Starting phenix.real_space_refine on Tue Aug 6 23:04:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9z_10742/08_2024/6y9z_10742.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9z_10742/08_2024/6y9z_10742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9z_10742/08_2024/6y9z_10742.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9z_10742/08_2024/6y9z_10742.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9z_10742/08_2024/6y9z_10742.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9z_10742/08_2024/6y9z_10742.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 11607 2.51 5 N 3207 2.21 5 O 3466 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 79": "OE1" <-> "OE2" Residue "D ARG 82": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D GLU 159": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "G GLU 29": "OE1" <-> "OE2" Residue "G GLU 71": "OE1" <-> "OE2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G GLU 175": "OE1" <-> "OE2" Residue "G GLU 213": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "H GLU 29": "OE1" <-> "OE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H GLU 128": "OE1" <-> "OE2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H GLU 175": "OE1" <-> "OE2" Residue "H GLU 213": "OE1" <-> "OE2" Residue "N GLU 175": "OE1" <-> "OE2" Residue "N GLU 187": "OE1" <-> "OE2" Residue "Y GLU 28": "OE1" <-> "OE2" Residue "Y GLU 71": "OE1" <-> "OE2" Residue "Y GLU 79": "OE1" <-> "OE2" Residue "Y ARG 82": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Y GLU 128": "OE1" <-> "OE2" Residue "Y ARG 132": "NH1" <-> "NH2" Residue "d GLU 28": "OE1" <-> "OE2" Residue "d GLU 71": "OE1" <-> "OE2" Residue "d GLU 79": "OE1" <-> "OE2" Residue "d ARG 82": "NH1" <-> "NH2" Residue "d ARG 100": "NH1" <-> "NH2" Residue "d GLU 128": "OE1" <-> "OE2" Residue "d ARG 132": "NH1" <-> "NH2" Residue "d GLU 159": "OE1" <-> "OE2" Residue "d GLU 175": "OE1" <-> "OE2" Residue "e ARG 18": "NH1" <-> "NH2" Residue "e GLU 45": "OE1" <-> "OE2" Residue "e GLU 98": "OE1" <-> "OE2" Residue "e GLU 159": "OE1" <-> "OE2" Residue "e GLU 180": "OE1" <-> "OE2" Residue "j GLU 159": "OE1" <-> "OE2" Residue "j GLU 180": "OE1" <-> "OE2" Residue "k ARG 18": "NH1" <-> "NH2" Residue "k GLU 28": "OE1" <-> "OE2" Residue "k ARG 82": "NH1" <-> "NH2" Residue "k GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18418 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1132 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "B" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "C" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "D" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "G" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "H" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "J" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1258 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 157} Chain: "N" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "Y" Number of atoms: 1132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1132 Classifications: {'peptide': 146} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 134} Chain: "d" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Chain: "e" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 202} Chain: "j" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 584 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 4, 'TRANS': 69} Chain: "k" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1716 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 203} Time building chain proxies: 9.07, per 1000 atoms: 0.49 Number of scatterers: 18418 At special positions: 0 Unit cell: (139.92, 182.32, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 3466 8.00 N 3207 7.00 C 11607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS d 198 " - pdb=" SG CYS d 218 " distance=2.03 Simple disulfide: pdb=" SG CYS e 198 " - pdb=" SG CYS e 218 " distance=2.03 Simple disulfide: pdb=" SG CYS j 198 " - pdb=" SG CYS j 218 " distance=2.03 Simple disulfide: pdb=" SG CYS k 198 " - pdb=" SG CYS k 218 " distance=2.03 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: 7.26 Conformation dependent library (CDL) restraints added in 3.4 seconds 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4402 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 8 sheets defined 64.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 16 through 31 Processing helix chain 'A' and resid 35 through 44 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 62 through 84 Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 120 Processing helix chain 'A' and resid 125 through 145 Processing helix chain 'B' and resid 16 through 27 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 145 Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.526A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.792A pdb=" N TRP B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU B 187 " --> pdb=" O ASN B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.595A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.805A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.008A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.536A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.872A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 174 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.766A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 Processing helix chain 'G' and resid 35 through 44 Processing helix chain 'G' and resid 48 through 58 Processing helix chain 'G' and resid 62 through 84 Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 125 through 145 Processing helix chain 'G' and resid 160 through 175 Processing helix chain 'G' and resid 178 through 193 removed outlier: 3.896A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL G 191 " --> pdb=" O GLU G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 206 Processing helix chain 'G' and resid 210 through 218 Processing helix chain 'H' and resid 16 through 31 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 145 Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 3.895A pdb=" N TRP H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'J' and resid 29 through 42 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 135 through 144 removed outlier: 4.121A pdb=" N ARG J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.526A pdb=" N ILE N 153 " --> pdb=" O ILE N 150 " (cutoff:3.500A) Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 190 removed outlier: 3.789A pdb=" N TRP N 184 " --> pdb=" O GLU N 180 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 187 " --> pdb=" O ASN N 183 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.592A pdb=" N LEU N 205 " --> pdb=" O ILE N 201 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 removed outlier: 3.800A pdb=" N CYS N 218 " --> pdb=" O MET N 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 30 removed outlier: 3.676A pdb=" N LEU Y 20 " --> pdb=" O SER Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 44 Processing helix chain 'Y' and resid 48 through 58 Processing helix chain 'Y' and resid 62 through 83 Processing helix chain 'Y' and resid 100 through 105 Processing helix chain 'Y' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.672A pdb=" N LEU d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'd' and resid 35 through 44 Processing helix chain 'd' and resid 48 through 58 Processing helix chain 'd' and resid 62 through 83 Processing helix chain 'd' and resid 100 through 105 Processing helix chain 'd' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN d 114 " --> pdb=" O THR d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 146 removed outlier: 3.602A pdb=" N ARG d 132 " --> pdb=" O GLU d 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 174 Processing helix chain 'd' and resid 178 through 193 removed outlier: 4.765A pdb=" N LEU d 190 " --> pdb=" O THR d 186 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N VAL d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) Processing helix chain 'd' and resid 195 through 206 Processing helix chain 'd' and resid 210 through 218 Processing helix chain 'e' and resid 16 through 31 Processing helix chain 'e' and resid 35 through 44 Processing helix chain 'e' and resid 48 through 58 Processing helix chain 'e' and resid 62 through 84 Processing helix chain 'e' and resid 100 through 105 Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 125 through 145 Processing helix chain 'e' and resid 149 through 153 Processing helix chain 'e' and resid 160 through 175 Processing helix chain 'e' and resid 178 through 189 removed outlier: 3.692A pdb=" N GLU e 187 " --> pdb=" O ASN e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 206 removed outlier: 3.905A pdb=" N ILE e 201 " --> pdb=" O ASP e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 218 removed outlier: 3.510A pdb=" N MET e 214 " --> pdb=" O THR e 210 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 153 Processing helix chain 'j' and resid 160 through 175 Processing helix chain 'j' and resid 178 through 189 removed outlier: 3.690A pdb=" N GLU j 187 " --> pdb=" O ASN j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 195 through 206 removed outlier: 3.905A pdb=" N ILE j 201 " --> pdb=" O ASP j 197 " (cutoff:3.500A) Processing helix chain 'j' and resid 210 through 218 removed outlier: 3.511A pdb=" N MET j 214 " --> pdb=" O THR j 210 " (cutoff:3.500A) Processing helix chain 'k' and resid 16 through 31 removed outlier: 3.523A pdb=" N LEU k 20 " --> pdb=" O SER k 16 " (cutoff:3.500A) Processing helix chain 'k' and resid 36 through 44 Processing helix chain 'k' and resid 48 through 58 Processing helix chain 'k' and resid 62 through 84 Processing helix chain 'k' and resid 100 through 105 Processing helix chain 'k' and resid 110 through 119 Processing helix chain 'k' and resid 125 through 145 Processing helix chain 'k' and resid 160 through 176 Processing helix chain 'k' and resid 179 through 193 removed outlier: 4.359A pdb=" N LEU k 190 " --> pdb=" O THR k 186 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N VAL k 191 " --> pdb=" O GLU k 187 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN k 193 " --> pdb=" O LEU k 189 " (cutoff:3.500A) Processing helix chain 'k' and resid 195 through 204 Processing helix chain 'k' and resid 210 through 219 removed outlier: 3.922A pdb=" N CYS k 218 " --> pdb=" O MET k 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'B' and resid 2 through 3 removed outlier: 3.668A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.600A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'J' and resid 53 through 57 removed outlier: 4.394A pdb=" N ILE J 97 " --> pdb=" O CYS J 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET J 100 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 128 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER J 21 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL J 12 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 18 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP J 160 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA J 11 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE J 158 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 2 through 3 removed outlier: 3.665A pdb=" N VAL e 3 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL e 11 " --> pdb=" O VAL e 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'k' and resid 3 through 4 removed outlier: 3.539A pdb=" N VAL k 3 " --> pdb=" O VAL k 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL k 11 " --> pdb=" O VAL k 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1037 hydrogen bonds defined for protein. 3081 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.98 Time building geometry restraints manager: 7.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.44: 7779 1.44 - 1.67: 10790 1.67 - 1.90: 252 1.90 - 2.13: 0 2.13 - 2.36: 3 Bond restraints: 18824 Sorted by residual: bond pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 1.331 2.237 -0.907 1.23e-02 6.61e+03 5.43e+03 bond pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 1.522 2.365 -0.843 1.37e-02 5.33e+03 3.79e+03 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.456 2.273 -0.816 1.33e-02 5.65e+03 3.77e+03 bond pdb=" C HIS e 84 " pdb=" N PRO e 85 " ideal model delta sigma weight residual 1.330 1.513 -0.183 1.22e-02 6.72e+03 2.25e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.292 0.082 1.10e-02 8.26e+03 5.51e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 64.14 - 80.44: 1 80.44 - 96.73: 2 96.73 - 113.03: 10886 113.03 - 129.32: 14523 129.32 - 145.62: 155 Bond angle restraints: 25567 Sorted by residual: angle pdb=" N ARG C 18 " pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 113.23 64.14 49.09 1.24e+00 6.50e-01 1.57e+03 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" O ARG C 18 " ideal model delta sigma weight residual 119.27 92.00 27.27 1.17e+00 7.31e-01 5.43e+02 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" N THR C 19 " ideal model delta sigma weight residual 118.21 145.62 -27.41 1.36e+00 5.41e-01 4.06e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.30 108.72 13.58 1.36e+00 5.41e-01 9.97e+01 angle pdb=" C HIS e 84 " pdb=" N PRO e 85 " pdb=" CA PRO e 85 " ideal model delta sigma weight residual 120.03 129.81 -9.78 9.90e-01 1.02e+00 9.76e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10634 17.97 - 35.93: 714 35.93 - 53.90: 179 53.90 - 71.86: 19 71.86 - 89.83: 13 Dihedral angle restraints: 11559 sinusoidal: 4764 harmonic: 6795 Sorted by residual: dihedral pdb=" C ARG e 97 " pdb=" N ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual -122.60 -163.17 40.57 0 2.50e+00 1.60e-01 2.63e+02 dihedral pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual 122.80 158.73 -35.93 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N ARG C 18 " pdb=" C ARG C 18 " pdb=" CA ARG C 18 " pdb=" CB ARG C 18 " ideal model delta harmonic sigma weight residual 122.80 96.15 26.65 0 2.50e+00 1.60e-01 1.14e+02 ... (remaining 11556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.945: 2846 0.945 - 1.889: 1 1.889 - 2.834: 0 2.834 - 3.778: 0 3.778 - 4.723: 1 Chirality restraints: 2848 Sorted by residual: chirality pdb=" CA ARG C 18 " pdb=" N ARG C 18 " pdb=" C ARG C 18 " pdb=" CB ARG C 18 " both_signs ideal model delta sigma weight residual False 2.51 7.23 -4.72 2.00e-01 2.50e+01 5.58e+02 chirality pdb=" CA ARG e 97 " pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CB