: 0.8174 (t) REVERT: C 11 ARG cc_start: 0.7820 (tpt170) cc_final: 0.7399 (ttp-110) REVERT: C 84 LYS cc_start: 0.7606 (ttpt) cc_final: 0.7288 (ttpp) REVERT: D 24 LYS cc_start: 0.7268 (tttt) cc_final: 0.6579 (ttmm) REVERT: D 37 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7850 (mmtt) REVERT: D 67 ARG cc_start: 0.7718 (mtp180) cc_final: 0.7261 (mtm180) REVERT: E 4 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8143 (ptpp) REVERT: E 52 MET cc_start: 0.7274 (mmm) cc_final: 0.6737 (mmt) REVERT: E 75 TYR cc_start: 0.8415 (p90) cc_final: 0.8175 (p90) REVERT: F 69 GLN cc_start: 0.6849 (mm110) cc_final: 0.6429 (mm110) REVERT: G 58 GLU cc_start: 0.5500 (pt0) cc_final: 0.5153 (tt0) REVERT: H 43 VAL cc_start: 0.6890 (p) cc_final: 0.6374 (m) REVERT: H 63 LEU cc_start: 0.7336 (OUTLIER) cc_final: 0.6997 (tt) REVERT: J 3 LYS cc_start: 0.7061 (pttm) cc_final: 0.6386 (ptmt) REVERT: J 35 LYS cc_start: 0.8200 (tppt) cc_final: 0.7189 (tttm) REVERT: J 41 ASP cc_start: 0.3951 (OUTLIER) cc_final: 0.2646 (m-30) REVERT: M 29 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6986 (mmtt) REVERT: M 43 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7866 (tp) REVERT: N 27 MET cc_start: 0.8033 (pmm) cc_final: 0.7579 (pmm) REVERT: O 38 ARG cc_start: 0.6205 (ptp-170) cc_final: 0.5673 (ptm-80) REVERT: O 39 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: Q 55 MET cc_start: 0.6942 (mmm) cc_final: 0.6510 (mmt) REVERT: R 24 MET cc_start: 0.7846 (ptm) cc_final: 0.7543 (ptp) REVERT: R 36 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: V 62 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7496 (mmmt) REVERT: V 137 GLN cc_start: 0.6511 (OUTLIER) cc_final: 0.4803 (mp10) REVERT: W 17 ARG cc_start: 0.7528 (mmm-85) cc_final: 0.6915 (mtm-85) REVERT: W 53 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6409 (mptt) REVERT: W 54 LYS cc_start: 0.7588 (ttmt) cc_final: 0.7202 (ttpp) REVERT: W 76 TYR cc_start: 0.9114 (m-80) cc_final: 0.8787 (m-80) REVERT: W 113 LYS cc_start: 0.7932 (tptt) cc_final: 0.7073 (ttmm) REVERT: Y 55 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7277 (m) REVERT: Y 76 LYS cc_start: 0.8309 (tttp) cc_final: 0.7598 (mttp) REVERT: Y 136 GLU cc_start: 0.2647 (OUTLIER) cc_final: 0.2214 (pt0) REVERT: Z 29 ARG cc_start: 0.7505 (ttm110) cc_final: 0.7171 (ttt180) REVERT: Z 61 ASN cc_start: 0.8220 (m-40) cc_final: 0.7892 (m-40) REVERT: Z 64 LYS cc_start: 0.8150 (mttt) cc_final: 0.7739 (mttt) REVERT: a 102 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6671 (p-80) outliers start: 139 outliers final: 106 residues processed: 470 average time/residue: 0.8193 time to fit residues: 643.1126 Evaluate side-chains 490 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 369 time to evaluate : 4.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 173 MET Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 62 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 20 ASN Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 500 optimal weight: 8.9990 chunk 58 optimal weight: 0.8980 chunk 296 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 293 optimal weight: 10.0000 chunk 437 optimal weight: 6.9990 chunk 290 optimal weight: 7.9990 chunk 517 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 315 optimal weight: 7.9990 chunk 238 optimal weight: 0.8980 overall best weight: 4.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN R 36 GLN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN a 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 88598 Z= 0.435 Angle : 0.826 10.037 133457 Z= 0.409 Chirality : 0.047 0.373 17200 Planarity : 0.006 0.061 6443 Dihedral : 23.850 179.376 46393 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 7.17 % Allowed : 20.04 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.02 (0.14), residues: 2617 helix: -2.41 (0.19), residues: 577 sheet: -1.01 (0.22), residues: 542 loop : -2.28 (0.13), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 213 HIS 0.008 0.002 HIS Q 31 PHE 0.028 0.003 PHE X 50 TYR 0.022 0.003 TYR V 76 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 365 time to evaluate : 3.172 Fit side-chains REVERT: A 51 LYS cc_start: 0.8562 (pttt) cc_final: 0.8258 (ptpt) REVERT: A 65 LYS cc_start: 0.8134 (ptmm) cc_final: 0.7827 (ptmt) REVERT: A 111 ARG cc_start: 0.6827 (OUTLIER) cc_final: 0.5856 (ptt-90) REVERT: B 111 GLU cc_start: 0.3507 (OUTLIER) cc_final: 0.1724 (tm-30) REVERT: B 175 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8355 (ttm170) REVERT: B 186 SER cc_start: 0.8447 (m) cc_final: 0.8216 (t) REVERT: C 11 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7419 (ttp-110) REVERT: C 84 LYS cc_start: 0.7741 (ttpt) cc_final: 0.7412 (ttpp) REVERT: D 24 LYS cc_start: 0.7391 (tttt) cc_final: 0.6660 (ttmm) REVERT: D 37 LYS cc_start: 0.8275 (mtpt) cc_final: 0.7806 (mmtt) REVERT: D 67 ARG cc_start: 0.7731 (mtp180) cc_final: 0.7245 (mtm180) REVERT: E 4 LYS cc_start: 0.8723 (ptmt) cc_final: 0.8133 (ptpp) REVERT: F 69 GLN cc_start: 0.6839 (mm110) cc_final: 0.6437 (mm110) REVERT: G 58 GLU cc_start: 0.5597 (pt0) cc_final: 0.5214 (tt0) REVERT: G 100 GLU cc_start: 0.6698 (mp0) cc_final: 0.6377 (mp0) REVERT: H 63 LEU cc_start: 0.7367 (OUTLIER) cc_final: 0.7063 (tt) REVERT: J 3 LYS cc_start: 0.7088 (pttm) cc_final: 0.6413 (ptmt) REVERT: J 35 LYS cc_start: 0.8294 (tppt) cc_final: 0.7294 (tttm) REVERT: J 41 ASP cc_start: 0.4060 (OUTLIER) cc_final: 0.2757 (m-30) REVERT: J 45 LYS cc_start: 0.5599 (OUTLIER) cc_final: 0.4212 (ttpt) REVERT: M 29 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.6985 (mmtt) REVERT: M 43 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.7921 (tp) REVERT: N 27 MET cc_start: 0.8024 (pmm) cc_final: 0.7630 (pmm) REVERT: O 38 ARG cc_start: 0.6230 (ptp-170) cc_final: 0.5807 (ptm-80) REVERT: Q 55 MET cc_start: 0.6965 (mmm) cc_final: 0.6515 (mmt) REVERT: R 24 MET cc_start: 0.7863 (ptm) cc_final: 0.7508 (ptp) REVERT: R 36 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: V 62 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7526 (mmmt) REVERT: V 137 GLN cc_start: 0.6634 (OUTLIER) cc_final: 0.4843 (mp10) REVERT: V 144 ARG cc_start: 0.5678 (OUTLIER) cc_final: 0.5235 (ptt180) REVERT: W 17 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.6901 (mtm-85) REVERT: W 53 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.6387 (mptt) REVERT: W 76 TYR cc_start: 0.9188 (m-80) cc_final: 0.8888 (m-80) REVERT: X 81 GLN cc_start: 0.7641 (OUTLIER) cc_final: 0.7400 (mt0) REVERT: Y 76 LYS cc_start: 0.8229 (tttp) cc_final: 0.7558 (mttp) REVERT: Z 29 ARG cc_start: 0.7478 (ttm110) cc_final: 0.7103 (ttt180) REVERT: Z 41 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8166 (ttm170) REVERT: Z 61 ASN cc_start: 0.8245 (m-40) cc_final: 0.7925 (m-40) REVERT: Z 64 LYS cc_start: 0.8132 (mttt) cc_final: 0.7924 (mttt) outliers start: 160 outliers final: 136 residues processed: 476 average time/residue: 0.8334 time to fit residues: 662.2927 Evaluate side-chains 512 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 361 time to evaluate : 3.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain R residue 36 GLN Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 194 ILE Chi-restraints excluded: chain V residue 11 ASN Chi-restraints excluded: chain V residue 44 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 62 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 12 SER Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 81 GLN Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 320 optimal weight: 4.9990 chunk 206 optimal weight: 0.2980 chunk 309 optimal weight: 4.9990 chunk 155 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 329 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 chunk 255 