ARG e 97 " both_signs ideal model delta sigma weight residual False 2.51 0.89 1.62 2.00e-01 2.50e+01 6.58e+01 chirality pdb=" CA PRO J 30 " pdb=" N PRO J 30 " pdb=" C PRO J 30 " pdb=" CB PRO J 30 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.53e+00 ... (remaining 2845 not shown) Planarity restraints: 3345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 60 " 0.124 2.00e-02 2.50e+03 7.91e-02 1.09e+02 pdb=" CG PHE J 60 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE J 60 " -0.093 2.00e-02 2.50e+03 pdb=" CD2 PHE J 60 " -0.074 2.00e-02 2.50e+03 pdb=" CE1 PHE J 60 " 0.023 2.00e-02 2.50e+03 pdb=" CE2 PHE J 60 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE J 60 " 0.093 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 147 " -0.065 2.00e-02 2.50e+03 9.96e-02 9.93e+01 pdb=" C PRO C 147 " 0.171 2.00e-02 2.50e+03 pdb=" O PRO C 147 " -0.068 2.00e-02 2.50e+03 pdb=" N THR C 148 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG e 97 " 0.039 2.00e-02 2.50e+03 7.85e-02 6.16e+01 pdb=" C ARG e 97 " -0.136 2.00e-02 2.50e+03 pdb=" O ARG e 97 " 0.053 2.00e-02 2.50e+03 pdb=" N GLU e 98 " 0.044 2.00e-02 2.50e+03 ... (remaining 3342 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 6 2.29 - 2.94: 7722 2.94 - 3.59: 27516 3.59 - 4.25: 40149 4.25 - 4.90: 65743 Nonbonded interactions: 141136 Sorted by model distance: nonbonded pdb=" CG2 VAL G 181 " pdb=" OE1 GLU d 180 " model vdw 1.631 3.460 nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.829 3.120 nonbonded pdb=" OE1 GLU D 180 " pdb=" CG2 VAL H 181 " model vdw 1.926 3.460 nonbonded pdb=" CD2 LEU C 151 " pdb=" OE1 GLN k 192 " model vdw 2.058 3.460 nonbonded pdb=" NH2 ARG C 143 " pdb=" O GLN C 176 " model vdw 2.124 3.120 ... (remaining 141131 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'Y' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' selection = chain 'd' selection = chain 'e' selection = chain 'k' } ncs_group { reference = chain 'N' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.150 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: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 47.490 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.160 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.012 0.907 18824 Z= 0.832 Angle : 1.068 49.088 25567 Z= 0.727 Chirality : 0.108 4.723 2848 Planarity : 0.007 0.100 3345 Dihedral : 13.054 89.825 7127 Min Nonbonded Distance : 1.631 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.93 % Favored : 98.03 % Rotamer: Outliers : 0.45 % Allowed : 3.00 % Favored : 96.55 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.96 (0.16), residues: 2336 helix: -0.33 (0.13), residues: 1402 sheet: -1.56 (0.60), residues: 65 loop : -0.85 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 121 HIS 0.009 0.001 HIS J 70 PHE 0.124 0.009 PHE J 60 TYR 0.099 0.003 TYR J 48 ARG 0.018 0.001 ARG J 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4672 Ramachandran restraints generated. 2336 Oldfield, 0 Emsley, 2336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1185 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9334 (mp10) cc_final: 0.9089 (pp30) REVERT: A 27 VAL cc_start: 0.9711 (t) cc_final: 0.9259 (t) REVERT: A 49 PRO cc_start: 0.9711 (Cg_exo) cc_final: 0.9399 (Cg_endo) REVERT: A 55 MET cc_start: 0.9348 (mtp) cc_final: 0.9137 (mtp) REVERT: A 67 GLN cc_start: 0.9635 (tp40) cc_final: 0.9397 (tm-30) REVERT: A 72 THR cc_start: 0.9752 (m) cc_final: 0.9389 (p) REVERT: A 79 GLU cc_start: 0.9671 (tm-30) cc_final: 0.9457 (pp20) REVERT: A 114 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8352 (pt0) REVERT: A 125 PRO cc_start: 0.9091 (Cg_exo) cc_final: 0.8768 (Cg_endo) REVERT: A 135 ILE cc_start: 0.9473 (mt) cc_final: 0.9151 (mt) REVERT: B 5 ASN cc_start: 0.9137 (t0) cc_final: 0.8863 (m110) REVERT: B 28 GLU cc_start: 0.9350 (tt0) cc_final: 0.9134 (mt-10) REVERT: B 30 LYS cc_start: 0.8752 (mmtp) cc_final: 0.7826 (mmtm) REVERT: B 35 GLU cc_start: 0.9335 (pm20) cc_final: 0.8957 (pp20) REVERT: B 39 MET cc_start: 0.9497 (tpp) cc_final: 0.8999 (tpp) REVERT: B 51 ASP cc_start: 0.9007 (m-30) cc_final: 0.8782 (m-30) REVERT: B 59 VAL cc_start: 0.9548 (t) cc_final: 0.9293 (t) REVERT: B 75 GLU cc_start: 0.9567 (tt0) cc_final: 0.9354 (pt0) REVERT: B 114 GLN cc_start: 0.9224 (mt0) cc_final: 0.8554 (mt0) REVERT: B 118 MET cc_start: 0.9530 (mtm) cc_final: 0.9172 (mmm) REVERT: B 165 VAL cc_start: 0.9714 (p) cc_final: 0.8913 (m) REVERT: B 169 TYR cc_start: 0.9134 (m-10) cc_final: 0.8838 (m-10) REVERT: B 181 VAL cc_start: 0.9521 (t) cc_final: 0.9205 (t) REVERT: B 187 GLU cc_start: 0.9434 (mt-10) cc_final: 0.9191 (pp20) REVERT: B 193 ASN cc_start: 0.9108 (m110) cc_final: 0.8901 (m-40) REVERT: B 203 LYS cc_start: 0.7898 (mtpt) cc_final: 0.7696 (mtmt) REVERT: B 213 GLU cc_start: 0.9395 (mm-30) cc_final: 0.9128 (pt0) REVERT: C 23 TRP cc_start: 0.9387 (t-100) cc_final: 0.9006 (t-100) REVERT: C 26 VAL cc_start: 0.9507 (p) cc_final: 0.9241 (p) REVERT: C 32 PHE cc_start: 0.8316 (m-80) cc_final: 0.7847 (m-80) REVERT: C 43 LEU cc_start: 0.9433 (mt) cc_final: 0.8606 (mm) REVERT: C 51 ASP cc_start: 0.9568 (m-30) cc_final: 0.9156 (m-30) REVERT: C 53 ASN cc_start: 0.9492 (m-40) cc_final: 0.9238 (m110) REVERT: C 55 MET cc_start: 0.8965 (mtp) cc_final: 0.8753 (ttp) REVERT: C 72 THR cc_start: 0.9049 (m) cc_final: 0.8503 (p) REVERT: C 75 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9094 (pt0) REVERT: C 76 GLU cc_start: 0.9521 (mm-30) cc_final: 0.8962 (mm-30) REVERT: C 96 MET cc_start: -0.4731 (mmt) cc_final: -0.5321 (mtm) REVERT: C 103 ASP cc_start: 0.8946 (m-30) cc_final: 0.8516 (m-30) REVERT: C 104 ILE cc_start: 0.8580 (mm) cc_final: 0.8349 (tt) REVERT: C 118 MET cc_start: 0.8987 (ttm) cc_final: 0.8585 (ttm) REVERT: C 129 ILE cc_start: 0.9540 (mt) cc_final: 0.9322 (mt) REVERT: C 140 LYS cc_start: 0.9260 (mttt) cc_final: 0.8803 (tptp) REVERT: C 159 GLU cc_start: 0.9345 (tt0) cc_final: 0.9053 (mp0) REVERT: C 179 GLN cc_start: 0.9009 (tm-30) cc_final: 0.8560 (tm-30) REVERT: C 199 LYS cc_start: 0.9505 (tttt) cc_final: 0.9165 (tptp) REVERT: D 23 TRP cc_start: 0.9605 (t-100) cc_final: 0.8949 (t60) REVERT: D 24 VAL cc_start: 0.9609 (m) cc_final: 0.9398 (p) REVERT: D 49 PRO cc_start: 0.9559 (Cg_exo) cc_final: 0.9320 (Cg_endo) REVERT: D 52 LEU cc_start: 0.9739 (mt) cc_final: 0.9508 (mt) REVERT: D 55 MET cc_start: 0.9467 (mtp) cc_final: 0.8961 (ttp) REVERT: D 104 ILE cc_start: 0.9006 (tt) cc_final: 0.8618 (tt) REVERT: D 111 LEU cc_start: 0.9178 (tp) cc_final: 0.8836 (pp) REVERT: D 129 ILE cc_start: 0.9582 (mt) cc_final: 0.9239 (tp) REVERT: D 130 TYR cc_start: 0.8768 (t80) cc_final: 0.8501 (t80) REVERT: D 131 LYS cc_start: 0.9488 (ttmt) cc_final: 0.9116 (ptpt) REVERT: D 140 LYS cc_start: 0.9600 (mttt) cc_final: 0.9354 (tptp) REVERT: D 151 LEU cc_start: 0.8291 (mt) cc_final: 0.7994 (mt) REVERT: D 170 LYS cc_start: 0.9347 (tttt) cc_final: 0.9127 (ptmm) REVERT: D 172 LEU cc_start: 0.9649 (tp) cc_final: 0.9424 (tp) REVERT: D 215 MET cc_start: 0.8722 (mtm) cc_final: 0.7947 (mtm) REVERT: G 55 MET cc_start: 0.9630 (mtp) cc_final: 0.9339 (mtp) REVERT: G 66 MET cc_start: 0.9668 (mmm) cc_final: 0.9388 (ptp) REVERT: G 104 ILE cc_start: 0.9380 (tt) cc_final: 0.9121 (pt) REVERT: G 130 TYR cc_start: 0.9475 (t80) cc_final: 0.8954 (t80) REVERT: G 141 ILE cc_start: 0.9054 (mt) cc_final: 0.8598 (mt) REVERT: G 151 LEU cc_start: 0.9118 (mt) cc_final: 0.8690 (mt) REVERT: G 153 ILE cc_start: 0.7593 (mt) cc_final: 0.7150 (tp) REVERT: G 187 GLU cc_start: 0.9785 (mt-10) cc_final: 0.9381 (mm-30) REVERT: G 205 LEU cc_start: 0.8576 (tt) cc_final: 0.8355 (tt) REVERT: G 215 MET cc_start: 0.9380 (mtm) cc_final: 0.9143 (ppp) REVERT: H 10 MET cc_start: 0.6095 (ptt) cc_final: 0.5459 (ttm) REVERT: H 23 TRP cc_start: 0.9547 (t-100) cc_final: 0.8571 (t60) REVERT: H 33 SER cc_start: 0.8507 (m) cc_final: 0.8299 (p) REVERT: H 55 MET cc_start: 0.9006 (mtp) cc_final: 0.8589 (mmt) REVERT: H 66 MET cc_start: 0.9380 (mmm) cc_final: 0.9002 (mmm) REVERT: H 67 GLN cc_start: 0.9322 (tp40) cc_final: 0.8766 (mt0) REVERT: H 68 MET cc_start: 0.9352 (mtp) cc_final: 0.8946 (mmm) REVERT: H 114 GLN cc_start: 0.9407 (mm-40) cc_final: 0.9109 (pt0) REVERT: H 128 GLU cc_start: 0.9592 (mm-30) cc_final: 0.9222 (mp0) REVERT: H 131 LYS cc_start: 0.9367 (ttmt) cc_final: 0.9152 (tttp) REVERT: H 143 ARG cc_start: 0.9493 (mtt180) cc_final: 0.9253 (mtm180) REVERT: H 144 MET cc_start: 0.9442 (ttp) cc_final: 0.9106 (tmm) REVERT: H 152 ASP cc_start: 0.9448 (m-30) cc_final: 0.9016 (p0) REVERT: H 168 PHE cc_start: 0.9405 (t80) cc_final: 0.9059 (t80) REVERT: H 193 ASN cc_start: 0.8118 (m-40) cc_final: 0.7759 (m-40) REVERT: J 29 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8054 (p) REVERT: J 40 SER cc_start: 0.8505 (m) cc_final: 0.8063 (p) REVERT: J 44 LYS cc_start: 0.9216 (mmtm) cc_final: 0.8973 (mmtp) REVERT: J 113 PHE cc_start: 0.9130 (p90) cc_final: 0.8875 (p90) REVERT: J 138 ILE cc_start: 0.4674 (mm) cc_final: 0.4311 (mm) REVERT: J 152 THR cc_start: 0.7922 (p) cc_final: 0.7528 (t) REVERT: J 158 ILE cc_start: 0.8915 (mt) cc_final: 0.8612 (mt) REVERT: N 153 ILE cc_start: 0.8547 (mm) cc_final: 0.8316 (tp) REVERT: Y 49 PRO cc_start: 0.9614 (Cg_exo) cc_final: 0.9311 (Cg_endo) REVERT: Y 57 ASN cc_start: 0.9448 (m-40) cc_final: 0.9008 (p0) REVERT: Y 63 GLN cc_start: 0.9351 (mm-40) cc_final: 0.8392 (mp10) REVERT: Y 103 ASP cc_start: 0.9133 (t0) cc_final: 0.8930 (t70) REVERT: Y 120 ASN cc_start: 0.9126 (t0) cc_final: 0.8484 (p0) REVERT: Y 121 ASN cc_start: 0.9137 (m-40) cc_final: 0.8910 (m110) REVERT: Y 131 LYS cc_start: 0.9098 (ttmt) cc_final: 0.8832 (ptpt) REVERT: Y 136 LEU cc_start: 0.9789 (mt) cc_final: 0.9524 (mt) REVERT: d 15 ILE cc_start: 0.8154 (pt) cc_final: 0.7730 (mt) REVERT: d 23 TRP cc_start: 0.9523 (t-100) cc_final: 0.8908 (t60) REVERT: d 25 LYS cc_start: 0.9282 (tttt) cc_final: 0.8991 (tptp) REVERT: d 30 LYS cc_start: 0.7751 (mttm) cc_final: 0.7452 (mtpt) REVERT: d 55 MET cc_start: 0.9396 (mtp) cc_final: 0.8923 (ptm) REVERT: d 67 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8934 (mt0) REVERT: d 76 GLU cc_start: 0.9752 (mm-30) cc_final: 0.9350 (mt-10) REVERT: d 168 PHE cc_start: 0.9454 (t80) cc_final: 0.8924 (t80) REVERT: e 25 LYS cc_start: 0.9754 (mttt) cc_final: 0.9510 (ptpp) REVERT: e 43 LEU cc_start: 0.8892 (mt) cc_final: 0.8579 (mp) REVERT: e 113 GLU cc_start: 0.9285 (mt-10) cc_final: 0.9035 (mt-10) REVERT: e 139 ASN cc_start: 0.9751 (m-40) cc_final: 0.9465 (t0) REVERT: e 140 LYS cc_start: 0.9651 (mttt) cc_final: 0.9196 (mttp) REVERT: e 145 TYR cc_start: 0.7325 (m-80) cc_final: 0.7021 (m-80) REVERT: e 169 TYR cc_start: 0.9261 (m-10) cc_final: 0.9055 (m-10) REVERT: e 214 MET cc_start: 0.8849 (mtt) cc_final: 0.8555 (mmt) REVERT: j 181 VAL cc_start: 0.9609 (t) cc_final: 0.9346 (t) REVERT: j 191 VAL cc_start: 0.8698 (t) cc_final: 0.8016 (p) REVERT: k 52 LEU cc_start: 0.9686 (mt) cc_final: 0.9265 (mt) REVERT: k 72 THR cc_start: 0.9408 (m) cc_final: 0.9112 (p) REVERT: k 79 GLU cc_start: 0.9658 (mt-10) cc_final: 0.9216 (tp30) REVERT: k 80 TRP cc_start: 0.9614 (t-100) cc_final: 0.9334 (t-100) REVERT: k 81 ASP cc_start: 0.9524 (t70) cc_final: 0.9284 (m-30) REVERT: k 82 ARG cc_start: 0.9187 (ttp80) cc_final: 0.8631 (ttp80) REVERT: k 83 VAL cc_start: 0.9737 (p) cc_final: 0.8947 (p) REVERT: k 104 ILE cc_start: 0.8484 (mm) cc_final: 0.7994 (mm) REVERT: k 130 TYR cc_start: 0.9377 (t80) cc_final: 0.9097 (t80) REVERT: k 140 LYS cc_start: 0.9476 (mttt) cc_final: 0.8932 (tmtt) REVERT: k 168 PHE cc_start: 0.9588 (t80) cc_final: 0.9058 (t80) REVERT: k 179 GLN cc_start: 0.9390 (tp-100) cc_final: 0.8946 (tp-100) REVERT: k 180 GLU cc_start: 0.9338 (mp0) cc_final: 0.9128 (mp0) REVERT: k 182 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9089 (ptpt) REVERT: k 185 MET cc_start: 0.9501 (mtm) cc_final: 0.9074 (mtm) REVERT: k 187 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9318 (pt0) REVERT: k 191 VAL cc_start: 0.9036 (m) cc_final: 0.8609 (m) REVERT: k 193 ASN cc_start: 0.8937 (m110) cc_final: 0.8309 (m-40) REVERT: k 212 GLU cc_start: 0.9486 (tt0) cc_final: 0.9220 (pm20) outliers start: 9 outliers final: 2 residues processed: 1187 average time/residue: 0.3541 time to fit residues: 589.5589 Evaluate side-chains 760 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 757 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 20.0000 chunk 177 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 119 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 183 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 212 optimal weight: 50.