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 406 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN E 61 ASN ** S 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 88598 Z= 0.198 Angle : 0.651 9.694 133457 Z= 0.338 Chirality : 0.039 0.328 17200 Planarity : 0.005 0.053 6443 Dihedral : 23.760 177.654 46393 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 6.95 % Allowed : 20.48 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.80 (0.15), residues: 2617 helix: -2.18 (0.19), residues: 573 sheet: -0.89 (0.22), residues: 544 loop : -2.14 (0.14), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 213 HIS 0.005 0.001 HIS Q 31 PHE 0.034 0.002 PHE X 50 TYR 0.015 0.002 TYR S 99 ARG 0.004 0.000 ARG O 2 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 370 time to evaluate : 3.154 Fit side-chains REVERT: A 51 LYS cc_start: 0.8535 (pttt) cc_final: 0.8297 (ptpt) REVERT: A 65 LYS cc_start: 0.8016 (ptmm) cc_final: 0.7768 (ptmt) REVERT: A 111 ARG cc_start: 0.6788 (OUTLIER) cc_final: 0.5727 (ptt-90) REVERT: B 111 GLU cc_start: 0.3403 (OUTLIER) cc_final: 0.1587 (tm-30) REVERT: B 167 LYS cc_start: 0.7391 (mptt) cc_final: 0.6904 (mmtp) REVERT: B 175 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8379 (ttm170) REVERT: B 186 SER cc_start: 0.8425 (m) cc_final: 0.8195 (t) REVERT: C 11 ARG cc_start: 0.7816 (tpt170) cc_final: 0.7387 (ttp-110) REVERT: C 84 LYS cc_start: 0.7677 (ttpt) cc_final: 0.7362 (ttpp) REVERT: D 24 LYS cc_start: 0.7262 (tttt) cc_final: 0.6569 (ttmm) REVERT: D 37 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7869 (mmtt) REVERT: D 67 ARG cc_start: 0.7710 (mtp180) cc_final: 0.7271 (mtm180) REVERT: E 4 LYS cc_start: 0.8725 (ptmt) cc_final: 0.8136 (ptpp) REVERT: E 52 MET cc_start: 0.7268 (mmm) cc_final: 0.6733 (mmt) REVERT: E 75 TYR cc_start: 0.8428 (p90) cc_final: 0.8186 (p90) REVERT: F 69 GLN cc_start: 0.6836 (mm110) cc_final: 0.6430 (mm110) REVERT: G 58 GLU cc_start: 0.5494 (pt0) cc_final: 0.5118 (tt0) REVERT: G 100 GLU cc_start: 0.6699 (mp0) cc_final: 0.6381 (mp0) REVERT: H 63 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7013 (tt) REVERT: J 3 LYS cc_start: 0.7010 (pttm) cc_final: 0.6351 (ptmt) REVERT: J 35 LYS cc_start: 0.8301 (tppt) cc_final: 0.7349 (tttm) REVERT: J 41 ASP cc_start: 0.4000 (OUTLIER) cc_final: 0.2667 (m-30) REVERT: J 45 LYS cc_start: 0.5448 (OUTLIER) cc_final: 0.4192 (ttpt) REVERT: M 29 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.6960 (mmtt) REVERT: M 43 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7822 (tp) REVERT: N 27 MET cc_start: 0.8015 (pmm) cc_final: 0.7572 (pmm) REVERT: O 38 ARG cc_start: 0.6196 (ptp-170) cc_final: 0.5657 (ptm-80) REVERT: O 39 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5741 (mp0) REVERT: Q 55 MET cc_start: 0.6918 (mmm) cc_final: 0.6485 (mmt) REVERT: R 24 MET cc_start: 0.7860 (ptm) cc_final: 0.7555 (ptp) REVERT: S 195 THR cc_start: 0.7202 (OUTLIER) cc_final: 0.6831 (p) REVERT: V 137 GLN cc_start: 0.6535 (OUTLIER) cc_final: 0.4820 (mp10) REVERT: V 144 ARG cc_start: 0.5668 (OUTLIER) cc_final: 0.5205 (ptt180) REVERT: W 17 ARG cc_start: 0.7500 (mmm-85) cc_final: 0.6840 (mtm-85) REVERT: W 53 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6210 (mptt) REVERT: W 76 TYR cc_start: 0.9161 (m-80) cc_final: 0.8823 (m-80) REVERT: X 81 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: Y 55 THR cc_start: 0.7389 (OUTLIER) cc_final: 0.7159 (m) REVERT: Y 76 LYS cc_start: 0.8219 (tttp) cc_final: 0.7542 (mttp) REVERT: Y 136 GLU cc_start: 0.2660 (OUTLIER) cc_final: 0.2239 (pt0) REVERT: Z 29 ARG cc_start: 0.7506 (ttm110) cc_final: 0.7159 (ttt180) REVERT: Z 41 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.8131 (ttm170) REVERT: Z 61 ASN cc_start: 0.8214 (m-40) cc_final: 0.7886 (m-40) REVERT: Z 64 LYS cc_start: 0.8132 (mttt) cc_final: 0.7717 (mttt) REVERT: a 102 HIS cc_start: 0.7039 (OUTLIER) cc_final: 0.6765 (p-80) outliers