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN B 7 GLN B 9 GLN B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 GLN B 183 ASN B 219 GLN C 57 ASN C 62 HIS C 192 GLN C 219 GLN D 4 GLN D 95 GLN D 114 GLN G 4 GLN G 84 HIS G 179 GLN G 183 ASN H 4 GLN H 183 ASN H 193 ASN N 219 GLN Y 4 GLN Y 21 ASN Y 95 GLN d 4 GLN d 95 GLN e 4 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 GLN j 219 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 GLN k 112 GLN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 18824 Z= 0.256 Angle : 0.700 8.320 25567 Z= 0.367 Chirality : 0.046 0.291 2848 Planarity : 0.006 0.075 3345 Dihedral : 4.217 27.951 2500 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.35 % Allowed : 4.55 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.15 (0.17), residues: 2338 helix: 0.25 (0.13), residues: 1440 sheet: -1.56 (0.62), residues: 67 loop : -0.38 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 133 HIS 0.006 0.001 HIS B 62 PHE 0.038 0.003 PHE J 60 TYR 0.017 0.002 TYR D 169 ARG 0.008 0.001 ARG d 173 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 938 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9450 (mp10) cc_final: 0.9055 (pp30) REVERT: A 27 VAL cc_start: 0.9685 (t) cc_final: 0.9435 (t) REVERT: A 28 GLU cc_start: 0.9633 (mm-30) cc_final: 0.9305 (mm-30) REVERT: A 52 LEU cc_start: 0.9801 (mt) cc_final: 0.9272 (mt) REVERT: A 56 LEU cc_start: 0.9814 (mt) cc_final: 0.9329 (mt) REVERT: A 67 GLN cc_start: 0.9557 (tp40) cc_final: 0.9239 (tm-30) REVERT: A 68 MET cc_start: 0.9318 (mtm) cc_final: 0.9021 (ptp) REVERT: A 72 THR cc_start: 0.9781 (m) cc_final: 0.9277 (p) REVERT: A 100 ARG cc_start: 0.9597 (ttm-80) cc_final: 0.9230 (tpp80) REVERT: A 125 PRO cc_start: 0.9009 (Cg_exo) cc_final: 0.8690 (Cg_endo) REVERT: A 135 ILE cc_start: 0.9343 (mt) cc_final: 0.9106 (mt) REVERT: B 5 ASN cc_start: 0.8978 (t0) cc_final: 0.8651 (m110) REVERT: B 25 LYS cc_start: 0.9600 (ptpp) cc_final: 0.9395 (pttm) REVERT: B 30 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8449 (mppt) REVERT: B 32 PHE cc_start: 0.8255 (m-10) cc_final: 0.8003 (m-80) REVERT: B 39 MET cc_start: 0.9540 (tpp) cc_final: 0.9046 (tpt) REVERT: B 68 MET cc_start: 0.9555 (mtm) cc_final: 0.9221 (mtt) REVERT: B 118 MET cc_start: 0.9568 (mtm) cc_final: 0.9256 (mmm) REVERT: B 128 GLU cc_start: 0.9374 (mp0) cc_final: 0.9154 (mp0) REVERT: B 141 ILE cc_start: 0.9510 (pt) cc_final: 0.9297 (mm) REVERT: B 144 MET cc_start: 0.8867 (ttt) cc_final: 0.8654 (ttt) REVERT: B 169 TYR cc_start: 0.9409 (m-10) cc_final: 0.8797 (m-10) REVERT: B 181 VAL cc_start: 0.9589 (t) cc_final: 0.8885 (p) REVERT: B 185 MET cc_start: 0.9739 (ptp) cc_final: 0.9345 (ptp) REVERT: B 187 GLU cc_start: 0.9531 (mt-10) cc_final: 0.9252 (pp20) REVERT: B 213 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9115 (pt0) REVERT: B 214 MET cc_start: 0.9185 (mtt) cc_final: 0.8925 (mtt) REVERT: C 10 MET cc_start: 0.8530 (mtt) cc_final: 0.8289 (ttm) REVERT: C 15 ILE cc_start: 0.8599 (tp) cc_final: 0.8322 (tp) REVERT: C 23 TRP cc_start: 0.9477 (t-100) cc_final: 0.8971 (t-100) REVERT: C 43 LEU cc_start: 0.9505 (mt) cc_final: 0.8830 (mm) REVERT: C 55 MET cc_start: 0.9163 (mtp) cc_final: 0.8875 (mtt) REVERT: C 76 GLU cc_start: 0.9506 (mm-30) cc_final: 0.8986 (mm-30) REVERT: C 96 MET cc_start: -0.5428 (mmt) cc_final: -0.5806 (mtm) REVERT: C 103 ASP cc_start: 0.8809 (m-30) cc_final: 0.8485 (m-30) REVERT: C 104 ILE cc_start: 0.8340 (mm) cc_final: 0.7678 (mm) REVERT: C 114 GLN cc_start: 0.9676 (mt0) cc_final: 0.9398 (mt0) REVERT: C 133 TRP cc_start: 0.8917 (m-10) cc_final: 0.8529 (m100) REVERT: C 140 LYS cc_start: 0.9282 (mttt) cc_final: 0.8807 (tptp) REVERT: C 144 MET cc_start: 0.8787 (tmm) cc_final: 0.8537 (tmm) REVERT: C 153 ILE cc_start: 0.9313 (mt) cc_final: 0.9095 (mt) REVERT: C 166 ASP cc_start: 0.8923 (t0) cc_final: 0.7685 (t70) REVERT: D 23 TRP cc_start: 0.9563 (t-100) cc_final: 0.8948 (t60) REVERT: D 24 VAL cc_start: 0.9714 (m) cc_final: 0.9511 (m) REVERT: D 39 MET cc_start: 0.9696 (mmp) cc_final: 0.9288 (mmm) REVERT: D 49 PRO cc_start: 0.9493 (Cg_exo) cc_final: 0.9271 (Cg_endo) REVERT: D 52 LEU cc_start: 0.9721 (mt) cc_final: 0.9376 (mt) REVERT: D 53 ASN cc_start: 0.9200 (m-40) cc_final: 0.8940 (m110) REVERT: D 55 MET cc_start: 0.9594 (mtp) cc_final: 0.9070 (ttp) REVERT: D 129 ILE cc_start: 0.9556 (mt) cc_final: 0.9276 (tp) REVERT: D 130 TYR cc_start: 0.8784 (t80) cc_final: 0.8411 (t80) REVERT: D 131 LYS cc_start: 0.9532 (ttmt) cc_final: 0.8992 (mttp) REVERT: D 140 LYS cc_start: 0.9625 (mttt) cc_final: 0.9355 (tptp) REVERT: D 215 MET cc_start: 0.8337 (mtm) cc_final: 0.7516 (mtm) REVERT: G 25 LYS cc_start: 0.9395 (ptpp) cc_final: 0.9184 (ptpp) REVERT: G 112 GLN cc_start: 0.9621 (mp10) cc_final: 0.9415 (mp10) REVERT: G 140 LYS cc_start: 0.9718 (mtpp) cc_final: 0.9457 (mtpp) REVERT: G 168 PHE cc_start: 0.9213 (t80) cc_final: 0.8950 (t80) REVERT: G 188 THR cc_start: 0.9213 (p) cc_final: 0.8969 (p) REVERT: H 25 LYS cc_start: 0.9735 (tttt) cc_final: 0.9476 (tppt) REVERT: H 30 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7189 (ptpt) REVERT: H 33 SER cc_start: 0.8676 (m) cc_final: 0.8389 (t) REVERT: H 39 MET cc_start: 0.9166 (mtt) cc_final: 0.8933 (mtt) REVERT: H 55 MET cc_start: 0.9081 (mtp) cc_final: 0.8839 (mmt) REVERT: H 66 MET cc_start: 0.9452 (mmm) cc_final: 0.9017 (mmm) REVERT: H 67 GLN cc_start: 0.9343 (tp40) cc_final: 0.8943 (mt0) REVERT: H 100 ARG cc_start: 0.9234 (ttt-90) cc_final: 0.8587 (mmp-170) REVERT: H 118 MET cc_start: 0.8665 (mmm) cc_final: 0.8037 (mmm) REVERT: H 128 GLU cc_start: 0.9706 (mm-30) cc_final: 0.9356 (mp0) REVERT: H 143 ARG cc_start: 0.9490 (mtt180) cc_final: 0.9250 (mtm180) REVERT: H 145 TYR cc_start: 0.9006 (m-80) cc_final: 0.8654 (m-10) REVERT: H 152 ASP cc_start: 0.9556 (m-30) cc_final: 0.9060 (p0) REVERT: H 161 PHE cc_start: 0.8699 (t80) cc_final: 0.8337 (t80) REVERT: H 182 LYS cc_start: 0.9765 (pttp) cc_final: 0.9490 (pttp) REVERT: J 29 VAL cc_start: 0.8838 (t) cc_final: 0.8540 (p) REVERT: J 36 PHE cc_start: 0.9597 (t80) cc_final: 0.9394 (t80) REVERT: J 40 SER cc_start: 0.8798 (m) cc_final: 0.7854 (p) REVERT: J 48 TYR cc_start: 0.8481 (m-10) cc_final: 0.8172 (m-80) REVERT: J 60 PHE cc_start: 0.7523 (t80) cc_final: 0.6733 (t80) REVERT: J 83 PHE cc_start: 0.8407 (p90) cc_final: 0.7907 (p90) REVERT: J 84 GLU cc_start: 0.7941 (pm20) cc_final: 0.7485 (pp20) REVERT: J 113 PHE cc_start: 0.9058 (p90) cc_final: 0.8639 (p90) REVERT: J 119 THR cc_start: 0.7216 (p) cc_final: 0.6278 (m) REVERT: J 156 ILE cc_start: 0.8981 (tp) cc_final: 0.8741 (tp) REVERT: N 166 ASP cc_start: 0.9174 (t0) cc_final: 0.8913 (t70) REVERT: N 178 SER cc_start: 0.8599 (p) cc_final: 0.8206 (t) REVERT: N 180 GLU cc_start: 0.9158 (pm20) cc_final: 0.8948 (pm20) REVERT: N 203 LYS cc_start: 0.7795 (pttt) cc_final: 0.7576 (pttt) REVERT: N 213 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9214 (pt0) REVERT: Y 10 MET cc_start: 0.9121 (pmm) cc_final: 0.8708 (mmp) REVERT: Y 28 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9147 (mm-30) REVERT: Y 32 PHE cc_start: 0.8120 (m-80) cc_final: 0.7790 (m-10) REVERT: Y 63 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8745 (mp10) REVERT: Y 67 GLN cc_start: 0.9756 (mm-40) cc_final: 0.9431 (mm-40) REVERT: Y 68 MET cc_start: 0.9484 (mtm) cc_final: 0.9090 (mtp) REVERT: Y 71 GLU cc_start: 0.9565 (mt-10) cc_final: 0.9279 (mt-10) REVERT: Y 75 GLU cc_start: 0.9487 (OUTLIER) cc_final: 0.9063 (mp0) REVERT: Y 79 GLU cc_start: 0.9450 (tp30) cc_final: 0.9198 (pp20) REVERT: Y 100 ARG cc_start: 0.9148 (ttm-80) cc_final: 0.8734 (tpp80) REVERT: Y 103 ASP cc_start: 0.9248 (t0) cc_final: 0.8924 (t70) REVERT: Y 131 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8846 (ptpt) REVERT: d 15 ILE cc_start: 0.7990 (pt) cc_final: 0.7548 (mp) REVERT: d 25 LYS cc_start: 0.9282 (tttt) cc_final: 0.9025 (tptp) REVERT: d 30 LYS cc_start: 0.8018 (mttm) cc_final: 0.7782 (mtpt) REVERT: d 39 MET cc_start: 0.8956 (mtm) cc_final: 0.8036 (mtt) REVERT: d 67 GLN cc_start: 0.9252 (tp-100) cc_final: 0.8773 (mt0) REVERT: d 68 MET cc_start: 0.9004 (mmm) cc_final: 0.8766 (mmp) REVERT: d 76 GLU cc_start: 0.9407 (mm-30) cc_final: 0.9084 (mt-10) REVERT: d 143 ARG cc_start: 0.8843 (tpt170) cc_final: 0.8615 (tpt170) REVERT: d 168 PHE cc_start: 0.9402 (t80) cc_final: 0.9178 (t80) REVERT: e 10 MET cc_start: 0.9082 (mmm) cc_final: 0.8612 (tpp) REVERT: e 23 TRP cc_start: 0.9364 (t-100) cc_final: 0.8861 (t-100) REVERT: e 39 MET cc_start: 0.9664 (mtm) cc_final: 0.9239 (mtm) REVERT: e 55 MET cc_start: 0.9488 (mtp) cc_final: 0.9219 (tpp) REVERT: e 57 ASN cc_start: 0.9588 (m110) cc_final: 0.9323 (p0) REVERT: e 104 ILE cc_start: 0.8371 (mt) cc_final: 0.7787 (mt) REVERT: e 128 GLU cc_start: 0.9650 (mp0) cc_final: 0.9388 (mp0) REVERT: e 140 LYS cc_start: 0.9703 (mttt) cc_final: 0.9037 (mttp) REVERT: e 166 ASP cc_start: 0.8915 (t0) cc_final: 0.8697 (t0) REVERT: e 167 ARG cc_start: 0.8495 (ptp-110) cc_final: 0.8130 (mtm110) REVERT: e 169 TYR cc_start: 0.9641 (m-10) cc_final: 0.8889 (m-10) REVERT: e 170 LYS cc_start: 0.9755 (tttt) cc_final: 0.9497 (pptt) REVERT: e 182 LYS cc_start: 0.9575 (mttt) cc_final: 0.9102 (mmmm) REVERT: e 205 LEU cc_start: 0.7567 (mp) cc_final: 0.5188 (tp) REVERT: j 150 ILE cc_start: 0.9214 (tp) cc_final: 0.8982 (tp) REVERT: j 153 ILE cc_start: 0.8782 (tp) cc_final: 0.8426 (tp) REVERT: j 172 LEU cc_start: 0.9742 (tp) cc_final: 0.9503 (mm) REVERT: j 182 LYS cc_start: 0.9446 (mttt) cc_final: 0.9125 (mmtp) REVERT: k 52 LEU cc_start: 0.9631 (mt) cc_final: 0.9309 (mt) REVERT: k 56 LEU cc_start: 0.9521 (mt) cc_final: 0.9266 (mt) REVERT: k 66 MET cc_start: 0.9618 (tpt) cc_final: 0.9184 (tpt) REVERT: k 68 MET cc_start: 0.9405 (mtp) cc_final: 0.8948 (mtp) REVERT: k 104 ILE cc_start: 0.8626 (mm) cc_final: 0.8258 (mm) REVERT: k 111 LEU cc_start: 0.9260 (tp) cc_final: 0.8799 (tp) REVERT: k 115 ILE cc_start: 0.9616 (mm) cc_final: 0.9254 (mm) REVERT: k 130 TYR cc_start: 0.9512 (t80) cc_final: 0.9245 (t80) REVERT: k 159 GLU cc_start: 0.8479 (mp0) cc_final: 0.7802 (pt0) REVERT: k 168 PHE cc_start: 0.9583 (t80) cc_final: 0.9139 (t80) REVERT: k 179 GLN cc_start: 0.9516 (tp-100) cc_final: 0.9202 (tp-100) REVERT: k 180 GLU cc_start: 0.9491 (mp0) cc_final: 0.9244 (mp0) REVERT: k 185 MET cc_start: 0.9325 (mtm) cc_final: 0.9084 (mtm) REVERT: k 187 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9209 (pt0) REVERT: k 193 ASN cc_start: 0.9166 (m110) cc_final: 0.7871 (t0) REVERT: k 203 LYS cc_start: 0.8969 (mmtm) cc_final: 0.8706 (mmtt) REVERT: k 212 GLU cc_start: 0.9603 (tt0) cc_final: 0.9328 (tm-30) REVERT: k 214 MET cc_start: 0.9308 (mmp) cc_final: 0.9050 (mmp) outliers start: 7 outliers final: 2 residues processed: 941 average time/residue: 0.3702 time to fit residues: 494.5591 Evaluate side-chains 728 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 725 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 58 optimal weight: 0.0470 chunk 212 optimal weight: 9.9990 chunk 229 optimal weight: 40.0000 chunk 189 optimal weight: 2.9990 chunk 211 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 0.3980 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS B 87 HIS B 95 GLN G 53 ASN G 183 ASN ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 7 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN j 155 GLN ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18824 Z= 0.200 Angle : 0.670 9.118 25567 Z= 0.345 Chirality : 0.046 0.306 2848 Planarity : 0.006 0.094 3345 Dihedral : 4.258 20.069 2500 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.15 % Allowed : 4.00 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.08 (0.17), residues: 2338 helix: 0.22 (0.13), residues: 1451 sheet: -1.41 (0.62), residues: 73 loop : -0.15 (0.22), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP e 117 HIS 0.003 0.001 HIS d 62 PHE 0.029 0.002 PHE H 168 TYR 0.014 0.002 TYR d 130 ARG 0.018 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 901 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9475 (mp10) cc_final: 0.9254 (pm20) REVERT: A 23 TRP cc_start: 0.9207 (t-100) cc_final: 0.8956 (t-100) REVERT: A 27 VAL cc_start: 0.9729 (t) cc_final: 0.9317 (t) REVERT: A 28 GLU cc_start: 0.9672 (mm-30) cc_final: 0.9392 (mm-30) REVERT: A 67 GLN cc_start: 0.9563 (tp40) cc_final: 0.9266 (tm-30) REVERT: A 72 THR cc_start: 0.9806 (m) cc_final: 0.9100 (m) REVERT: A 100 ARG cc_start: 0.9600 (ttm-80) cc_final: 0.9277 (tpp80) REVERT: A 103 ASP cc_start: 0.9572 (m-30) cc_final: 0.9113 (m-30) REVERT: A 114 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8585 (pt0) REVERT: A 141 ILE cc_start: 0.9319 (mm) cc_final: 0.8927 (mm) REVERT: B 5 ASN cc_start: 0.8910 (t0) cc_final: 0.8624 (m110) REVERT: B 23 TRP cc_start: 0.9020 (t-100) cc_final: 0.8604 (t-100) REVERT: B 30 LYS cc_start: 0.8927 (mmtp) cc_final: 0.8366 (mppt) REVERT: B 39 MET cc_start: 0.9560 (tpp) cc_final: 0.8997 (tpt) REVERT: B 40 PHE cc_start: 0.9460 (t80) cc_final: 0.8890 (t80) REVERT: B 100 ARG cc_start: 0.9013 (ttp-110) cc_final: 0.8759 (ttp-110) REVERT: B 118 MET cc_start: 0.9580 (mtm) cc_final: 0.9248 (mmm) REVERT: B 133 TRP cc_start: 0.8749 (m-10) cc_final: 0.8242 (m-10) REVERT: B 140 LYS cc_start: 0.9629 (tttt) cc_final: 0.9206 (mmmt) REVERT: B 169 TYR cc_start: 0.9255 (m-10) cc_final: 0.8778 (m-10) REVERT: B 181 VAL cc_start: 0.9660 (t) cc_final: 0.9432 (t) REVERT: B 185 MET cc_start: 0.9705 (ptp) cc_final: 0.9468 (ptt) REVERT: B 213 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9106 (pt0) REVERT: B 214 MET cc_start: 0.9183 (mtt) cc_final: 0.8974 (mtt) REVERT: C 40 PHE cc_start: 0.9683 (t80) cc_final: 0.9482 (t80) REVERT: C 51 ASP cc_start: 0.9508 (m-30) cc_final: 0.9303 (m-30) REVERT: C 52 LEU cc_start: 0.9695 (mt) cc_final: 0.9451 (mt) REVERT: C 75 GLU cc_start: 0.9513 (mt-10) cc_final: 0.8908 (pt0) REVERT: C 76 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9000 (mm-30) REVERT: C 96 MET cc_start: -0.5533 (mmt) cc_final: -0.5792 (mtm) REVERT: C 104 ILE cc_start: 0.8312 (mm) cc_final: 0.7813 (mm) REVERT: C 140 LYS cc_start: 0.9286 (mttt) cc_final: 0.8812 (tptp) REVERT: C 166 ASP cc_start: 0.8489 (t0) cc_final: 0.7790 (t0) REVERT: C 175 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7955 (tm-30) REVERT: C 193 ASN cc_start: 0.8278 (m110) cc_final: 0.6710 (t0) REVERT: D 23 TRP cc_start: 0.9536 (t-100) cc_final: 0.8935 (t60) REVERT: D 39 MET cc_start: 0.9431 (mmm) cc_final: 0.9067 (mmm) REVERT: D 52 LEU cc_start: 0.9700 (mt) cc_final: 0.9319 (mt) REVERT: D 53 ASN cc_start: 0.9171 (m-40) cc_final: 0.8884 (m110) REVERT: D 54 THR cc_start: 0.9622 (p) cc_final: 0.9419 (p) REVERT: D 55 MET cc_start: 0.9614 (mtp) cc_final: 0.9176 (ttp) REVERT: D 62 HIS cc_start: 0.8148 (m90) cc_final: 0.7884 (m90) REVERT: D 66 MET cc_start: 0.9735 (mmp) cc_final: 0.9510 (mmm) REVERT: D 96 MET cc_start: 0.6792 (ttt) cc_final: 0.6465 (ttm) REVERT: D 129 ILE cc_start: 0.9541 (mt) cc_final: 0.9246 (tp) REVERT: D 130 TYR cc_start: 0.8837 (t80) cc_final: 0.8482 (t80) REVERT: D 131 LYS cc_start: 0.9508 (ttmt) cc_final: 0.8913 (mttt) REVERT: D 140 LYS cc_start: 0.9623 (mttt) cc_final: 0.9338 (tptp) REVERT: D 144 MET cc_start: 0.4805 (ttt) cc_final: 0.4538 (ttt) REVERT: D 151 LEU cc_start: 0.9005 (mt) cc_final: 0.8762 (mt) REVERT: D 205 LEU cc_start: 0.8721 (tt) cc_final: 0.8398 (tt) REVERT: D 215 MET cc_start: 0.8458 (mtm) cc_final: 0.7633 (mtm) REVERT: G 11 VAL cc_start: 0.8577 (t) cc_final: 0.7942 (m) REVERT: G 18 ARG cc_start: 0.9444 (mmm-85) cc_final: 0.9225 (mmp80) REVERT: G 25 LYS cc_start: 0.9455 (ptpp) cc_final: 0.9197 (ptpp) REVERT: G 55 MET cc_start: 0.9549 (ttp) cc_final: 0.9181 (tmm) REVERT: G 140 LYS cc_start: 0.9698 (mtpp) cc_final: 0.9470 (mtpp) REVERT: G 168 PHE cc_start: 0.9258 (t80) cc_final: 0.8946 (t80) REVERT: G 181 VAL cc_start: 0.9380 (t) cc_final: 0.9158 (t) REVERT: G 215 MET cc_start: 0.8822 (ppp) cc_final: 0.8430 (ppp) REVERT: H 25 LYS cc_start: 0.9734 (tttt) cc_final: 0.9381 (tppt) REVERT: H 30 LYS cc_start: 0.7799 (ptpt) cc_final: 0.7200 (ptmm) REVERT: H 39 MET cc_start: 0.9130 (mtt) cc_final: 0.8907 (mtt) REVERT: H 55 MET cc_start: 0.9212 (mtp) cc_final: 0.8868 (mmt) REVERT: H 67 GLN cc_start: 0.9333 (tp40) cc_final: 0.8958 (mt0) REVERT: H 100 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8573 (mmp-170) REVERT: H 111 LEU cc_start: 0.9474 (pt) cc_final: 0.9149 (pt) REVERT: H 114 GLN cc_start: 0.9656 (mm-40) cc_final: 0.9158 (pt0) REVERT: H 118 MET cc_start: 0.8506 (mmm) cc_final: 0.8065 (mmm) REVERT: H 128 GLU cc_start: 0.9697 (mm-30) cc_final: 0.9354 (mp0) REVERT: H 145 TYR cc_start: 0.9027 (m-80) cc_final: 0.8686 (m-10) REVERT: H 182 LYS cc_start: 0.9794 (pttp) cc_final: 0.9469 (pmtt) REVERT: J 29 VAL cc_start: 0.9005 (t) cc_final: 0.8668 (p) REVERT: J 36 PHE cc_start: 0.9597 (t80) cc_final: 0.9264 (t80) REVERT: J 37 ARG cc_start: 0.9299 (ptm-80) cc_final: 0.9018 (ptm-80) REVERT: J 40 SER cc_start: 0.8301 (m) cc_final: 0.7322 (p) REVERT: J 41 THR cc_start: 0.6433 (t) cc_final: 0.6098 (t) REVERT: J 60 PHE cc_start: 0.7570 (t80) cc_final: 0.6853 (t80) REVERT: J 61 MET cc_start: 0.7083 (ppp) cc_final: 0.6357 (ppp) REVERT: J 84 GLU cc_start: 0.8144 (pm20) cc_final: 0.7890 (pm20) REVERT: J 100 MET cc_start: 0.9159 (mtm) cc_final: 0.8847 (ptp) REVERT: J 119 THR cc_start: 0.7186 (p) cc_final: 0.6470 (m) REVERT: J 138 ILE cc_start: 0.5150 (mm) cc_final: 0.4792 (mm) REVERT: J 142 MET cc_start: 0.9041 (mtt) cc_final: 0.8649 (mtp) REVERT: J 158 ILE cc_start: 0.9056 (mt) cc_final: 0.8675 (mt) REVERT: N 170 LYS cc_start: 0.8825 (tptt) cc_final: 0.8617 (tppt) REVERT: N 178 SER cc_start: 0.8678 (p) cc_final: 0.8138 (t) REVERT: N 180 GLU cc_start: 0.9172 (pm20) cc_final: 0.8906 (pm20) REVERT: N 212 GLU cc_start: 0.9232 (pm20) cc_final: 0.8902 (pm20) REVERT: N 213 GLU cc_start: 0.9520 (mm-30) cc_final: 0.9272 (pt0) REVERT: Y 10 MET cc_start: 0.9088 (pmm) cc_final: 0.8763 (mmp) REVERT: Y 28 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9189 (mm-30) REVERT: Y 63 GLN cc_start: 0.8957 (mm-40) cc_final: 0.8653 (mp10) REVERT: Y 67 GLN cc_start: 0.9732 (mm-40) cc_final: 0.9505 (mt0) REVERT: Y 68 MET cc_start: 0.9340 (mtm) cc_final: 0.9072 (mtp) REVERT: Y 71 GLU cc_start: 0.9558 (mt-10) cc_final: 0.9240 (mt-10) REVERT: Y 100 ARG cc_start: 0.9204 (ttm-80) cc_final: 0.8901 (tpp80) REVERT: Y 103 ASP cc_start: 0.9268 (t0) cc_final: 0.9008 (t0) REVERT: d 15 ILE cc_start: 0.8002 (pt) cc_final: 0.7619 (mp) REVERT: d 21 ASN cc_start: 0.9512 (m-40) cc_final: 0.9297 (m-40) REVERT: d 25 LYS cc_start: 0.9251 (tttt) cc_final: 0.9002 (tptp) REVERT: d 30 LYS cc_start: 0.7972 (mttm) cc_final: 0.7675 (mtpt) REVERT: d 57 ASN cc_start: 0.9485 (m-40) cc_final: 0.9271 (t0) REVERT: d 66 MET cc_start: 0.9558 (mpp) cc_final: 0.9266 (mpp) REVERT: d 67 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8760 (mt0) REVERT: d 132 ARG cc_start: 0.9395 (ttm110) cc_final: 0.9162 (ttp-110) REVERT: d 143 ARG cc_start: 0.8741 (tpt170) cc_final: 0.8491 (tpt170) REVERT: d 168 PHE cc_start: 0.9432 (t80) cc_final: 0.9176 (t80) REVERT: e 23 TRP cc_start: 0.9431 (t-100) cc_final: 0.9050 (t-100) REVERT: e 39 MET cc_start: 0.9730 (mtm) cc_final: 0.9143 (mtm) REVERT: e 43 LEU cc_start: 0.8966 (mp) cc_final: 0.8741 (mp) REVERT: e 50 GLN cc_start: 0.9296 (mt0) cc_final: 0.8957 (mt0) REVERT: e 57 ASN cc_start: 0.9595 (m110) cc_final: 0.9284 (p0) REVERT: e 83 VAL cc_start: 0.9293 (t) cc_final: 0.9084 (m) REVERT: e 104 ILE cc_start: 0.8442 (mt) cc_final: 0.8010 (mt) REVERT: e 111 LEU cc_start: 0.9411 (tp) cc_final: 0.9087 (tp) REVERT: e 131 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8746 (ttmt) REVERT: e 140 LYS cc_start: 0.9517 (mttt) cc_final: 0.9060 (mttp) REVERT: e 141 ILE cc_start: 0.9604 (tp) cc_final: 0.9370 (tp) REVERT: e 166 ASP cc_start: 0.8852 (t0) cc_final: 0.8634 (t0) REVERT: e 167 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8598 (ptp-110) REVERT: e 170 LYS cc_start: 0.9730 (tttt) cc_final: 0.9168 (pptt) REVERT: e 182 LYS cc_start: 0.9745 (mttt) cc_final: 0.9111 (mmmm) REVERT: e 185 MET cc_start: 0.9779 (ptp) cc_final: 0.9507 (ptt) REVERT: e 203 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7484 (tttt) REVERT: e 211 LEU cc_start: 0.9117 (tp) cc_final: 0.8776 (tp) REVERT: j 188 THR cc_start: 0.7968 (m) cc_final: 0.7503 (m) REVERT: k 52 LEU cc_start: 0.9552 (mt) cc_final: 0.9267 (mt) REVERT: k 66 MET cc_start: 0.9524 (tpt) cc_final: 0.9190 (tpt) REVERT: k 68 MET cc_start: 0.9438 (mtp) cc_final: 0.9043 (mtp) REVERT: k 76 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8971 (mm-30) REVERT: k 83 VAL cc_start: 0.9659 (p) cc_final: 0.8921 (p) REVERT: k 100 ARG cc_start: 0.8951 (ptp-110) cc_final: 0.8677 (ptp-110) REVERT: k 104 ILE cc_start: 0.8736 (mm) cc_final: 0.8388 (mm) REVERT: k 131 LYS cc_start: 0.9389 (tttt) cc_final: 0.9026 (tptt) REVERT: k 132 ARG cc_start: 0.9414 (ptp90) cc_final: 0.9130 (ptp-170) REVERT: k 143 ARG cc_start: 0.9386 (mtt180) cc_final: 0.9166 (ttm110) REVERT: k 159 GLU cc_start: 0.8403 (mp0) cc_final: 0.7772 (pt0) REVERT: k 168 PHE cc_start: 0.9519 (t80) cc_final: 0.9164 (t80) REVERT: k 179 GLN cc_start: 0.9528 (tp-100) cc_final: 0.8948 (tp-100) REVERT: k 180 GLU cc_start: 0.9460 (mp0) cc_final: 0.9225 (mp0) REVERT: k 181 VAL cc_start: 0.8798 (p) cc_final: 0.8232 (p) REVERT: k 182 LYS cc_start: 0.9460 (ttmm) cc_final: 0.8927 (ttpp) REVERT: k 185 MET cc_start: 0.9345 (mtm) cc_final: 0.8956 (mtm) REVERT: k 193 ASN cc_start: 0.9217 (m110) cc_final: 0.7946 (t0) REVERT: k 215 MET cc_start: 0.9398 (ppp) cc_final: 0.9102 (ppp) outliers start: 3 outliers final: 0 residues processed: 903 average time/residue: 0.3593 time to fit residues: 461.9818 Evaluate side-chains 702 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 702 time to evaluate : 2.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 20.0000 chunk 160 optimal weight: 30.0000 chunk 110 optimal weight: 9.9990 chunk 23 optimal weight: 0.0270 chunk 101 optimal weight: 20.0000 chunk 142 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 202 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 overall best weight: 3.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 62 HIS d 112 GLN e 4 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18824 Z= 0.206 Angle : 0.664 8.899 25567 Z= 0.350 Chirality : 0.046 0.284 2848 Planarity : 0.005 0.063 3345 Dihedral : 4.316 22.731 2500 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.22 % Favored : 97.73 % Rotamer: Outliers : 0.10 % Allowed : 3.10 % Favored : 96.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.26 (0.17), residues: 2338 helix: 0.07 (0.13), residues: 1486 sheet: -1.33 (0.65), residues: 61 loop : -0.25 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 23 HIS 0.003 0.001 HIS C 62 PHE 0.029 0.002 PHE H 168 TYR 0.025 0.002 TYR J 48 ARG 0.007 0.001 ARG Y 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 875 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 873 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9465 (mp10) cc_final: 0.9254 (pm20) REVERT: A 16 SER cc_start: 0.9363 (m) cc_final: 0.9069 (p) REVERT: A 23 TRP cc_start: 0.9239 (t-100) cc_final: 0.8908 (t-100) REVERT: A 27 VAL cc_start: 0.9753 (t) cc_final: 0.9402 (t) REVERT: A 28 GLU cc_start: 0.9681 (mm-30) cc_final: 0.9454 (mm-30) REVERT: A 39 MET cc_start: 0.9093 (mtt) cc_final: 0.8842 (mtt) REVERT: A 63 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8689 (tp-100) REVERT: A 67 GLN cc_start: 0.9561 (tp40) cc_final: 0.9312 (tm-30) REVERT: A 70 LYS cc_start: 0.9567 (pttm) cc_final: 0.9035 (pttp) REVERT: A 76 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 96 MET cc_start: 0.6669 (mtp) cc_final: 0.6356 (mtp) REVERT: A 100 ARG cc_start: 0.9604 (ttm-80) cc_final: 0.9268 (tpp80) REVERT: A 103 ASP cc_start: 0.9630 (m-30) cc_final: 0.9150 (m-30) REVERT: A 114 GLN cc_start: 0.9125 (mm-40) cc_final: 0.8663 (pt0) REVERT: B 5 ASN cc_start: 0.8957 (t0) cc_final: 0.8682 (m110) REVERT: B 20 LEU cc_start: 0.9606 (mt) cc_final: 0.9399 (mt) REVERT: B 23 TRP cc_start: 0.8987 (t-100) cc_final: 0.8504 (t-100) REVERT: B 30 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8388 (mppt) REVERT: B 39 MET cc_start: 0.9571 (tpp) cc_final: 0.9036 (tpt) REVERT: B 40 PHE cc_start: 0.9450 (t80) cc_final: 0.8511 (t80) REVERT: B 118 MET cc_start: 0.9603 (mtm) cc_final: 0.9318 (mmm) REVERT: B 128 GLU cc_start: 0.9341 (mp0) cc_final: 0.9043 (mp0) REVERT: B 132 ARG cc_start: 0.9527 (ptp90) cc_final: 0.9132 (ptp-170) REVERT: B 144 MET cc_start: 0.8814 (ttt) cc_final: 0.8571 (tpp) REVERT: B 159 GLU cc_start: 0.8853 (tm-30) cc_final: 0.8349 (tm-30) REVERT: B 169 TYR cc_start: 0.9306 (m-10) cc_final: 0.8691 (m-10) REVERT: B 181 VAL cc_start: 0.9652 (t) cc_final: 0.9151 (p) REVERT: B 185 MET cc_start: 0.9690 (ptp) cc_final: 0.9403 (ptt) REVERT: B 213 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9121 (pt0) REVERT: C 10 MET cc_start: 0.8253 (tpp) cc_final: 0.7423 (tpp) REVERT: C 23 TRP cc_start: 0.9455 (t-100) cc_final: 0.9175 (t-100) REVERT: C 32 PHE cc_start: 0.8783 (m-80) cc_final: 0.8398 (m-80) REVERT: C 43 LEU cc_start: 0.9550 (mt) cc_final: 0.8950 (mp) REVERT: C 55 MET cc_start: 0.9540 (ttt) cc_final: 0.8206 (ttm) REVERT: C 76 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8718 (mm-30) REVERT: C 96 MET cc_start: -0.5701 (mmt) cc_final: -0.6008 (mtm) REVERT: C 103 ASP cc_start: 0.8936 (m-30) cc_final: 0.8725 (m-30) REVERT: C 129 ILE cc_start: 0.9718 (mt) cc_final: 0.9152 (mt) REVERT: C 133 TRP cc_start: 0.8861 (m-10) cc_final: 0.8499 (m-10) REVERT: C 144 MET cc_start: 0.8533 (tmm) cc_final: 0.7916 (tmm) REVERT: C 166 ASP cc_start: 0.8559 (t0) cc_final: 0.7810 (t0) REVERT: C 175 GLU cc_start: 0.8378 (tm-30) cc_final: 0.8010 (tm-30) REVERT: C 185 MET cc_start: 0.9347 (mtt) cc_final: 0.9066 (mtt) REVERT: C 215 MET cc_start: 0.9492 (tmm) cc_final: 0.8711 (tmm) REVERT: D 10 MET cc_start: 0.7760 (mpp) cc_final: 0.6988 (mmt) REVERT: D 21 ASN cc_start: 0.9594 (t0) cc_final: 0.9354 (t0) REVERT: D 25 LYS cc_start: 0.9767 (ttpt) cc_final: 0.9510 (ptmt) REVERT: D 39 MET cc_start: 0.9450 (mmm) cc_final: 0.9132 (mmm) REVERT: D 52 LEU cc_start: 0.9704 (mt) cc_final: 0.9314 (mt) REVERT: D 53 ASN cc_start: 0.9247 (m-40) cc_final: 0.8918 (m110) REVERT: D 62 HIS cc_start: 0.8086 (m90) cc_final: 0.7856 (m90) REVERT: D 66 MET cc_start: 0.9729 (mmp) cc_final: 0.9503 (mmm) REVERT: D 96 MET cc_start: 0.7054 (ttt) cc_final: 0.6641 (ttm) REVERT: D 129 ILE cc_start: 0.9586 (mt) cc_final: 0.9324 (tp) REVERT: D 130 TYR cc_start: 0.8861 (t80) cc_final: 0.8475 (t80) REVERT: D 131 LYS cc_start: 0.9501 (ttmt) cc_final: 0.9004 (ptpt) REVERT: D 140 LYS cc_start: 0.9619 (mttt) cc_final: 0.9335 (tptp) REVERT: D 144 MET cc_start: 0.4802 (ttt) cc_final: 0.4543 (ttt) REVERT: D 181 VAL cc_start: 0.9513 (p) cc_final: 0.9277 (m) REVERT: D 215 MET cc_start: 0.8406 (mtm) cc_final: 0.7096 (ppp) REVERT: G 11 VAL cc_start: 0.8348 (t) cc_final: 0.8146 (m) REVERT: G 18 ARG cc_start: 0.9429 (mmm-85) cc_final: 0.9203 (mmp80) REVERT: G 140 LYS cc_start: 0.9696 (mtpp) cc_final: 0.9479 (mtpp) REVERT: G 168 PHE cc_start: 0.9260 (t80) cc_final: 0.8948 (t80) REVERT: G 188 THR cc_start: 0.9325 (p) cc_final: 0.9113 (p) REVERT: H 13 GLN cc_start: 0.9152 (pp30) cc_final: 0.8894 (pm20) REVERT: H 51 ASP cc_start: 0.9128 (m-30) cc_final: 0.8748 (m-30) REVERT: H 66 MET cc_start: 0.9507 (mmp) cc_final: 0.9126 (mmm) REVERT: H 67 GLN cc_start: 0.9304 (tp40) cc_final: 0.8943 (mt0) REVERT: H 100 ARG cc_start: 0.9132 (ttt-90) cc_final: 0.8595 (mmp-170) REVERT: H 111 LEU cc_start: 0.9468 (pt) cc_final: 0.9130 (pt) REVERT: H 114 GLN cc_start: 0.9701 (mm-40) cc_final: 0.9195 (pt0) REVERT: H 118 MET cc_start: 0.8518 (mmm) cc_final: 0.8076 (mmm) REVERT: H 128 GLU cc_start: 0.9719 (mm-30) cc_final: 0.9388 (mp0) REVERT: H 145 TYR cc_start: 0.9070 (m-80) cc_final: 0.8729 (m-10) REVERT: H 152 ASP cc_start: 0.9582 (m-30) cc_final: 0.9307 (m-30) REVERT: H 166 ASP cc_start: 0.8897 (m-30) cc_final: 0.8664 (m-30) REVERT: H 167 ARG cc_start: 0.9071 (ptt180) cc_final: 0.8813 (ptt90) REVERT: J 25 PHE cc_start: 0.9049 (m-80) cc_final: 0.8760 (m-80) REVERT: J 29 VAL cc_start: 0.9048 (t) cc_final: 0.8683 (p) REVERT: J 37 ARG cc_start: 0.9345 (ptm-80) cc_final: 0.9053 (ptm-80) REVERT: J 40 SER cc_start: 0.8611 (m) cc_final: 0.7390 (p) REVERT: J 48 TYR cc_start: 0.8625 (m-80) cc_final: 0.8307 (m-80) REVERT: J 60 PHE cc_start: 0.7593 (t80) cc_final: 0.6968 (t80) REVERT: J 61 MET cc_start: 0.7037 (ppp) cc_final: 0.6736 (ppp) REVERT: J 83 PHE cc_start: 0.8281 (p90) cc_final: 0.7976 (p90) REVERT: J 84 GLU cc_start: 0.8236 (pm20) cc_final: 0.7713 (pp20) REVERT: J 119 THR cc_start: 0.7078 (p) cc_final: 0.6263 (m) REVERT: J 138 ILE cc_start: 0.5564 (mm) cc_final: 0.5185 (mm) REVERT: J 142 MET cc_start: 0.9149 (mtt) cc_final: 0.8681 (mtp) REVERT: N 178 SER cc_start: 0.8717 (p) cc_final: 0.8106 (t) REVERT: N 180 GLU cc_start: 0.9245 (pm20) cc_final: 0.8960 (pm20) REVERT: Y 10 MET cc_start: 0.9118 (pmm) cc_final: 0.8801 (mmp) REVERT: Y 27 VAL cc_start: 0.9636 (p) cc_final: 0.9379 (m) REVERT: Y 63 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8798 (mp10) REVERT: Y 67 GLN cc_start: 0.9793 (mm-40) cc_final: 0.9211 (mm-40) REVERT: Y 68 MET cc_start: 0.9342 (mtm) cc_final: 0.9065 (mtp) REVERT: Y 71 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9232 (mt-10) REVERT: Y 100 ARG cc_start: 0.9283 (ttm-80) cc_final: 0.8982 (tpp80) REVERT: Y 103 ASP cc_start: 0.9330 (t0) cc_final: 0.9085 (t0) REVERT: Y 115 ILE cc_start: 0.9208 (mm) cc_final: 0.8707 (mm) REVERT: Y 124 ILE cc_start: 0.8909 (tp) cc_final: 0.8662 (tp) REVERT: Y 126 VAL cc_start: 0.9407 (t) cc_final: 0.9082 (t) REVERT: Y 129 ILE cc_start: 0.9476 (mt) cc_final: 0.9139 (tt) REVERT: Y 136 LEU cc_start: 0.9731 (mt) cc_final: 0.9478 (mt) REVERT: d 15 ILE cc_start: 0.7592 (pt) cc_final: 0.7231 (mp) REVERT: d 21 ASN cc_start: 0.9507 (m-40) cc_final: 0.9291 (m-40) REVERT: d 23 TRP cc_start: 0.9418 (t-100) cc_final: 0.8909 (t-100) REVERT: d 25 LYS cc_start: 0.9208 (tttt) cc_final: 0.8948 (tptp) REVERT: d 30 LYS cc_start: 0.8096 (mttm) cc_final: 0.7761 (mtpt) REVERT: d 39 MET cc_start: 0.8922 (mtm) cc_final: 0.7906 (mtt) REVERT: d 55 MET cc_start: 0.9311 (ppp) cc_final: 0.9105 (ppp) REVERT: d 67 GLN cc_start: 0.9207 (tp-100) cc_final: 0.8782 (tp40) REVERT: d 68 MET cc_start: 0.9091 (mmm) cc_final: 0.8572 (mmm) REVERT: d 111 LEU cc_start: 0.9543 (pp) cc_final: 0.9341 (pp) REVERT: d 132 ARG cc_start: 0.9392 (ttm110) cc_final: 0.9011 (ttp-110) REVERT: d 143 ARG cc_start: 0.8683 (tpt170) cc_final: 0.8388 (tpt170) REVERT: d 144 MET cc_start: 0.9152 (tmm) cc_final: 0.8918 (tmm) REVERT: d 215 MET cc_start: 0.4257 (mmt) cc_final: 0.3744 (mtp) REVERT: e 10 MET cc_start: 0.9086 (mmm) cc_final: 0.8645 (tpp) REVERT: e 23 TRP cc_start: 0.9443 (t-100) cc_final: 0.8749 (t-100) REVERT: e 50 GLN cc_start: 0.9303 (mt0) cc_final: 0.8910 (mt0) REVERT: e 57 ASN cc_start: 0.9590 (m110) cc_final: 0.9279 (p0) REVERT: e 104 ILE cc_start: 0.8429 (mt) cc_final: 0.8059 (mt) REVERT: e 111 LEU cc_start: 0.9344 (tp) cc_final: 0.9054 (tp) REVERT: e 131 LYS cc_start: 0.9042 (ttmt) cc_final: 0.8609 (ttmt) REVERT: e 141 ILE cc_start: 0.9569 (tp) cc_final: 0.9278 (tp) REVERT: e 167 ARG cc_start: 0.8875 (ptp-110) cc_final: 0.8548 (ptp-110) REVERT: e 169 TYR cc_start: 0.9561 (m-10) cc_final: 0.8929 (m-10) REVERT: e 170 LYS cc_start: 0.9457 (tttt) cc_final: 0.9254 (tmmt) REVERT: e 185 MET cc_start: 0.9820 (ptp) cc_final: 0.9610 (ptt) REVERT: e 203 LYS cc_start: 0.8030 (ptpt) cc_final: 0.7452 (tttt) REVERT: e 205 LEU cc_start: 0.7750 (mt) cc_final: 0.6930 (mt) REVERT: e 211 LEU cc_start: 0.9105 (tp) cc_final: 0.8870 (tp) REVERT: j 188 THR cc_start: 0.7976 (m) cc_final: 0.7669 (p) REVERT: k 43 LEU cc_start: 0.9624 (mp) cc_final: 0.8844 (mp) REVERT: k 52 LEU cc_start: 0.9537 (mt) cc_final: 0.9243 (mt) REVERT: k 56 LEU cc_start: 0.9564 (mt) cc_final: 0.9361 (mt) REVERT: k 66 MET cc_start: 0.9547 (tpt) cc_final: 0.9246 (tpt) REVERT: k 76 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9122 (mm-30) REVERT: k 131 LYS cc_start: 0.9379 (tttt) cc_final: 0.9004 (tptt) REVERT: k 139 ASN cc_start: 0.9635 (m110) cc_final: 0.9325 (m110) REVERT: k 163 ASP cc_start: 0.9450 (m-30) cc_final: 0.9113 (m-30) REVERT: k 168 PHE cc_start: 0.9527 (t80) cc_final: 0.9213 (t80) REVERT: k 179 GLN cc_start: 0.9530 (tp-100) cc_final: 0.9237 (tp-100) REVERT: k 180 GLU cc_start: 0.9510 (mp0) cc_final: 0.9250 (mp0) REVERT: k 185 MET cc_start: 0.9341 (mtm) cc_final: 0.8982 (mtt) REVERT: k 193 ASN cc_start: 0.9309 (m110) cc_final: 0.8356 (t0) REVERT: k 215 MET cc_start: 0.9349 (ppp) cc_final: 0.9097 (ppp) outliers start: 2 outliers final: 0 residues processed: 873 average time/residue: 0.3725 time to fit residues: 463.9979 Evaluate side-chains 699 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 699 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 20.0000 chunk 128 optimal weight: 20.0000 chunk 3 optimal weight: 0.8980 chunk 168 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 4.9990 chunk 156 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 115 optimal weight: 20.0000 chunk 203 optimal weight: 30.0000 chunk 57 optimal weight: 30.0000 overall best weight: 10.