start: 155 outliers final: 126 residues processed: 475 average time/residue: 0.8148 time to fit residues: 645.9403 Evaluate side-chains 515 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 371 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 10 SER Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain V residue 144 ARG Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 81 GLN Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 470 optimal weight: 10.0000 chunk 495 optimal weight: 9.9990 chunk 452 optimal weight: 9.9990 chunk 482 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 210 optimal weight: 0.9990 chunk 378 optimal weight: 8.9990 chunk 148 optimal weight: 0.0050 chunk 435 optimal weight: 8.9990 chunk 456 optimal weight: 7.9990 chunk 480 optimal weight: 7.9990 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 ASN M 5 GLN ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN a 37 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 88598 Z= 0.439 Angle : 0.831 10.048 133457 Z= 0.411 Chirality : 0.047 0.377 17200 Planarity : 0.006 0.065 6443 Dihedral : 23.842 179.794 46393 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 7.17 % Allowed : 20.84 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -3.00 (0.14), residues: 2617 helix: -2.39 (0.19), residues: 577 sheet: -1.04 (0.22), residues: 553 loop : -2.25 (0.14), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 213 HIS 0.008 0.002 HIS Q 31 PHE 0.027 0.003 PHE X 50 TYR 0.023 0.003 TYR V 76 ARG 0.007 0.001 ARG I 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 366 time to evaluate : 3.241 Fit side-chains REVERT: A 51 LYS cc_start: 0.8542 (pttt) cc_final: 0.8291 (ptpt) REVERT: A 65 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7777 (ptmt) REVERT: A 111 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.5767 (ptt-90) REVERT: B 111 GLU cc_start: 0.3496 (OUTLIER) cc_final: 0.1712 (tm-30) REVERT: B 175 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.8215 (ttm170) REVERT: B 186 SER cc_start: 0.8487 (m) cc_final: 0.8272 (t) REVERT: C 11 ARG cc_start: 0.7750 (tpt170) cc_final: 0.7357 (ttp-110) REVERT: C 84 LYS cc_start: 0.7753 (ttpt) cc_final: 0.7423 (ttpp) REVERT: D 24 LYS cc_start: 0.7391 (tttt) cc_final: 0.6653 (ttmm) REVERT: D 37 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7805 (mmtt) REVERT: E 4 LYS cc_start: 0.8719 (ptmt) cc_final: 0.8131 (ptpp) REVERT: E 52 MET cc_start: 0.7300 (mmm) cc_final: 0.6752 (mmt) REVERT: E 75 TYR cc_start: 0.8440 (p90) cc_final: 0.8153 (p90) REVERT: F 69 GLN cc_start: 0.6851 (mm110) cc_final: 0.6597 (mm110) REVERT: G 58 GLU cc_start: 0.5598 (pt0) cc_final: 0.5194 (tt0) REVERT: H 63 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.7062 (tt) REVERT: J 3 LYS cc_start: 0.7089 (pttm) cc_final: 0.6415 (ptmt) REVERT: J 35 LYS cc_start: 0.8342 (tppt) cc_final: 0.7361 (tttm) REVERT: J 41 ASP cc_start: 0.4007 (OUTLIER) cc_final: 0.2692 (m-30) REVERT: J 45 LYS cc_start: 0.5527 (OUTLIER) cc_final: 0.4158 (ttpt) REVERT: M 29 LYS cc_start: 0.7858 (OUTLIER) cc_final: 0.6980 (mmtt) REVERT: M 43 ILE cc_start: 0.8396 (OUTLIER) cc_final: 0.7924 (tp) REVERT: N 27 MET cc_start: 0.7997 (pmm) cc_final: 0.7631 (pmm) REVERT: O 38 ARG cc_start: 0.6186 (ptp-170) cc_final: 0.5758 (ptm-80) REVERT: Q 55 MET cc_start: 0.6971 (mmm) cc_final: 0.6519 (mmt) REVERT: R 24 MET cc_start: 0.7866 (ptm) cc_final: 0.7512 (ptp) REVERT: S 195 THR cc_start: 0.7219 (OUTLIER) cc_final: 0.6851 (p) REVERT: V 62 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7573 (mmmt) REVERT: V 137 GLN cc_start: 0.6640 (OUTLIER) cc_final: 0.4912 (mp10) REVERT: W 17 ARG cc_start: 0.7595 (mmm-85) cc_final: 0.6970 (mtm-85) REVERT: W 53 LYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6468 (mptt) REVERT: W 76 TYR cc_start: 0.9188 (m-80) cc_final: 0.8878 (m-80) REVERT: X 81 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7367 (mt0) REVERT: Y 76 LYS cc_start: 0.8226 (tttp) cc_final: 0.7558 (mttp) REVERT: Y 136 GLU cc_start: 0.2623 (OUTLIER) cc_final: 0.2181 (pt0) REVERT: Z 29 ARG cc_start: 0.7473 (ttm110) cc_final: 0.7097 (ttt180) REVERT: Z 41 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8165 (ttm170) REVERT: Z 61 ASN cc_start: 0.8285 (m-40) cc_final: 0.7960 (m-40) REVERT: Z 64 LYS cc_start: 0.8114 (mttt) cc_final: 0.7697 (mttt) outliers start: 160 outliers final: 135 residues processed: 479 average time/residue: 0.8199 time to fit residues: 655.7187 Evaluate side-chains 512 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 362 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 37 ARG Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 62 LYS Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 81 GLN Chi-restraints excluded: chain X residue 84 LYS Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 68 ILE Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 316 optimal weight: 7.9990 chunk 510 optimal weight: 10.0000 chunk 311 optimal weight: 4.9990 chunk 241 optimal weight: 9.9990 chunk 354 optimal weight: 10.0000 chunk 534 optimal weight: 0.8980 chunk 492 optimal weight: 5.9990 chunk 426 optimal weight: 10.0000 chunk 44 optimal weight: 0.9990 chunk 329 optimal weight: 4.9990 chunk 261 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN E 61 ASN ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 11 ASN a 37 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 88598 Z= 0.323 Angle : 0.754 9.987 133457 Z= 0.380 Chirality : 0.043 0.345 17200 Planarity : 0.006 0.059 6443 Dihedral : 23.816 179.802 46390 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 7.04 % Allowed : 20.98 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % 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: -2.99 (0.14), residues: 2617 helix: -2.40 (0.19), residues: 583 sheet: -1.04 (0.22), residues: 553 loop : -2.23 (0.14), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 213 HIS 0.007 0.001 HIS Q 31 PHE 0.028 0.002 PHE X 50 TYR 0.019 0.002 TYR S 99 ARG 0.010 0.001 ARG F 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5234 Ramachandran restraints generated. 2617 Oldfield, 0 Emsley, 2617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 363 time to evaluate : 3.182 Fit side-chains REVERT: A 51 LYS cc_start: 0.8547 (pttt) cc_final: 0.8305 (ptpt) REVERT: A 65 LYS cc_start: 0.8033 (ptmm) cc_final: 0.7718 (ptmt) REVERT: A 111 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.5746 (ptt-90) REVERT: B 111 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.1678 (tm-30) REVERT: B 175 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8368 (ttm170) REVERT: B 186 SER cc_start: 0.8479 (m) cc_final: 0.8266 (t) REVERT: C 11 ARG cc_start: 0.7850 (tpt170) cc_final: 0.7410 (ttp-110) REVERT: C 84 LYS cc_start: 0.7731 (ttpt) cc_final: 0.7403 (ttpp) REVERT: D 24 LYS cc_start: 0.7344 (tttt) cc_final: 0.6619 (ttmm) REVERT: D 37 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7767 (mmtt) REVERT: D 67 ARG cc_start: 0.7651 (mtp180) cc_final: 0.7263 (mtm180) REVERT: E 4 LYS cc_start: 0.8721 (ptmt) cc_final: 0.8129 (ptpp) REVERT: E 52 MET cc_start: 0.7294 (mmm) cc_final: 0.6745 (mmt) REVERT: E 75 TYR cc_start: 0.8456 (p90) cc_final: 0.8196 (p90) REVERT: F 69 GLN cc_start: 0.6852 (mm110) cc_final: 0.6584 (mm110) REVERT: G 58 GLU cc_start: 0.5584 (pt0) cc_final: 0.5177 (tt0) REVERT: H 63 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7006 (tt) REVERT: J 3 LYS cc_start: 0.7074 (pttm) cc_final: 0.6405 (ptmt) REVERT: J 35 LYS cc_start: 0.8327 (tppt) cc_final: 0.7353 (tttm) REVERT: J 41 ASP cc_start: 0.4003 (OUTLIER) cc_final: 0.2684 (m-30) REVERT: J 45 LYS cc_start: 0.5508 (OUTLIER) cc_final: 0.4171 (ttpt) REVERT: M 29 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.6984 (mmtt) REVERT: M 43 