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 HIS B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN C 183 ASN D 74 ASN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 HIS ** d 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.6887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18824 Z= 0.325 Angle : 0.742 7.618 25567 Z= 0.398 Chirality : 0.047 0.258 2848 Planarity : 0.006 0.080 3345 Dihedral : 4.616 24.792 2500 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.05 % Allowed : 3.05 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.53 (0.16), residues: 2338 helix: -0.15 (0.13), residues: 1471 sheet: -1.51 (0.51), residues: 79 loop : -0.30 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 184 HIS 0.008 0.002 HIS k 12 PHE 0.033 0.003 PHE H 168 TYR 0.021 0.002 TYR H 130 ARG 0.011 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 826 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9451 (mp10) cc_final: 0.9226 (pm20) REVERT: A 23 TRP cc_start: 0.9380 (t-100) cc_final: 0.8944 (t-100) REVERT: A 25 LYS cc_start: 0.9670 (tptt) cc_final: 0.9381 (tppt) REVERT: A 29 GLU cc_start: 0.8966 (pp20) cc_final: 0.8493 (pp20) REVERT: A 39 MET cc_start: 0.9140 (mtt) cc_final: 0.8830 (mtt) REVERT: A 63 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8634 (tp-100) REVERT: A 67 GLN cc_start: 0.9560 (tp40) cc_final: 0.9260 (tm-30) REVERT: A 68 MET cc_start: 0.9391 (ptp) cc_final: 0.8854 (ptp) REVERT: A 76 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8591 (mt-10) REVERT: A 96 MET cc_start: 0.6999 (mtp) cc_final: 0.6687 (mtp) REVERT: A 100 ARG cc_start: 0.9693 (ttm-80) cc_final: 0.9372 (tpp80) REVERT: A 103 ASP cc_start: 0.9687 (m-30) cc_final: 0.9468 (m-30) REVERT: A 132 ARG cc_start: 0.9395 (mtm110) cc_final: 0.9180 (mtm110) REVERT: B 5 ASN cc_start: 0.9236 (t0) cc_final: 0.8879 (m110) REVERT: B 23 TRP cc_start: 0.8990 (t-100) cc_final: 0.8502 (t-100) REVERT: B 25 LYS cc_start: 0.9694 (pttm) cc_final: 0.9391 (mmtt) REVERT: B 28 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9439 (mt-10) REVERT: B 30 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8711 (mmmt) REVERT: B 39 MET cc_start: 0.9570 (tpp) cc_final: 0.9136 (tpt) REVERT: B 40 PHE cc_start: 0.9469 (t80) cc_final: 0.8717 (t80) REVERT: B 114 GLN cc_start: 0.9218 (mt0) cc_final: 0.8960 (mt0) REVERT: B 118 MET cc_start: 0.9613 (mtm) cc_final: 0.9316 (mmm) REVERT: B 169 TYR cc_start: 0.9390 (m-10) cc_final: 0.8745 (m-10) REVERT: B 170 LYS cc_start: 0.9458 (tppt) cc_final: 0.9231 (tppt) REVERT: B 181 VAL cc_start: 0.9696 (t) cc_final: 0.9212 (t) REVERT: B 185 MET cc_start: 0.9763 (ptp) cc_final: 0.9292 (ptp) REVERT: B 187 GLU cc_start: 0.9507 (mt-10) cc_final: 0.9268 (pp20) REVERT: B 213 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9193 (pt0) REVERT: B 214 MET cc_start: 0.9171 (mtt) cc_final: 0.8963 (mtt) REVERT: C 10 MET cc_start: 0.8324 (tpp) cc_final: 0.7769 (tpp) REVERT: C 23 TRP cc_start: 0.9600 (t-100) cc_final: 0.9179 (t-100) REVERT: C 32 PHE cc_start: 0.8922 (m-80) cc_final: 0.8522 (m-80) REVERT: C 43 LEU cc_start: 0.9580 (mt) cc_final: 0.8954 (mp) REVERT: C 55 MET cc_start: 0.9610 (ttt) cc_final: 0.8209 (ttm) REVERT: C 59 VAL cc_start: 0.8684 (t) cc_final: 0.8380 (p) REVERT: C 76 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9111 (mm-30) REVERT: C 79 GLU cc_start: 0.9014 (pm20) cc_final: 0.8702 (pm20) REVERT: C 81 ASP cc_start: 0.8929 (m-30) cc_final: 0.8588 (m-30) REVERT: C 96 MET cc_start: -0.5376 (mmt) cc_final: -0.5715 (mtm) REVERT: C 133 TRP cc_start: 0.8992 (m-10) cc_final: 0.8512 (m-10) REVERT: C 166 ASP cc_start: 0.8808 (t0) cc_final: 0.7796 (t70) REVERT: C 167 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8395 (mmp80) REVERT: C 175 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8358 (tm-30) REVERT: C 185 MET cc_start: 0.9366 (mtt) cc_final: 0.9129 (mtt) REVERT: D 21 ASN cc_start: 0.9620 (t0) cc_final: 0.9299 (t0) REVERT: D 25 LYS cc_start: 0.9750 (ttpt) cc_final: 0.9494 (ptmt) REVERT: D 52 LEU cc_start: 0.9615 (mt) cc_final: 0.9397 (mt) REVERT: D 53 ASN cc_start: 0.9218 (m-40) cc_final: 0.8967 (m-40) REVERT: D 68 MET cc_start: 0.8169 (mtt) cc_final: 0.7833 (mtp) REVERT: D 128 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8955 (mp0) REVERT: D 129 ILE cc_start: 0.9573 (mt) cc_final: 0.9312 (tp) REVERT: D 130 TYR cc_start: 0.9029 (t80) cc_final: 0.8790 (t80) REVERT: D 131 LYS cc_start: 0.9521 (ttmt) cc_final: 0.9090 (ptpt) REVERT: D 140 LYS cc_start: 0.9644 (mttt) cc_final: 0.9358 (tptp) REVERT: D 215 MET cc_start: 0.8626 (mtm) cc_final: 0.7945 (mtp) REVERT: G 18 ARG cc_start: 0.9553 (mmm-85) cc_final: 0.9279 (mmp80) REVERT: G 25 LYS cc_start: 0.9425 (ptpp) cc_final: 0.9149 (ptpp) REVERT: G 140 LYS cc_start: 0.9685 (mtpp) cc_final: 0.9439 (mtpp) REVERT: G 159 GLU cc_start: 0.8277 (tt0) cc_final: 0.8007 (tt0) REVERT: G 168 PHE cc_start: 0.9295 (t80) cc_final: 0.9010 (t80) REVERT: G 188 THR cc_start: 0.9392 (p) cc_final: 0.9157 (p) REVERT: H 13 GLN cc_start: 0.9308 (pp30) cc_final: 0.9062 (pm20) REVERT: H 25 LYS cc_start: 0.9573 (tttt) cc_final: 0.9247 (tppt) REVERT: H 30 LYS cc_start: 0.8216 (ptmt) cc_final: 0.7979 (ptmt) REVERT: H 32 PHE cc_start: 0.6980 (m-10) cc_final: 0.6723 (m-10) REVERT: H 55 MET cc_start: 0.9256 (mtp) cc_final: 0.8894 (mmm) REVERT: H 67 GLN cc_start: 0.9404 (tp40) cc_final: 0.9039 (mt0) REVERT: H 68 MET cc_start: 0.9364 (mmt) cc_final: 0.9000 (mmm) REVERT: H 87 HIS cc_start: 0.7765 (m-70) cc_final: 0.7044 (t-90) REVERT: H 100 ARG cc_start: 0.9138 (ttt-90) cc_final: 0.8546 (mmp-170) REVERT: H 128 GLU cc_start: 0.9728 (mm-30) cc_final: 0.9365 (mp0) REVERT: H 144 MET cc_start: 0.9587 (ttt) cc_final: 0.9363 (ttt) REVERT: H 145 TYR cc_start: 0.9181 (m-80) cc_final: 0.8628 (m-10) REVERT: H 152 ASP cc_start: 0.9592 (m-30) cc_final: 0.9309 (m-30) REVERT: H 182 LYS cc_start: 0.9618 (pttm) cc_final: 0.9350 (pttt) REVERT: J 5 THR cc_start: 0.8698 (m) cc_final: 0.8423 (m) REVERT: J 24 LEU cc_start: 0.9622 (mt) cc_final: 0.9372 (mt) REVERT: J 37 ARG cc_start: 0.9431 (ptm-80) cc_final: 0.9226 (ptm-80) REVERT: J 40 SER cc_start: 0.8728 (m) cc_final: 0.7575 (p) REVERT: J 48 TYR cc_start: 0.8852 (m-80) cc_final: 0.8188 (m-80) REVERT: J 57 ILE cc_start: 0.7515 (tt) cc_final: 0.6404 (tt) REVERT: J 60 PHE cc_start: 0.7882 (t80) cc_final: 0.7462 (t80) REVERT: J 100 MET cc_start: 0.9386 (ptp) cc_final: 0.9094 (pmm) REVERT: J 119 THR cc_start: 0.7127 (p) cc_final: 0.6105 (m) REVERT: J 122 LEU cc_start: 0.8624 (mt) cc_final: 0.8243 (mt) REVERT: J 142 MET cc_start: 0.9159 (mtt) cc_final: 0.8711 (mtp) REVERT: N 178 SER cc_start: 0.8823 (p) cc_final: 0.8411 (t) REVERT: N 180 GLU cc_start: 0.9127 (pm20) cc_final: 0.8875 (pm20) REVERT: N 205 LEU cc_start: 0.8104 (tp) cc_final: 0.7764 (tp) REVERT: N 213 GLU cc_start: 0.9571 (mm-30) cc_final: 0.9225 (pt0) REVERT: N 215 MET cc_start: 0.8835 (tmm) cc_final: 0.8579 (tmm) REVERT: Y 10 MET cc_start: 0.9123 (pmm) cc_final: 0.8795 (mmp) REVERT: Y 63 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8764 (mp10) REVERT: Y 66 MET cc_start: 0.8787 (ptp) cc_final: 0.8393 (ptp) REVERT: Y 67 GLN cc_start: 0.9791 (mm-40) cc_final: 0.9296 (mm-40) REVERT: Y 68 MET cc_start: 0.9350 (mtm) cc_final: 0.9108 (mtp) REVERT: Y 71 GLU cc_start: 0.9470 (mt-10) cc_final: 0.9147 (mt-10) REVERT: Y 100 ARG cc_start: 0.9301 (ttm-80) cc_final: 0.9041 (tpp80) REVERT: Y 129 ILE cc_start: 0.9531 (mt) cc_final: 0.9218 (mt) REVERT: d 23 TRP cc_start: 0.9479 (t-100) cc_final: 0.8988 (t-100) REVERT: d 25 LYS cc_start: 0.9246 (tttt) cc_final: 0.8994 (tptp) REVERT: d 30 LYS cc_start: 0.8290 (mttm) cc_final: 0.7882 (mtpt) REVERT: d 39 MET cc_start: 0.9137 (mtm) cc_final: 0.8113 (mtt) REVERT: d 66 MET cc_start: 0.9590 (mpp) cc_final: 0.9176 (mpp) REVERT: d 67 GLN cc_start: 0.9146 (tp-100) cc_final: 0.8688 (tp40) REVERT: d 111 LEU cc_start: 0.9464 (pp) cc_final: 0.9239 (pp) REVERT: d 132 ARG cc_start: 0.9451 (ttm110) cc_final: 0.9049 (ttp-110) REVERT: d 143 ARG cc_start: 0.8707 (tpt170) cc_final: 0.8417 (tpt170) REVERT: d 168 PHE cc_start: 0.9356 (t80) cc_final: 0.9102 (t80) REVERT: e 32 PHE cc_start: 0.8965 (m-80) cc_final: 0.8713 (m-80) REVERT: e 35 GLU cc_start: 0.9391 (pm20) cc_final: 0.9157 (pm20) REVERT: e 39 MET cc_start: 0.9665 (mtm) cc_final: 0.9194 (mtm) REVERT: e 50 GLN cc_start: 0.9368 (mt0) cc_final: 0.8975 (mt0) REVERT: e 76 GLU cc_start: 0.9550 (mm-30) cc_final: 0.9266 (mm-30) REVERT: e 104 ILE cc_start: 0.8324 (mt) cc_final: 0.7897 (mt) REVERT: e 111 LEU cc_start: 0.9245 (tp) cc_final: 0.8993 (tp) REVERT: e 114 GLN cc_start: 0.9393 (pt0) cc_final: 0.9077 (pt0) REVERT: e 118 MET cc_start: 0.9448 (mmt) cc_final: 0.9070 (ptp) REVERT: e 167 ARG cc_start: 0.9009 (ptp-110) cc_final: 0.8575 (ptp-110) REVERT: e 169 TYR cc_start: 0.9672 (m-10) cc_final: 0.9324 (m-10) REVERT: e 185 MET cc_start: 0.9841 (ptp) cc_final: 0.9523 (ptt) REVERT: e 203 LYS cc_start: 0.8046 (ptpt) cc_final: 0.7426 (tttt) REVERT: e 211 LEU cc_start: 0.9209 (tp) cc_final: 0.8929 (tp) REVERT: j 188 THR cc_start: 0.7937 (m) cc_final: 0.7531 (m) REVERT: k 39 MET cc_start: 0.9462 (tpt) cc_final: 0.9212 (tpt) REVERT: k 43 LEU cc_start: 0.9586 (mp) cc_final: 0.8992 (mp) REVERT: k 52 LEU cc_start: 0.9607 (mt) cc_final: 0.9299 (mt) REVERT: k 66 MET cc_start: 0.9678 (tpt) cc_final: 0.9376 (tpt) REVERT: k 76 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9180 (mm-30) REVERT: k 131 LYS cc_start: 0.9405 (tttt) cc_final: 0.9021 (tptt) REVERT: k 163 ASP cc_start: 0.9396 (m-30) cc_final: 0.9099 (m-30) REVERT: k 167 ARG cc_start: 0.8929 (mtm-85) cc_final: 0.8464 (ptt-90) REVERT: k 168 PHE cc_start: 0.9553 (t80) cc_final: 0.9285 (t80) REVERT: k 185 MET cc_start: 0.9370 (mtm) cc_final: 0.9014 (mtt) REVERT: k 193 ASN cc_start: 0.9444 (m110) cc_final: 0.8189 (t0) REVERT: k 203 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8758 (mmtt) REVERT: k 215 MET cc_start: 0.9416 (ppp) cc_final: 0.9117 (ppp) outliers start: 1 outliers final: 0 residues processed: 827 average time/residue: 0.3601 time to fit residues: 419.5472 Evaluate side-chains 655 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 655 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 6.9990 chunk 203 optimal weight: 20.0000 chunk 44 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 55 optimal weight: 5.9990 chunk 226 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 104 optimal weight: 0.7980 chunk 18 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 87 HIS B 95 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 ASN ** Y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 21 ASN ** e 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18824 Z= 0.216 Angle : 0.696 9.601 25567 Z= 0.367 Chirality : 0.047 0.239 2848 Planarity : 0.005 0.047 3345 Dihedral : 4.500 22.048 2500 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.25 % Allowed : 1.70 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.36 (0.17), residues: 2338 helix: 0.03 (0.13), residues: 1460 sheet: -1.74 (0.49), residues: 88 loop : -0.26 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Y 23 HIS 0.004 0.001 HIS C 84 PHE 0.032 0.002 PHE H 168 TYR 0.017 0.002 TYR d 130 ARG 0.012 0.001 ARG B 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 841 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9461 (mp10) cc_final: 0.9243 (pm20) REVERT: A 23 TRP cc_start: 0.9417 (t-100) cc_final: 0.9009 (t-100) REVERT: A 25 LYS cc_start: 0.9630 (tptt) cc_final: 0.9317 (tppt) REVERT: A 29 GLU cc_start: 0.8787 (pp20) cc_final: 0.8585 (pp20) REVERT: A 39 MET cc_start: 0.9119 (mtt) cc_final: 0.8824 (mtt) REVERT: A 67 GLN cc_start: 0.9572 (tp40) cc_final: 0.9195 (tm-30) REVERT: A 76 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8641 (mt-10) REVERT: A 96 MET cc_start: 0.6533 (mtp) cc_final: 0.6223 (mtp) REVERT: A 100 ARG cc_start: 0.9655 (ttm-80) cc_final: 0.9312 (tpp80) REVERT: A 141 ILE cc_start: 0.9685 (mm) cc_final: 0.9260 (mm) REVERT: B 5 ASN cc_start: 0.9227 (t0) cc_final: 0.8840 (m110) REVERT: B 23 TRP cc_start: 0.9018 (t-100) cc_final: 0.8547 (t-100) REVERT: B 28 GLU cc_start: 0.9646 (mm-30) cc_final: 0.9383 (mt-10) REVERT: B 30 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8595 (mmmt) REVERT: B 39 MET cc_start: 0.9543 (tpp) cc_final: 0.9103 (tpt) REVERT: B 40 PHE cc_start: 0.9422 (t80) cc_final: 0.8655 (t80) REVERT: B 113 GLU cc_start: 0.9623 (mt-10) cc_final: 0.9134 (mt-10) REVERT: B 117 TRP cc_start: 0.8596 (m-10) cc_final: 0.7719 (m-90) REVERT: B 118 MET cc_start: 0.9669 (mtm) cc_final: 0.9413 (mmm) REVERT: B 128 GLU cc_start: 0.9447 (mp0) cc_final: 0.9185 (pm20) REVERT: B 169 TYR cc_start: 0.9421 (m-10) cc_final: 0.8849 (m-10) REVERT: B 170 LYS cc_start: 0.9493 (tppt) cc_final: 0.9230 (tppt) REVERT: B 181 VAL cc_start: 0.9680 (t) cc_final: 0.9176 (t) REVERT: B 185 MET cc_start: 0.9716 (ptp) cc_final: 0.9328 (ptp) REVERT: B 213 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9073 (pt0) REVERT: C 10 MET cc_start: 0.8303 (tpp) cc_final: 0.7675 (tpp) REVERT: C 23 TRP cc_start: 0.9610 (t-100) cc_final: 0.9153 (t-100) REVERT: C 43 LEU cc_start: 0.9528 (mt) cc_final: 0.8941 (mp) REVERT: C 55 MET cc_start: 0.9628 (ttt) cc_final: 0.8019 (ttm) REVERT: C 59 VAL cc_start: 0.8521 (t) cc_final: 0.8232 (p) REVERT: C 76 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9073 (mm-30) REVERT: C 96 MET cc_start: -0.5440 (mmt) cc_final: -0.5768 (mtm) REVERT: C 144 MET cc_start: 0.8459 (tmm) cc_final: 0.8138 (tmm) REVERT: C 153 ILE cc_start: 0.9223 (mt) cc_final: 0.8946 (mt) REVERT: C 166 ASP cc_start: 0.8818 (t0) cc_final: 0.8023 (t0) REVERT: C 167 ARG cc_start: 0.8742 (mmp80) cc_final: 0.8500 (mmp80) REVERT: C 175 GLU cc_start: 0.8726 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 185 MET cc_start: 0.9378 (mtt) cc_final: 0.9046 (mtt) REVERT: C 203 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8818 (mmmm) REVERT: C 215 MET cc_start: 0.9611 (tmm) cc_final: 0.8997 (tmm) REVERT: D 10 MET cc_start: 0.7737 (mpp) cc_final: 0.6446 (mmt) REVERT: D 21 ASN cc_start: 0.9607 (t0) cc_final: 0.9288 (t0) REVERT: D 25 LYS cc_start: 0.9756 (ttpt) cc_final: 0.9495 (ptmt) REVERT: D 52 LEU cc_start: 0.9641 (mt) cc_final: 0.9385 (mt) REVERT: D 68 MET cc_start: 0.8266 (mtt) cc_final: 0.7955 (mtp) REVERT: D 128 GLU cc_start: 0.9236 (mm-30) cc_final: 0.9003 (mp0) REVERT: D 129 ILE cc_start: 0.9559 (mt) cc_final: 0.9282 (tp) REVERT: D 130 TYR cc_start: 0.9026 (t80) cc_final: 0.8726 (t80) REVERT: D 131 LYS cc_start: 0.9423 (ttmt) cc_final: 0.9022 (ptpt) REVERT: D 140 LYS cc_start: 0.9615 (mttt) cc_final: 0.9331 (tptp) REVERT: G 40 PHE cc_start: 0.9717 (t80) cc_final: 0.9465 (t80) REVERT: G 58 THR cc_start: 0.9282 (p) cc_final: 0.8907 (p) REVERT: G 140 LYS cc_start: 0.9678 (mtpp) cc_final: 0.9432 (mtpp) REVERT: G 159 GLU cc_start: 0.8283 (tt0) cc_final: 0.7987 (tt0) REVERT: G 168 PHE cc_start: 0.9284 (t80) cc_final: 0.8999 (t80) REVERT: G 176 GLN cc_start: 0.9377 (tm-30) cc_final: 0.9018 (tm-30) REVERT: G 188 THR cc_start: 0.9393 (p) cc_final: 0.9165 (p) REVERT: H 13 GLN cc_start: 0.9342 (pp30) cc_final: 0.9078 (pm20) REVERT: H 25 LYS cc_start: 0.9532 (tttt) cc_final: 0.9180 (tppt) REVERT: H 29 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: H 32 PHE cc_start: 0.6937 (m-10) cc_final: 0.6647 (m-10) REVERT: H 39 MET cc_start: 0.9161 (mtm) cc_final: 0.8884 (mpp) REVERT: H 66 MET cc_start: 0.9557 (mmp) cc_final: 0.9182 (mmm) REVERT: H 67 GLN cc_start: 0.9318 (tp40) cc_final: 0.8741 (mt0) REVERT: H 81 ASP cc_start: 0.9465 (m-30) cc_final: 0.9232 (m-30) REVERT: H 87 HIS cc_start: 0.7835 (m-70) cc_final: 0.7065 (t-90) REVERT: H 118 MET cc_start: 0.8637 (mmm) cc_final: 0.8175 (mmt) REVERT: H 124 ILE cc_start: 0.6783 (mm) cc_final: 0.6391 (mp) REVERT: H 128 GLU cc_start: 0.9738 (mm-30) cc_final: 0.9370 (mp0) REVERT: H 145 TYR cc_start: 0.9097 (m-80) cc_final: 0.8625 (m-10) REVERT: H 152 ASP cc_start: 0.9593 (m-30) cc_final: 0.9314 (m-30) REVERT: H 182 LYS cc_start: 0.9657 (pttm) cc_final: 0.9362 (pttp) REVERT: H 185 MET cc_start: 0.9608 (mtm) cc_final: 0.9374 (mtm) REVERT: J 24 LEU cc_start: 0.9705 (mt) cc_final: 0.9452 (mt) REVERT: J 29 VAL cc_start: 0.9145 (t) cc_final: 0.8822 (p) REVERT: J 40 SER cc_start: 0.8589 (m) cc_final: 0.7628 (p) REVERT: J 41 THR cc_start: 0.6665 (t) cc_final: 0.6185 (t) REVERT: J 48 TYR cc_start: 0.8767 (m-80) cc_final: 0.8162 (m-80) REVERT: J 57 ILE cc_start: 0.7383 (tt) cc_final: 0.6941 (tt) REVERT: J 60 PHE cc_start: 0.7784 (t80) cc_final: 0.7441 (t80) REVERT: J 61 MET cc_start: 0.6000 (ppp) cc_final: 0.5596 (ppp) REVERT: J 78 ILE cc_start: 0.9258 (pt) cc_final: 0.8960 (pt) REVERT: J 119 THR cc_start: 0.7123 (p) cc_final: 0.6285 (m) REVERT: J 133 LYS cc_start: 0.9367 (tppt) cc_final: 0.9079 (mttt) REVERT: J 142 MET cc_start: 0.9154 (mtt) cc_final: 0.8752 (mtp) REVERT: N 178 SER cc_start: 0.8823 (p) cc_final: 0.8153 (t) REVERT: N 180 GLU cc_start: 0.9218 (pm20) cc_final: 0.8909 (pm20) REVERT: Y 10 MET cc_start: 0.9125 (pmm) cc_final: 0.8842 (mmp) REVERT: Y 32 PHE cc_start: 0.7893 (m-10) cc_final: 0.7664 (m-10) REVERT: Y 43 LEU cc_start: 0.9355 (mm) cc_final: 0.9135 (mm) REVERT: Y 53 ASN cc_start: 0.9622 (m-40) cc_final: 0.9275 (m-40) REVERT: Y 67 GLN cc_start: 0.9790 (mm-40) cc_final: 0.9500 (mm-40) REVERT: Y 68 MET cc_start: 0.9281 (mtm) cc_final: 0.9022 (mtp) REVERT: Y 71 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9150 (mt-10) REVERT: Y 115 ILE cc_start: 0.9457 (mm) cc_final: 0.9212 (mm) REVERT: Y 124 ILE cc_start: 0.8925 (tp) cc_final: 0.8635 (tp) REVERT: Y 126 VAL cc_start: 0.9244 (t) cc_final: 0.8876 (t) REVERT: Y 129 ILE cc_start: 0.9524 (mt) cc_final: 0.9240 (tt) REVERT: d 10 MET cc_start: 0.7054 (tpp) cc_final: 0.6803 (tpp) REVERT: d 23 TRP cc_start: 0.9429 (t-100) cc_final: 0.8775 (t-100) REVERT: d 25 LYS cc_start: 0.9205 (tttt) cc_final: 0.8961 (tptp) REVERT: d 30 LYS cc_start: 0.8260 (mttm) cc_final: 0.7963 (ttpp) REVERT: d 39 MET cc_start: 0.9108 (mtm) cc_final: 0.8115 (mtt) REVERT: d 55 MET cc_start: 0.9362 (ppp) cc_final: 0.8905 (ppp) REVERT: d 58 THR cc_start: 0.9354 (p) cc_final: 0.9132 (p) REVERT: d 67 GLN cc_start: 0.9121 (tp-100) cc_final: 0.8644 (tp40) REVERT: d 111 LEU cc_start: 0.9433 (pp) cc_final: 0.9204 (pp) REVERT: d 132 ARG cc_start: 0.9434 (ttm110) cc_final: 0.9087 (ttp-110) REVERT: d 143 ARG cc_start: 0.8601 (tpt170) cc_final: 0.8366 (tpt170) REVERT: d 168 PHE cc_start: 0.9422 (t80) cc_final: 0.9062 (t80) REVERT: e 10 MET cc_start: 0.8390 (tpp) cc_final: 0.7784 (tpp) REVERT: e 39 MET cc_start: 0.9623 (mtm) cc_final: 0.9145 (mtm) REVERT: e 50 GLN cc_start: 0.9278 (mt0) cc_final: 0.8805 (mt0) REVERT: e 104 ILE cc_start: 0.8280 (mt) cc_final: 0.7816 (mt) REVERT: e 111 LEU cc_start: 0.9300 (tp) cc_final: 0.9096 (tp) REVERT: e 114 GLN cc_start: 0.9425 (pt0) cc_final: 0.9049 (pt0) REVERT: e 118 MET cc_start: 0.9381 (mmt) cc_final: 0.8964 (ptp) REVERT: e 167 ARG cc_start: 0.8877 (ptp-110) cc_final: 0.8640 (ptp-110) REVERT: e 185 MET cc_start: 0.9845 (ptp) cc_final: 0.9469 (ptt) REVERT: e 203 LYS cc_start: 0.8013 (ptpt) cc_final: 0.7358 (tttt) REVERT: e 211 LEU cc_start: 0.9181 (tp) cc_final: 0.8756 (tp) REVERT: e 214 MET cc_start: 0.8774 (tpp) cc_final: 0.8566 (tpp) REVERT: j 188 THR cc_start: 0.8143 (m) cc_final: 0.7690 (m) REVERT: k 39 MET cc_start: 0.9482 (tpt) cc_final: 0.9227 (tpt) REVERT: k 43 LEU cc_start: 0.9591 (mp) cc_final: 0.9073 (mp) REVERT: k 52 LEU cc_start: 0.9595 (mt) cc_final: 0.9350 (mt) REVERT: k 55 MET cc_start: 0.9734 (ttt) cc_final: 0.9251 (ttt) REVERT: k 56 LEU cc_start: 0.9587 (mt) cc_final: 0.9290 (mt) REVERT: k 76 GLU cc_start: 0.9460 (mm-30) cc_final: 0.9171 (mm-30) REVERT: k 113 GLU cc_start: 0.9317 (tp30) cc_final: 0.9033 (tp30) REVERT: k 131 LYS cc_start: 0.9352 (tttt) cc_final: 0.8928 (tptt) REVERT: k 143 ARG cc_start: 0.8975 (mtt-85) cc_final: 0.8648 (mtp85) REVERT: k 163 ASP cc_start: 0.9311 (m-30) cc_final: 0.8930 (m-30) REVERT: k 167 ARG cc_start: 0.8916 (mtm-85) cc_final: 0.8450 (ptt-90) REVERT: k 168 PHE cc_start: 0.9486 (t80) cc_final: 0.9227 (t80) REVERT: k 173 ARG cc_start: 0.8842 (ttt180) cc_final: 0.8571 (ttp-170) REVERT: k 179 GLN cc_start: 0.9554 (tp-100) cc_final: 0.9259 (tp-100) REVERT: k 185 MET cc_start: 0.9336 (mtm) cc_final: 0.8982 (mtt) REVERT: k 193 ASN cc_start: 0.9328 (m110) cc_final: 0.8083 (t0) REVERT: k 215 MET cc_start: 0.9352 (ppp) cc_final: 0.9124 (ppp) outliers start: 5 outliers final: 2 residues processed: 845 average time/residue: 0.3445 time to fit residues: 411.4996 Evaluate side-chains 680 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 677 time to evaluate : 2.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 6.9990 chunk 25 optimal weight: 9.9990 chunk 128 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 141 optimal weight: 0.0060 chunk 137 optimal weight: 8.9990 chunk 104 optimal weight: 0.0970 chunk 139 optimal weight: 30.0000 overall best weight: 4.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.7503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18824 Z= 0.218 Angle : 0.704 9.591 25567 Z= 0.374 Chirality : 0.048 0.422 2848 Planarity : 0.005 0.047 3345 Dihedral : 4.555 21.529 2500 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.05 % Allowed : 0.90 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.50 (0.17), residues: 2338 helix: -0.09 (0.13), residues: 1467 sheet: -1.51 (0.48), residues: 82 loop : -0.35 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 184 HIS 0.004 0.001 HIS k 62 PHE 0.033 0.002 PHE H 168 TYR 0.019 0.002 TYR H 130 ARG 0.008 0.001 ARG H 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 845 time to evaluate : 2.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9460 (mp10) cc_final: 0.9232 (pm20) REVERT: A 25 LYS cc_start: 0.9614 (tptt) cc_final: 0.9321 (tppt) REVERT: A 29 GLU cc_start: 0.8848 (pp20) cc_final: 0.8198 (pp20) REVERT: A 39 MET cc_start: 0.9197 (mtt) cc_final: 0.8878 (mtt) REVERT: A 67 GLN cc_start: 0.9527 (tp40) cc_final: 0.9247 (tm-30) REVERT: A 68 MET cc_start: 0.9459 (ptp) cc_final: 0.8805 (ptp) REVERT: A 70 LYS cc_start: 0.9619 (pttm) cc_final: 0.9359 (pttm) REVERT: A 76 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8539 (mt-10) REVERT: A 96 MET cc_start: 0.6651 (mtp) cc_final: 0.6345 (mtp) REVERT: A 100 ARG cc_start: 0.9646 (ttm-80) cc_final: 0.9290 (tpp80) REVERT: A 103 ASP cc_start: 0.9636 (m-30) cc_final: 0.9292 (m-30) REVERT: A 135 ILE cc_start: 0.9484 (mt) cc_final: 0.9219 (mt) REVERT: A 141 ILE cc_start: 0.9720 (mm) cc_final: 0.9364 (mm) REVERT: B 5 ASN cc_start: 0.9224 (t0) cc_final: 0.8851 (m110) REVERT: B 16 SER cc_start: 0.9027 (m) cc_final: 0.8783 (m) REVERT: B 20 LEU cc_start: 0.9570 (mt) cc_final: 0.9364 (mt) REVERT: B 23 TRP cc_start: 0.8977 (t-100) cc_final: 0.8436 (t-100) REVERT: B 30 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8640 (mmmt) REVERT: B 39 MET cc_start: 0.9536 (tpp) cc_final: 0.9117 (tpt) REVERT: B 40 PHE cc_start: 0.9408 (t80) cc_final: 0.8889 (t80) REVERT: B 55 MET cc_start: 0.9287 (ttm) cc_final: 0.8499 (ttm) REVERT: B 100 ARG cc_start: 0.8978 (ttp-110) cc_final: 0.8539 (ttp80) REVERT: B 117 TRP cc_start: 0.8839 (m-10) cc_final: 0.8435 (m-10) REVERT: B 118 MET cc_start: 0.9643 (mtm) cc_final: 0.9371 (mmm) REVERT: B 128 GLU cc_start: 0.9452 (mp0) cc_final: 0.9175 (pm20) REVERT: B 131 LYS cc_start: 0.9269 (ttmt) cc_final: 0.8813 (ttmt) REVERT: B 158 LYS cc_start: 0.8952 (tppt) cc_final: 0.8226 (mmtt) REVERT: B 167 ARG cc_start: 0.9225 (mtp-110) cc_final: 0.8936 (ttm110) REVERT: B 169 TYR cc_start: 0.9367 (m-10) cc_final: 0.8817 (m-10) REVERT: B 170 LYS cc_start: 0.9487 (tppt) cc_final: 0.9225 (tppt) REVERT: B 181 VAL cc_start: 0.9693 (t) cc_final: 0.9148 (t) REVERT: B 185 MET cc_start: 0.9717 (ptp) cc_final: 0.9327 (ptp) REVERT: B 213 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9158 (pt0) REVERT: B 214 MET cc_start: 0.9122 (mtt) cc_final: 0.8902 (mtt) REVERT: C 10 MET cc_start: 0.8291 (tpp) cc_final: 0.7709 (tpp) REVERT: C 23 TRP cc_start: 0.9621 (t-100) cc_final: 0.9058 (t-100) REVERT: C 43 LEU cc_start: 0.9513 (mt) cc_final: 0.8868 (mp) REVERT: C 55 MET cc_start: 0.9656 (ttt) cc_final: 0.8181 (ttm) REVERT: C 59 VAL cc_start: 0.8541 (t) cc_final: 0.8272 (p) REVERT: C 76 GLU cc_start: 0.9461 (mm-30) cc_final: 0.9149 (mm-30) REVERT: C 96 MET cc_start: -0.5597 (mmt) cc_final: -0.5920 (mtm) REVERT: C 129 ILE cc_start: 0.9717 (mt) cc_final: 0.9216 (mt) REVERT: C 133 TRP cc_start: 0.8887 (m-10) cc_final: 0.8505 (m-10) REVERT: C 144 MET cc_start: 0.8161 (tmm) cc_final: 0.7726 (tmm) REVERT: C 153 ILE cc_start: 0.9230 (mt) cc_final: 0.8937 (mt) REVERT: C 163 ASP cc_start: 0.9137 (m-30) cc_final: 0.8783 (t0) REVERT: C 166 ASP cc_start: 0.8859 (t0) cc_final: 0.7985 (t0) REVERT: C 167 ARG cc_start: 0.8935 (mmp80) cc_final: 0.8476 (mmp80) REVERT: C 175 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8325 (tm-30) REVERT: C 185 MET cc_start: 0.9338 (mtt) cc_final: 0.9074 (mtt) REVERT: C 203 LYS cc_start: 0.9073 (mmtt) cc_final: 0.8831 (mmmm) REVERT: C 215 MET cc_start: 0.9290 (tmm) cc_final: 0.9030 (tmm) REVERT: D 10 MET cc_start: 0.7767 (mpp) cc_final: 0.6705 (mmt) REVERT: D 21 ASN cc_start: 0.9603 (t0) cc_final: 0.9318 (t0) REVERT: D 25 LYS cc_start: 0.9752 (ttpt) cc_final: 0.9500 (ptmt) REVERT: D 52 LEU cc_start: 0.9597 (mt) cc_final: 0.9332 (mt) REVERT: D 68 MET cc_start: 0.8373 (mtt) cc_final: 0.8063 (mtp) REVERT: D 129 ILE cc_start: 0.9564 (mt) cc_final: 0.9135 (tp) REVERT: D 130 TYR cc_start: 0.9034 (t80) cc_final: 0.8641 (t80) REVERT: D 131 LYS cc_start: 0.9416 (ttmt) cc_final: 0.8884 (mttt) REVERT: D 132 ARG cc_start: 0.9687 (ttt180) cc_final: 0.9403 (tpp80) REVERT: D 140 LYS cc_start: 0.9608 (mttt) cc_final: 0.9310 (tptp) REVERT: D 215 MET cc_start: 0.8288 (mtm) cc_final: 0.7422 (mtm) REVERT: G 128 GLU cc_start: 0.9502 (pm20) cc_final: 0.9158 (pm20) REVERT: G 132 ARG cc_start: 0.9443 (ptp-110) cc_final: 0.8922 (ptt-90) REVERT: G 140 LYS cc_start: 0.9670 (mtpp) cc_final: 0.9353 (mtpp) REVERT: G 159 GLU cc_start: 0.8235 (tt0) cc_final: 0.7964 (tt0) REVERT: G 168 PHE cc_start: 0.9297 (t80) cc_final: 0.8997 (t80) REVERT: G 188 THR cc_start: 0.9396 (p) cc_final: 0.9170 (p) REVERT: G 213 GLU cc_start: 0.9169 (pt0) cc_final: 0.8946 (pp20) REVERT: G 214 MET cc_start: 0.9536 (mmp) cc_final: 0.9319 (mmm) REVERT: H 13 GLN cc_start: 0.9423 (pp30) cc_final: 0.9173 (pm20) REVERT: H 23 TRP cc_start: 0.9367 (t60) cc_final: 0.8754 (t60) REVERT: H 25 LYS cc_start: 0.9588 (tttt) cc_final: 0.9165 (tppt) REVERT: H 29 GLU cc_start: 0.8333 (pm20) cc_final: 0.7901 (pm20) REVERT: H 32 PHE cc_start: 0.7393 (m-10) cc_final: 0.7125 (m-10) REVERT: H 39 MET cc_start: 0.9126 (mtm) cc_final: 0.8905 (mmt) REVERT: H 55 MET cc_start: 0.9061 (mtp) cc_final: 0.8769 (mmm) REVERT: H 66 MET cc_start: 0.9562 (mmp) cc_final: 0.9222 (mmm) REVERT: H 67 GLN cc_start: 0.9300 (tp40) cc_final: 0.8874 (mt0) REVERT: H 68 MET cc_start: 0.9407 (mmt) cc_final: 0.9090 (mmm) REVERT: H 81 ASP cc_start: 0.9480 (m-30) cc_final: 