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.7868 (tp) REVERT: N 27 MET cc_start: 0.8003 (pmm) cc_final: 0.7620 (pmm) REVERT: O 38 ARG cc_start: 0.6172 (ptp-170) cc_final: 0.5618 (ptm-80) REVERT: O 39 GLU cc_start: 0.6449 (OUTLIER) cc_final: 0.5964 (mp0) REVERT: Q 55 MET cc_start: 0.6941 (mmm) cc_final: 0.6487 (mmt) REVERT: R 24 MET cc_start: 0.7851 (ptm) cc_final: 0.7495 (ptp) REVERT: S 195 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6839 (p) REVERT: V 137 GLN cc_start: 0.6572 (OUTLIER) cc_final: 0.4738 (mp10) REVERT: W 17 ARG cc_start: 0.7560 (mmm-85) cc_final: 0.6937 (mtm-85) REVERT: W 53 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6215 (mptt) REVERT: W 76 TYR cc_start: 0.9181 (m-80) cc_final: 0.8870 (m-80) REVERT: X 81 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7382 (mt0) REVERT: Y 76 LYS cc_start: 0.8221 (tttp) cc_final: 0.7551 (mttp) REVERT: Y 136 GLU cc_start: 0.2619 (OUTLIER) cc_final: 0.2197 (pt0) REVERT: Z 29 ARG cc_start: 0.7495 (ttm110) cc_final: 0.7127 (ttt180) REVERT: Z 41 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8182 (ttm170) REVERT: Z 61 ASN cc_start: 0.8275 (m-40) cc_final: 0.7952 (m-40) REVERT: Z 64 LYS cc_start: 0.8107 (mttt) cc_final: 0.7693 (mttt) REVERT: Z 106 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7683 (mt0) outliers start: 157 outliers final: 135 residues processed: 469 average time/residue: 0.8150 time to fit residues: 645.0623 Evaluate side-chains 517 residues out of total 2232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 366 time to evaluate : 3.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 111 ARG Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 117 GLU Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 139 THR Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 184 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 34 THR Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 95 LEU Chi-restraints excluded: chain E residue 35 ILE Chi-restraints excluded: chain E residue 67 ASP Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 108 SER Chi-restraints excluded: chain F residue 12 ILE Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 40 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 TYR Chi-restraints excluded: chain F residue 80 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 81 VAL Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 63 LEU Chi-restraints excluded: chain H residue 65 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 14 THR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 41 ASP Chi-restraints excluded: chain J residue 45 LYS Chi-restraints excluded: chain J residue 47 VAL Chi-restraints excluded: chain J residue 60 THR Chi-restraints excluded: chain K residue 10 THR Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 97 ASP Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain L residue 161 SER Chi-restraints excluded: chain L residue 176 ASN Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 194 VAL Chi-restraints excluded: chain L residue 209 VAL Chi-restraints excluded: chain L residue 215 ILE Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain M residue 36 VAL Chi-restraints excluded: chain M residue 43 ILE Chi-restraints excluded: chain N residue 46 CYS Chi-restraints excluded: chain O residue 14 ASP Chi-restraints excluded: chain O residue 16 ASN Chi-restraints excluded: chain O residue 39 GLU Chi-restraints excluded: chain O residue 43 THR Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 37 ARG Chi-restraints excluded: chain P residue 43 LEU Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 49 HIS Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 93 THR Chi-restraints excluded: chain S residue 110 LEU Chi-restraints excluded: chain S residue 118 VAL Chi-restraints excluded: chain S residue 127 ASP Chi-restraints excluded: chain