0.9237 (m-30) REVERT: H 87 HIS cc_start: 0.7900 (m-70) cc_final: 0.7067 (t-90) REVERT: H 118 MET cc_start: 0.8643 (mmm) cc_final: 0.8314 (mmt) REVERT: H 124 ILE cc_start: 0.6789 (mm) cc_final: 0.6515 (mp) REVERT: H 128 GLU cc_start: 0.9731 (mm-30) cc_final: 0.9391 (mp0) REVERT: H 143 ARG cc_start: 0.9169 (mtm-85) cc_final: 0.8959 (mtm-85) REVERT: H 145 TYR cc_start: 0.9060 (m-80) cc_final: 0.8755 (m-10) REVERT: H 152 ASP cc_start: 0.9585 (m-30) cc_final: 0.9298 (m-30) REVERT: H 167 ARG cc_start: 0.9185 (ptt180) cc_final: 0.8855 (ptt90) REVERT: H 182 LYS cc_start: 0.9684 (pttm) cc_final: 0.9389 (pttp) REVERT: J 24 LEU cc_start: 0.9691 (mt) cc_final: 0.9457 (mt) REVERT: J 40 SER cc_start: 0.8671 (m) cc_final: 0.7627 (p) REVERT: J 48 TYR cc_start: 0.8884 (m-80) cc_final: 0.8305 (m-80) REVERT: J 57 ILE cc_start: 0.7404 (tt) cc_final: 0.6269 (tt) REVERT: J 60 PHE cc_start: 0.7806 (t80) cc_final: 0.7360 (t80) REVERT: J 78 ILE cc_start: 0.9228 (pt) cc_final: 0.8977 (pt) REVERT: J 119 THR cc_start: 0.7041 (p) cc_final: 0.6060 (m) REVERT: J 122 LEU cc_start: 0.8698 (mt) cc_final: 0.8424 (mt) REVERT: J 142 MET cc_start: 0.9135 (mtt) cc_final: 0.8738 (mtp) REVERT: N 162 ARG cc_start: 0.9409 (mmm-85) cc_final: 0.9110 (mmp80) REVERT: N 178 SER cc_start: 0.8922 (p) cc_final: 0.8327 (t) REVERT: N 180 GLU cc_start: 0.9231 (pm20) cc_final: 0.8946 (pm20) REVERT: N 203 LYS cc_start: 0.8061 (pttt) cc_final: 0.7644 (pttt) REVERT: Y 10 MET cc_start: 0.9102 (pmm) cc_final: 0.8868 (mmp) REVERT: Y 23 TRP cc_start: 0.9500 (t-100) cc_final: 0.8949 (t60) REVERT: Y 53 ASN cc_start: 0.9614 (m-40) cc_final: 0.9296 (m-40) REVERT: Y 55 MET cc_start: 0.9324 (tmm) cc_final: 0.9104 (tmm) REVERT: Y 58 THR cc_start: 0.9464 (p) cc_final: 0.8897 (p) REVERT: Y 63 GLN cc_start: 0.8789 (mp10) cc_final: 0.8403 (mp10) REVERT: Y 66 MET cc_start: 0.9143 (ptp) cc_final: 0.8677 (ptt) REVERT: Y 67 GLN cc_start: 0.9777 (mm-40) cc_final: 0.9373 (mm-40) REVERT: Y 68 MET cc_start: 0.9274 (mtm) cc_final: 0.9008 (mtp) REVERT: Y 71 GLU cc_start: 0.9486 (mt-10) cc_final: 0.9063 (mt-10) REVERT: Y 129 ILE cc_start: 0.9537 (mt) cc_final: 0.9291 (tt) REVERT: d 10 MET cc_start: 0.7063 (tpp) cc_final: 0.6748 (tpp) REVERT: d 15 ILE cc_start: 0.7283 (pt) cc_final: 0.6404 (mp) REVERT: d 23 TRP cc_start: 0.9437 (t-100) cc_final: 0.8793 (t-100) REVERT: d 25 LYS cc_start: 0.9224 (tttt) cc_final: 0.8973 (tptp) REVERT: d 30 LYS cc_start: 0.8335 (mttm) cc_final: 0.8114 (ttpt) REVERT: d 39 MET cc_start: 0.9065 (mtm) cc_final: 0.8078 (mtt) REVERT: d 55 MET cc_start: 0.9365 (ppp) cc_final: 0.8818 (ppp) REVERT: d 58 THR cc_start: 0.9332 (p) cc_final: 0.9114 (p) REVERT: d 67 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8632 (tp40) REVERT: d 111 LEU cc_start: 0.9436 (pp) cc_final: 0.9187 (pp) REVERT: d 132 ARG cc_start: 0.9424 (ttm110) cc_final: 0.9067 (ttp-110) REVERT: d 143 ARG cc_start: 0.8575 (tpt170) cc_final: 0.8344 (tpt170) REVERT: d 215 MET cc_start: 0.4390 (mmt) cc_final: 0.3909 (mtp) REVERT: e 10 MET cc_start: 0.8530 (tpp) cc_final: 0.7971 (tpp) REVERT: e 23 TRP cc_start: 0.9352 (t-100) cc_final: 0.9078 (t-100) REVERT: e 28 GLU cc_start: 0.9696 (mp0) cc_final: 0.9472 (pm20) REVERT: e 32 PHE cc_start: 0.8917 (m-80) cc_final: 0.8660 (m-80) REVERT: e 35 GLU cc_start: 0.9321 (mp0) cc_final: 0.9087 (pm20) REVERT: e 39 MET cc_start: 0.9604 (mtm) cc_final: 0.9114 (mtm) REVERT: e 50 GLN cc_start: 0.9307 (mt0) cc_final: 0.8820 (mt0) REVERT: e 104 ILE cc_start: 0.8277 (mt) cc_final: 0.7752 (mt) REVERT: e 111 LEU cc_start: 0.9278 (tp) cc_final: 0.9066 (tp) REVERT: e 114 GLN cc_start: 0.9470 (pt0) cc_final: 0.9076 (pt0) REVERT: e 118 MET cc_start: 0.9410 (mmt) cc_final: 0.9129 (mtt) REVERT: e 169 TYR cc_start: 0.9579 (m-10) cc_final: 0.9291 (m-10) REVERT: e 175 GLU cc_start: 0.7527 (pp20) cc_final: 0.7272 (pp20) REVERT: e 182 LYS cc_start: 0.9606 (mttt) cc_final: 0.9073 (mmmm) REVERT: e 203 LYS cc_start: 0.8027 (ptpt) cc_final: 0.7336 (tttt) REVERT: j 188 THR cc_start: 0.8143 (m) cc_final: 0.7676 (m) REVERT: k 39 MET cc_start: 0.9573 (tpt) cc_final: 0.9225 (tpt) REVERT: k 43 LEU cc_start: 0.9596 (mp) cc_final: 0.9041 (mp) REVERT: k 52 LEU cc_start: 0.9580 (mt) cc_final: 0.9374 (mt) REVERT: k 55 MET cc_start: 0.9751 (ttt) cc_final: 0.9483 (ttt) REVERT: k 76 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9152 (mm-30) REVERT: k 113 GLU cc_start: 0.9310 (tp30) cc_final: 0.9015 (tp30) REVERT: k 131 LYS cc_start: 0.9293 (tttt) cc_final: 0.8859 (tptt) REVERT: k 143 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8580 (mtp85) REVERT: k 168 PHE cc_start: 0.9503 (t80) cc_final: 0.9275 (t80) REVERT: k 173 ARG cc_start: 0.8876 (ttt180) cc_final: 0.8622 (ttp-170) REVERT: k 179 GLN cc_start: 0.9566 (tp-100) cc_final: 0.9293 (tp-100) REVERT: k 185 MET cc_start: 0.9358 (mtm) cc_final: 0.8959 (mtm) REVERT: k 193 ASN cc_start: 0.9296 (m110) cc_final: 0.8068 (t0) REVERT: k 215 MET cc_start: 0.9410 (ppp) cc_final: 0.9120 (ppp) outliers start: 1 outliers final: 0 residues processed: 846 average time/residue: 0.3569 time to fit residues: 428.5584 Evaluate side-chains 680 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 680 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 20.0000 chunk 134 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 30.0000 chunk 43 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 177 optimal weight: 0.5980 chunk 205 optimal weight: 30.0000 overall best weight: 6.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 HIS ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.7802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 18824 Z= 0.246 Angle : 0.721 9.948 25567 Z= 0.385 Chirality : 0.047 0.185 2848 Planarity : 0.005 0.051 3345 Dihedral : 4.586 22.680 2500 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.53 (0.17), residues: 2338 helix: -0.17 (0.13), residues: 1461 sheet: -1.31 (0.56), residues: 64 loop : -0.31 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP G 117 HIS 0.005 0.001 HIS k 12 PHE 0.033 0.002 PHE H 168 TYR 0.018 0.002 TYR d 130 ARG 0.007 0.001 ARG k 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 827 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9466 (mp10) cc_final: 0.9243 (pm20) REVERT: A 39 MET cc_start: 0.9223 (mtt) cc_final: 0.8884 (mtt) REVERT: A 67 GLN cc_start: 0.9525 (tp40) cc_final: 0.9236 (tm-30) REVERT: A 68 MET cc_start: 0.9489 (ptp) cc_final: 0.8794 (ptp) REVERT: A 96 MET cc_start: 0.6632 (mtp) cc_final: 0.5328 (mtp) REVERT: A 100 ARG cc_start: 0.9652 (ttm-80) cc_final: 0.9304 (tpp80) REVERT: A 114 GLN cc_start: 0.9174 (mt0) cc_final: 0.8912 (mt0) REVERT: B 5 ASN cc_start: 0.9351 (t0) cc_final: 0.8907 (m110) REVERT: B 16 SER cc_start: 0.9089 (m) cc_final: 0.8861 (m) REVERT: B 20 LEU cc_start: 0.9523 (mt) cc_final: 0.9316 (mt) REVERT: B 30 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8653 (mmmt) REVERT: B 39 MET cc_start: 0.9519 (tpp) cc_final: 0.9133 (tpt) REVERT: B 68 MET cc_start: 0.9432 (mtm) cc_final: 0.9174 (mtt) REVERT: B 100 ARG cc_start: 0.9015 (ttp-110) cc_final: 0.8510 (ttp80) REVERT: B 108 THR cc_start: 0.9306 (p) cc_final: 0.9097 (p) REVERT: B 114 GLN cc_start: 0.9392 (pt0) cc_final: 0.9004 (pt0) REVERT: B 117 TRP cc_start: 0.8886 (m-10) cc_final: 0.8524 (m-10) REVERT: B 118 MET cc_start: 0.9643 (mtm) cc_final: 0.9407 (mmm) REVERT: B 128 GLU cc_start: 0.9463 (mp0) cc_final: 0.9197 (pm20) REVERT: B 144 MET cc_start: 0.8857 (ttt) cc_final: 0.8531 (tpp) REVERT: B 158 LYS cc_start: 0.9115 (tppt) cc_final: 0.8460 (mmtt) REVERT: B 167 ARG cc_start: 0.9243 (mtp-110) cc_final: 0.8954 (ttm110) REVERT: B 169 TYR cc_start: 0.9433 (m-10) cc_final: 0.8881 (m-10) REVERT: B 170 LYS cc_start: 0.9498 (tppt) cc_final: 0.9236 (tppt) REVERT: B 211 LEU cc_start: 0.7099 (tp) cc_final: 0.6877 (tp) REVERT: B 213 GLU cc_start: 0.9438 (mm-30) cc_final: 0.9102 (pt0) REVERT: C 10 MET cc_start: 0.8306 (tpp) cc_final: 0.7751 (tpp) REVERT: C 52 LEU cc_start: 0.9683 (mt) cc_final: 0.9467 (mt) REVERT: C 59 VAL cc_start: 0.8642 (t) cc_final: 0.8398 (p) REVERT: C 76 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9217 (mm-30) REVERT: C 96 MET cc_start: -0.5598 (mmt) cc_final: -0.5967 (mtm) REVERT: C 144 MET cc_start: 0.8281 (tmm) cc_final: 0.7985 (tmm) REVERT: C 153 ILE cc_start: 0.9149 (mt) cc_final: 0.8851 (mt) REVERT: C 166 ASP cc_start: 0.8860 (t0) cc_final: 0.7941 (t0) REVERT: C 167 ARG cc_start: 0.8950 (mmp80) cc_final: 0.8583 (mmp80) REVERT: C 175 GLU cc_start: 0.8846 (tm-30) cc_final: 0.8412 (tm-30) REVERT: C 185 MET cc_start: 0.9349 (mtt) cc_final: 0.9109 (mtt) REVERT: C 203 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8862 (mmmm) REVERT: C 215 MET cc_start: 0.9567 (tmm) cc_final: 0.9184 (tmm) REVERT: D 21 ASN cc_start: 0.9614 (t0) cc_final: 0.9282 (t0) REVERT: D 25 LYS cc_start: 0.9750 (ttpt) cc_final: 0.9493 (ptmt) REVERT: D 52 LEU cc_start: 0.9644 (mt) cc_final: 0.9433 (mt) REVERT: D 68 MET cc_start: 0.8432 (mtt) cc_final: 0.8082 (mtp) REVERT: D 96 MET cc_start: 0.7882 (ttt) cc_final: 0.7494 (ttt) REVERT: D 129 ILE cc_start: 0.9507 (mt) cc_final: 0.9164 (tp) REVERT: D 131 LYS cc_start: 0.9390 (ttmt) cc_final: 0.8923 (mttt) REVERT: D 140 LYS cc_start: 0.9610 (mttt) cc_final: 0.9313 (tptp) REVERT: G 23 TRP cc_start: 0.9420 (t60) cc_final: 0.8920 (t60) REVERT: G 58 THR cc_start: 0.9156 (p) cc_final: 0.8955 (p) REVERT: G 117 TRP cc_start: 0.8775 (m-10) cc_final: 0.8156 (m100) REVERT: G 140 LYS cc_start: 0.9668 (mtpp) cc_final: 0.9357 (mtpp) REVERT: G 159 GLU cc_start: 0.8220 (tt0) cc_final: 0.7953 (tt0) REVERT: G 168 PHE cc_start: 0.9312 (t80) cc_final: 0.9023 (t80) REVERT: G 188 THR cc_start: 0.9409 (p) cc_final: 0.9167 (p) REVERT: H 3 VAL cc_start: 0.9507 (p) cc_final: 0.9262 (m) REVERT: H 13 GLN cc_start: 0.9517 (pp30) cc_final: 0.9192 (pm20) REVERT: H 23 TRP cc_start: 0.9426 (t60) cc_final: 0.9075 (t60) REVERT: H 25 LYS cc_start: 0.9503 (tttt) cc_final: 0.9132 (tppt) REVERT: H 39 MET cc_start: 0.9464 (mtm) cc_final: 0.8982 (mtt) REVERT: H 53 ASN cc_start: 0.9683 (m-40) cc_final: 0.9402 (m-40) REVERT: H 66 MET cc_start: 0.9576 (mmp) cc_final: 0.9246 (mmm) REVERT: H 67 GLN cc_start: 0.9330 (tp40) cc_final: 0.8730 (mt0) REVERT: H 68 MET cc_start: 0.9389 (mmt) cc_final: 0.9047 (mmm) REVERT: H 80 TRP cc_start: 0.9590 (t-100) cc_final: 0.9157 (t60) REVERT: H 87 HIS cc_start: 0.7960 (m-70) cc_final: 0.7217 (t-170) REVERT: H 118 MET cc_start: 0.8590 (mmm) cc_final: 0.8248 (mmt) REVERT: H 124 ILE cc_start: 0.6884 (mm) cc_final: 0.6637 (mp) REVERT: H 128 GLU cc_start: 0.9740 (mm-30) cc_final: 0.9406 (mp0) REVERT: H 143 ARG cc_start: 0.9197 (mtm-85) cc_final: 0.8923 (mtm-85) REVERT: H 145 TYR cc_start: 0.9059 (m-80) cc_final: 0.8712 (m-10) REVERT: H 152 ASP cc_start: 0.9595 (m-30) cc_final: 0.9321 (m-30) REVERT: H 182 LYS cc_start: 0.9720 (pttm) cc_final: 0.9448 (pttp) REVERT: H 215 MET cc_start: 0.6035 (mtp) cc_final: 0.5835 (mtp) REVERT: J 24 LEU cc_start: 0.9652 (mt) cc_final: 0.9334 (mt) REVERT: J 25 PHE cc_start: 0.9132 (m-80) cc_final: 0.8914 (m-80) REVERT: J 36 PHE cc_start: 0.9661 (t80) cc_final: 0.9352 (t80) REVERT: J 40 SER cc_start: 0.8513 (m) cc_final: 0.7552 (p) REVERT: J 41 THR cc_start: 0.6615 (t) cc_final: 0.6236 (t) REVERT: J 48 TYR cc_start: 0.8792 (m-80) cc_final: 0.8283 (m-80) REVERT: J 60 PHE cc_start: 0.7892 (t80) cc_final: 0.7422 (t80) REVERT: J 78 ILE cc_start: 0.9229 (pt) cc_final: 0.9002 (pt) REVERT: J 119 THR cc_start: 0.7048 (p) cc_final: 0.5763 (m) REVERT: J 122 LEU cc_start: 0.8646 (mt) cc_final: 0.8132 (mt) REVERT: J 142 MET cc_start: 0.9153 (mtt) cc_final: 0.8784 (mtp) REVERT: J 158 ILE cc_start: 0.9067 (mt) cc_final: 0.8826 (mt) REVERT: N 178 SER cc_start: 0.8824 (p) cc_final: 0.8210 (t) REVERT: N 180 GLU cc_start: 0.9277 (pm20) cc_final: 0.9014 (pm20) REVERT: N 203 LYS cc_start: 0.7964 (pttt) cc_final: 0.7599 (pttt) REVERT: Y 53 ASN cc_start: 0.9540 (m-40) cc_final: 0.9276 (m-40) REVERT: Y 63 GLN cc_start: 0.8827 (mp10) cc_final: 0.8430 (mp10) REVERT: Y 66 MET cc_start: 0.9147 (ptp) cc_final: 0.8905 (ptt) REVERT: Y 67 GLN cc_start: 0.9757 (mm-40) cc_final: 0.9352 (mm-40) REVERT: Y 68 MET cc_start: 0.9268 (mtm) cc_final: 0.9038 (mtp) REVERT: Y 71 GLU cc_start: 0.9401 (mt-10) cc_final: 0.9006 (mt-10) REVERT: Y 115 ILE cc_start: 0.9612 (mm) cc_final: 0.9379 (mm) REVERT: Y 118 MET cc_start: 0.9306 (mmp) cc_final: 0.9089 (ptm) REVERT: Y 124 ILE cc_start: 0.8867 (tp) cc_final: 0.8539 (tp) REVERT: Y 126 VAL cc_start: 0.9251 (t) cc_final: 0.8911 (t) REVERT: Y 129 ILE cc_start: 0.9528 (mt) cc_final: 0.9276 (tt) REVERT: d 10 MET cc_start: 0.7087 (tpp) cc_final: 0.6786 (tpp) REVERT: d 15 ILE cc_start: 0.7314 (pt) cc_final: 0.6466 (mp) REVERT: d 23 TRP cc_start: 0.9449 (t-100) cc_final: 0.8812 (t-100) REVERT: d 25 LYS cc_start: 0.9230 (tttt) cc_final: 0.8980 (tptp) REVERT: d 30 LYS cc_start: 0.8421 (mttm) cc_final: 0.8154 (ttpt) REVERT: d 39 MET cc_start: 0.9152 (mtm) cc_final: 0.8190 (mtt) REVERT: d 55 MET cc_start: 0.9350 (ppp) cc_final: 0.8841 (ppp) REVERT: d 58 THR cc_start: 0.9348 (p) cc_final: 0.9138 (p) REVERT: d 67 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8576 (tp40) REVERT: d 68 MET cc_start: 0.9061 (mmm) cc_final: 0.8509 (mmm) REVERT: d 75 GLU cc_start: 0.8939 (pp20) cc_final: 0.8439 (pp20) REVERT: d 80 TRP cc_start: 0.9590 (t60) cc_final: 0.9359 (t60) REVERT: d 132 ARG cc_start: 0.9452 (ttm110) cc_final: 0.9095 (ttp-110) REVERT: d 143 ARG cc_start: 0.8663 (tpt170) cc_final: 0.8350 (tpt90) REVERT: d 168 PHE cc_start: 0.9450 (t80) cc_final: 0.9182 (t80) REVERT: d 215 MET cc_start: 0.4335 (mmt) cc_final: 0.3837 (mtp) REVERT: e 10 MET cc_start: 0.8461 (tpp) cc_final: 0.7893 (tpp) REVERT: e 32 PHE cc_start: 0.8967 (m-80) cc_final: 0.8664 (m-80) REVERT: e 50 GLN cc_start: 0.9327 (mt0) cc_final: 0.8895 (mt0) REVERT: e 66 MET cc_start: 0.9666 (ptm) cc_final: 0.9286 (ptp) REVERT: e 68 MET cc_start: 0.9235 (mtp) cc_final: 0.9025 (mtp) REVERT: e 76 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9344 (mm-30) REVERT: e 100 ARG cc_start: 0.8570 (mmp80) cc_final: 0.8275 (mmm160) REVERT: e 104 ILE cc_start: 0.8298 (mt) cc_final: 0.7813 (mt) REVERT: e 111 LEU cc_start: 0.9274 (tp) cc_final: 0.9039 (tp) REVERT: e 114 GLN cc_start: 0.9457 (pt0) cc_final: 0.9103 (pt0) REVERT: e 118 MET cc_start: 0.9434 (mmt) cc_final: 0.9137 (mtt) REVERT: e 169 TYR cc_start: 0.9581 (m-10) cc_final: 0.9282 (m-10) REVERT: e 185 MET cc_start: 0.9846 (ptp) cc_final: 0.9519 (ptt) REVERT: e 203 LYS cc_start: 0.7939 (ptpt) cc_final: 0.7239 (tttt) REVERT: j 150 ILE cc_start: 0.9426 (tp) cc_final: 