S residue 132 GLU Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 175 VAL Chi-restraints excluded: chain S residue 184 LEU Chi-restraints excluded: chain S residue 195 THR Chi-restraints excluded: chain V residue 11 ASN Chi-restraints excluded: chain V residue 49 VAL Chi-restraints excluded: chain V residue 61 SER Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 64 GLU Chi-restraints excluded: chain V residue 74 VAL Chi-restraints excluded: chain V residue 137 GLN Chi-restraints excluded: chain W residue 2 ILE Chi-restraints excluded: chain W residue 6 THR Chi-restraints excluded: chain W residue 51 VAL Chi-restraints excluded: chain W residue 52 VAL Chi-restraints excluded: chain W residue 53 LYS Chi-restraints excluded: chain W residue 58 VAL Chi-restraints excluded: chain W residue 67 SER Chi-restraints excluded: chain W residue 96 THR Chi-restraints excluded: chain X residue 23 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 81 GLN Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 107 SER Chi-restraints excluded: chain X residue 131 SER Chi-restraints excluded: chain Y residue 39 THR Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 MET Chi-restraints excluded: chain Y residue 127 VAL Chi-restraints excluded: chain Y residue 136 GLU Chi-restraints excluded: chain Z residue 40 VAL Chi-restraints excluded: chain Z residue 41 ARG Chi-restraints excluded: chain Z residue 58 SER Chi-restraints excluded: chain Z residue 69 VAL Chi-restraints excluded: chain Z residue 76 GLU Chi-restraints excluded: chain Z residue 77 THR Chi-restraints excluded: chain Z residue 78 THR Chi-restraints excluded: chain Z residue 80 THR Chi-restraints excluded: chain Z residue 88 GLU Chi-restraints excluded: chain Z residue 97 GLN Chi-restraints excluded: chain Z residue 101 THR Chi-restraints excluded: chain Z residue 106 GLN Chi-restraints excluded: chain Z residue 118 ILE Chi-restraints excluded: chain a residue 18 VAL Chi-restraints excluded: chain a residue 22 LEU Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain a residue 44 ILE Chi-restraints excluded: chain a residue 45 ILE Chi-restraints excluded: chain a residue 52 THR Chi-restraints excluded: chain a residue 80 ILE Chi-restraints excluded: chain a residue 105 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 49 ARG Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 75 VAL Chi-restraints excluded: chain I residue 87 VAL Chi-restraints excluded: chain I residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 537 random chunks: chunk 338 optimal weight: 7.9990 chunk 453 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 426 optimal weight: 10.0000 chunk 178 optimal weight: 0.2980 chunk 438 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 71 GLN E 61 ASN ** R 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.149028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.127954 restraints weight = 93205.810| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 0.76 r_work: 0.2871 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.158 88598 Z= 0.357 Angle : 0.788 59.189 133457 Z= 0.405 Chirality : 0.044 0.918 17200 Planarity : 0.006 0.059 6443 Dihedral : 23.817 179.808 46390 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.37 % Favored : 92.59 % Rotamer: Outliers : 7.08 % Allowed : 20.89 % Favored : 72.03 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.37 % 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: -3.00 (0.14), residues: 2617 helix: -2.41 (0.19), residues: 583 sheet: -1.03 (0.22), residues: 553 loop : -2.24 (0.14), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 213 HIS 0.007 0.001 HIS Q 31 PHE 0.029 0.002 PHE X 50 TYR 0.020 0.002 TYR S 99 ARG 0.005 0.001 ARG I 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12132.64 seconds wall clock time: 217 minutes 49.32 seconds (13069.32 seconds total)