0.9182 (tp) REVERT: j 172 LEU cc_start: 0.9658 (tp) cc_final: 0.9328 (mm) REVERT: j 182 LYS cc_start: 0.9334 (mmtt) cc_final: 0.8891 (mmtt) REVERT: j 188 THR cc_start: 0.8190 (m) cc_final: 0.7741 (m) REVERT: k 39 MET cc_start: 0.9635 (tpt) cc_final: 0.9258 (tpt) REVERT: k 43 LEU cc_start: 0.9598 (mp) cc_final: 0.9021 (mp) REVERT: k 52 LEU cc_start: 0.9617 (mt) cc_final: 0.9344 (mt) REVERT: k 76 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9253 (mm-30) REVERT: k 113 GLU cc_start: 0.9309 (tp30) cc_final: 0.9007 (tp30) REVERT: k 143 ARG cc_start: 0.8907 (mtt-85) cc_final: 0.8603 (mtp85) REVERT: k 173 ARG cc_start: 0.8891 (ttt180) cc_final: 0.8544 (ttt180) REVERT: k 185 MET cc_start: 0.9346 (mtm) cc_final: 0.8925 (mtt) REVERT: k 193 ASN cc_start: 0.9319 (m110) cc_final: 0.8052 (t0) REVERT: k 215 MET cc_start: 0.9347 (ppp) cc_final: 0.9101 (ptm) outliers start: 0 outliers final: 0 residues processed: 827 average time/residue: 0.3431 time to fit residues: 401.6493 Evaluate side-chains 665 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 665 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 91 optimal weight: 0.3980 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.8001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18824 Z= 0.226 Angle : 0.751 18.428 25567 Z= 0.395 Chirality : 0.048 0.263 2848 Planarity : 0.005 0.052 3345 Dihedral : 4.645 22.149 2500 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.61 (0.17), residues: 2338 helix: -0.22 (0.13), residues: 1457 sheet: -1.30 (0.58), residues: 64 loop : -0.37 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP G 23 HIS 0.003 0.001 HIS C 12 PHE 0.034 0.002 PHE H 168 TYR 0.025 0.002 TYR C 169 ARG 0.010 0.001 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 823 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9464 (mp10) cc_final: 0.9238 (pm20) REVERT: A 25 LYS cc_start: 0.9571 (tptp) cc_final: 0.9320 (tppt) REVERT: A 29 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8943 (pp20) REVERT: A 39 MET cc_start: 0.9227 (mtt) cc_final: 0.8888 (mtt) REVERT: A 67 GLN cc_start: 0.9532 (tp40) cc_final: 0.9133 (tm-30) REVERT: A 70 LYS cc_start: 0.9589 (pttm) cc_final: 0.9065 (tptp) REVERT: A 74 ASN cc_start: 0.9539 (m110) cc_final: 0.8974 (m110) REVERT: A 100 ARG cc_start: 0.9650 (ttm-80) cc_final: 0.9288 (tpp80) REVERT: A 114 GLN cc_start: 0.9183 (mt0) cc_final: 0.8952 (mt0) REVERT: B 5 ASN cc_start: 0.9411 (t0) cc_final: 0.8986 (m110) REVERT: B 23 TRP cc_start: 0.9228 (t-100) cc_final: 0.8670 (t-100) REVERT: B 30 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8701 (mmmt) REVERT: B 39 MET cc_start: 0.9537 (tpp) cc_final: 0.9064 (tpp) REVERT: B 55 MET cc_start: 0.9499 (ttm) cc_final: 0.8908 (ttm) REVERT: B 100 ARG cc_start: 0.8973 (ttp-110) cc_final: 0.8422 (ttp80) REVERT: B 108 THR cc_start: 0.9275 (p) cc_final: 0.9041 (p) REVERT: B 114 GLN cc_start: 0.9440 (pt0) cc_final: 0.8872 (pt0) REVERT: B 118 MET cc_start: 0.9639 (mtm) cc_final: 0.9205 (ptp) REVERT: B 128 GLU cc_start: 0.9453 (mp0) cc_final: 0.9159 (pm20) REVERT: B 131 LYS cc_start: 0.9335 (ttmt) cc_final: 0.8822 (ttmt) REVERT: B 144 MET cc_start: 0.8830 (ttt) cc_final: 0.8497 (tpp) REVERT: B 158 LYS cc_start: 0.9089 (tppt) cc_final: 0.8473 (mmtt) REVERT: B 167 ARG cc_start: 0.9251 (mtp-110) cc_final: 0.8963 (ttm110) REVERT: B 169 TYR cc_start: 0.9495 (m-10) cc_final: 0.8907 (m-10) REVERT: B 170 LYS cc_start: 0.9515 (tppt) cc_final: 0.9248 (tppt) REVERT: B 214 MET cc_start: 0.9154 (mtt) cc_final: 0.8879 (mtt) REVERT: C 10 MET cc_start: 0.8301 (tpp) cc_final: 0.7752 (tpp) REVERT: C 52 LEU cc_start: 0.9642 (mt) cc_final: 0.9410 (mt) REVERT: C 59 VAL cc_start: 0.8630 (t) cc_final: 0.8399 (p) REVERT: C 76 GLU cc_start: 0.9470 (mm-30) cc_final: 0.9151 (mm-30) REVERT: C 96 MET cc_start: -0.5846 (mmt) cc_final: -0.6264 (mtm) REVERT: C 129 ILE cc_start: 0.9719 (mt) cc_final: 0.9157 (mt) REVERT: C 133 TRP cc_start: 0.8909 (m-10) cc_final: 0.8477 (m-10) REVERT: C 144 MET cc_start: 0.8161 (tmm) cc_final: 0.7688 (tmm) REVERT: C 153 ILE cc_start: 0.9174 (mt) cc_final: 0.8906 (mt) REVERT: C 166 ASP cc_start: 0.8939 (t0) cc_final: 0.7806 (t0) REVERT: C 167 ARG cc_start: 0.8960 (mmp80) cc_final: 0.8536 (mmp80) REVERT: C 185 MET cc_start: 0.9322 (mtt) cc_final: 0.9082 (mtt) REVERT: C 203 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8822 (mmmm) REVERT: C 215 MET cc_start: 0.9568 (tmm) cc_final: 0.9202 (tmm) REVERT: D 21 ASN cc_start: 0.9610 (t0) cc_final: 0.9280 (t0) REVERT: D 25 LYS cc_start: 0.9747 (ttpt) cc_final: 0.9487 (ptmt) REVERT: D 68 MET cc_start: 0.8434 (mtt) cc_final: 0.8091 (mtp) REVERT: D 96 MET cc_start: 0.7675 (ttt) cc_final: 0.6856 (ttt) REVERT: D 129 ILE cc_start: 0.9342 (mt) cc_final: 0.8498 (tt) REVERT: D 131 LYS cc_start: 0.9350 (ttmt) cc_final: 0.9011 (ptpt) REVERT: D 140 LYS cc_start: 0.9598 (mttt) cc_final: 0.9291 (tptp) REVERT: D 215 MET cc_start: 0.8302 (mtm) cc_final: 0.7504 (mtm) REVERT: G 23 TRP cc_start: 0.9434 (t60) cc_final: 0.8960 (t60) REVERT: G 140 LYS cc_start: 0.9650 (mtpp) cc_final: 0.9340 (mtpp) REVERT: G 159 GLU cc_start: 0.8217 (tt0) cc_final: 0.7951 (tt0) REVERT: G 168 PHE cc_start: 0.9307 (t80) cc_final: 0.9021 (t80) REVERT: G 188 THR cc_start: 0.9416 (p) cc_final: 0.9182 (p) REVERT: H 3 VAL cc_start: 0.9520 (p) cc_final: 0.9309 (m) REVERT: H 13 GLN cc_start: 0.9524 (pp30) cc_final: 0.9233 (pm20) REVERT: H 25 LYS cc_start: 0.9470 (tttt) cc_final: 0.9076 (tppt) REVERT: H 32 PHE cc_start: 0.7285 (m-10) cc_final: 0.6936 (m-10) REVERT: H 52 LEU cc_start: 0.9857 (mt) cc_final: 0.9648 (mt) REVERT: H 53 ASN cc_start: 0.9719 (m-40) cc_final: 0.9425 (m110) REVERT: H 66 MET cc_start: 0.9564 (mmp) cc_final: 0.9182 (mmm) REVERT: H 67 GLN cc_start: 0.9310 (tp40) cc_final: 0.8922 (mt0) REVERT: H 68 MET cc_start: 0.9398 (mmt) cc_final: 0.8983 (mmm) REVERT: H 87 HIS cc_start: 0.8002 (m-70) cc_final: 0.6326 (t-170) REVERT: H 102 SER cc_start: 0.9359 (m) cc_final: 0.8986 (t) REVERT: H 108 THR cc_start: 0.9365 (p) cc_final: 0.9055 (p) REVERT: H 118 MET cc_start: 0.8486 (mmm) cc_final: 0.8141 (mmt) REVERT: H 128 GLU cc_start: 0.9751 (mm-30) cc_final: 0.9363 (mp0) REVERT: H 145 TYR cc_start: 0.9106 (m-80) cc_final: 0.8797 (m-10) REVERT: H 152 ASP cc_start: 0.9594 (m-30) cc_final: 0.9321 (m-30) REVERT: H 182 LYS cc_start: 0.9727 (pttm) cc_final: 0.9435 (pttp) REVERT: J 24 LEU cc_start: 0.9641 (mt) cc_final: 0.9407 (mt) REVERT: J 25 PHE cc_start: 0.9141 (m-80) cc_final: 0.8925 (m-80) REVERT: J 40 SER cc_start: 0.8890 (m) cc_final: 0.8165 (p) REVERT: J 43 GLU cc_start: 0.8828 (pm20) cc_final: 0.8422 (mp0) REVERT: J 48 TYR cc_start: 0.8939 (m-80) cc_final: 0.8258 (m-80) REVERT: J 60 PHE cc_start: 0.7844 (t80) cc_final: 0.7200 (t80) REVERT: J 78 ILE cc_start: 0.9244 (pt) cc_final: 0.8995 (pt) REVERT: J 119 THR cc_start: 0.7122 (p) cc_final: 0.5712 (m) REVERT: J 122 LEU cc_start: 0.8701 (mt) cc_final: 0.8148 (mt) REVERT: J 142 MET cc_start: 0.9154 (mtt) cc_final: 0.8771 (mtp) REVERT: N 162 ARG cc_start: 0.9443 (mmm-85) cc_final: 0.9075 (mmm-85) REVERT: N 178 SER cc_start: 0.8861 (p) cc_final: 0.8189 (t) REVERT: N 180 GLU cc_start: 0.9315 (pm20) cc_final: 0.9056 (pm20) REVERT: N 203 LYS cc_start: 0.7844 (pttt) cc_final: 0.7491 (pttt) REVERT: Y 23 TRP cc_start: 0.9525 (t-100) cc_final: 0.8992 (t60) REVERT: Y 28 GLU cc_start: 0.9636 (mm-30) cc_final: 0.9295 (mm-30) REVERT: Y 53 ASN cc_start: 0.9608 (m-40) cc_final: 0.9320 (m-40) REVERT: Y 58 THR cc_start: 0.9466 (p) cc_final: 0.9025 (p) REVERT: Y 63 GLN cc_start: 0.8751 (mp10) cc_final: 0.8517 (mp10) REVERT: Y 66 MET cc_start: 0.9173 (ptp) cc_final: 0.8514 (ptp) REVERT: Y 67 GLN cc_start: 0.9749 (mm-40) cc_final: 0.9196 (mm-40) REVERT: Y 115 ILE cc_start: 0.9595 (mm) cc_final: 0.9366 (mm) REVERT: Y 124 ILE cc_start: 0.8944 (tp) cc_final: 0.8615 (tp) REVERT: Y 126 VAL cc_start: 0.9248 (t) cc_final: 0.8895 (t) REVERT: Y 129 ILE cc_start: 0.9521 (mt) cc_final: 0.9170 (tt) REVERT: Y 132 ARG cc_start: 0.9745 (ptp-170) cc_final: 0.9521 (mtm110) REVERT: d 10 MET cc_start: 0.6894 (tpp) cc_final: 0.6588 (tpp) REVERT: d 15 ILE cc_start: 0.7283 (pt) cc_final: 0.6127 (pt) REVERT: d 23 TRP cc_start: 0.9434 (t-100) cc_final: 0.8807 (t-100) REVERT: d 25 LYS cc_start: 0.9223 (tttt) cc_final: 0.8977 (tptp) REVERT: d 30 LYS cc_start: 0.8462 (mttm) cc_final: 0.8233 (tttt) REVERT: d 39 MET cc_start: 0.9120 (mtm) cc_final: 0.8171 (mtt) REVERT: d 55 MET cc_start: 0.9334 (ppp) cc_final: 0.8848 (ppp) REVERT: d 67 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8535 (tp40) REVERT: d 68 MET cc_start: 0.9120 (mmm) cc_final: 0.8580 (mmm) REVERT: d 80 TRP cc_start: 0.9567 (t60) cc_final: 0.9346 (t60) REVERT: d 132 ARG cc_start: 0.9419 (ttm110) cc_final: 0.9061 (ttp-110) REVERT: d 143 ARG cc_start: 0.8640 (tpt170) cc_final: 0.8327 (tpt90) REVERT: d 168 PHE cc_start: 0.9426 (t80) cc_final: 0.9179 (t80) REVERT: e 10 MET cc_start: 0.8593 (tpp) cc_final: 0.8154 (tpp) REVERT: e 30 LYS cc_start: 0.9345 (mmmm) cc_final: 0.9058 (mmmm) REVERT: e 50 GLN cc_start: 0.9346 (mt0) cc_final: 0.8822 (mt0) REVERT: e 55 MET cc_start: 0.9065 (tpp) cc_final: 0.8813 (tpp) REVERT: e 68 MET cc_start: 0.9266 (mtp) cc_final: 0.8803 (mtp) REVERT: e 76 GLU cc_start: 0.9581 (mm-30) cc_final: 0.9332 (mm-30) REVERT: e 104 ILE cc_start: 0.8142 (mt) cc_final: 0.7910 (mt) REVERT: e 111 LEU cc_start: 0.9256 (tp) cc_final: 0.9037 (tp) REVERT: e 114 GLN cc_start: 0.9432 (pt0) cc_final: 0.8850 (pt0) REVERT: e 118 MET cc_start: 0.9426 (mmt) cc_final: 0.9182 (mtt) REVERT: e 169 TYR cc_start: 0.9579 (m-10) cc_final: 0.9305 (m-10) REVERT: e 185 MET cc_start: 0.9845 (ptp) cc_final: 0.9508 (ptt) REVERT: e 203 LYS cc_start: 0.7959 (ptpt) cc_final: 0.7269 (tttt) REVERT: j 150 ILE cc_start: 0.9387 (tp) cc_final: 0.9126 (tp) REVERT: j 172 LEU cc_start: 0.9670 (tp) cc_final: 0.9362 (mm) REVERT: j 182 LYS cc_start: 0.9343 (mmtt) cc_final: 0.8894 (mmtt) REVERT: j 188 THR cc_start: 0.8219 (m) cc_final: 0.7745 (m) REVERT: k 39 MET cc_start: 0.9679 (tpt) cc_final: 0.9264 (tpt) REVERT: k 43 LEU cc_start: 0.9594 (mp) cc_final: 0.8939 (mp) REVERT: k 55 MET cc_start: 0.9758 (ttt) cc_final: 0.9341 (ttt) REVERT: k 76 GLU cc_start: 0.9502 (mm-30) cc_final: 0.9249 (mm-30) REVERT: k 113 GLU cc_start: 0.9299 (tp30) cc_final: 0.9000 (tp30) REVERT: k 131 LYS cc_start: 0.9445 (tttp) cc_final: 0.8991 (tptt) REVERT: k 140 LYS cc_start: 0.9498 (mtmm) cc_final: 0.9244 (mtmm) REVERT: k 168 PHE cc_start: 0.9501 (t80) cc_final: 0.9296 (t80) REVERT: k 179 GLN cc_start: 0.9550 (tp-100) cc_final: 0.9288 (tp-100) REVERT: k 185 MET cc_start: 0.9332 (mtm) cc_final: 0.8959 (mtm) REVERT: k 193 ASN cc_start: 0.9319 (m110) cc_final: 0.7997 (t0) REVERT: k 215 MET cc_start: 0.9371 (ppp) cc_final: 0.9048 (ptm) outliers start: 0 outliers final: 0 residues processed: 823 average time/residue: 0.3674 time to fit residues: 434.0840 Evaluate side-chains 668 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 668 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.1980 chunk 135 optimal weight: 7.9990 chunk 105 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 233 optimal weight: 20.0000 chunk 214 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 147 optimal weight: 50.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 HIS ** B 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.8186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18824 Z= 0.225 Angle : 0.751 8.592 25567 Z= 0.403 Chirality : 0.048 0.365 2848 Planarity : 0.005 0.054 3345 Dihedral : 4.669 25.469 2500 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % 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: -0.65 (0.17), residues: 2338 helix: -0.31 (0.13), residues: 1457 sheet: -1.38 (0.58), residues: 64 loop : -0.27 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP G 23 HIS 0.007 0.001 HIS J 54 PHE 0.034 0.002 PHE H 168 TYR 0.017 0.002 TYR d 130 ARG 0.011 0.001 ARG e 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 GLN cc_start: 0.9460 (mp10) cc_final: 0.9229 (pm20) REVERT: A 25 LYS cc_start: 0.9562 (tptp) cc_final: 0.9324 (tppt) REVERT: A 29 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8930 (pp20) REVERT: A 39 MET cc_start: 0.9221 (mtt) cc_final: 0.8894 (mtt) REVERT: A 67 GLN cc_start: 0.9534 (tp40) cc_final: 0.9217 (tm-30) REVERT: A 70 LYS cc_start: 0.9580 (pttm) cc_final: 0.9327 (pttm) REVERT: A 76 GLU cc_start: 0.9399 (mt-10) cc_final: 0.9099 (mt-10) REVERT: A 114 GLN cc_start: 0.9196 (mt0) cc_final: 0.8875 (mt0) REVERT: B 5 ASN cc_start: 0.9427 (t0) cc_final: 0.8991 (m110) REVERT: B 23 TRP cc_start: 0.9197 (t-100) cc_final: 0.8544 (t-100) REVERT: B 30 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8564 (mmmt) REVERT: B 39 MET cc_start: 0.9535 (tpp) cc_final: 0.9070 (tpp) REVERT: B 55 MET cc_start: 0.9466 (ttm) cc_final: 0.8770 (ttm) REVERT: B 100 ARG cc_start: 0.8916 (ttp-110) cc_final: 0.8546 (ttp80) REVERT: B 118 MET cc_start: 0.9608 (mtm) cc_final: 0.9165 (ptp) REVERT: B 128 GLU cc_start: 0.9444 (mp0) cc_final: 0.9141 (pm20) REVERT: B 131 LYS cc_start: 0.9326 (ttmt) cc_final: 0.8800 (ttmt) REVERT: B 158 LYS cc_start: 0.9124 (tppt) cc_final: 0.8446 (mmtt) REVERT: B 167 ARG cc_start: 0.9255 (mtp-110) cc_final: 0.8972 (ttm110) REVERT: B 169 TYR cc_start: 0.9504 (m-10) cc_final: 0.8916 (m-10) REVERT: B 170 LYS cc_start: 0.9518 (tppt) cc_final: 0.9248 (tppt) REVERT: B 211 LEU cc_start: 0.7557 (tp) cc_final: 0.7141 (tp) REVERT: C 10 MET cc_start: 0.8322 (tpp) cc_final: 0.7778 (tpp) REVERT: C 52 LEU cc_start: 0.9611 (mt) cc_final: 0.9384 (mt) REVERT: C 76 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9182 (mm-30) REVERT: C 96 MET cc_start: -0.5941 (mmt) cc_final: -0.6400 (mtm) REVERT: C 129 ILE cc_start: 0.9712 (mt) cc_final: 0.9170 (mt) REVERT: C 133 TRP cc_start: 0.8870 (m-10) cc_final: 0.8489 (m-10) REVERT: C 144 MET cc_start: 0.8116 (tmm) cc_final: 0.7628 (tmm) REVERT: C 153 ILE cc_start: 0.9149 (mt) cc_final: 0.8884 (mt) REVERT: C 166 ASP cc_start: 0.8872 (t0) cc_final: 0.7721 (t0) REVERT: C 167 ARG cc_start: 0.8939 (mmp80) cc_final: 0.8515 (mmp80) REVERT: C 185 MET cc_start: 0.9333 (mtt) cc_final: 0.9048 (mtt) REVERT: C 192 GLN cc_start: 0.9211 (mp10) cc_final: 0.8967 (mp10) REVERT: D 21 ASN cc_start: 0.9610 (t0) cc_final: 0.9289 (t0) REVERT: D 25 LYS cc_start: 0.9731 (ttpt) cc_final: 0.9465 (ptmt) REVERT: D 68 MET cc_start: 0.8511 (mtt) cc_final: 0.8177 (mtp) REVERT: D 96 MET cc_start: 0.7707 (ttt) cc_final: 0.6835 (ttt) REVERT: D 131 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8911 (mttt) REVERT: D 140 LYS cc_start: 0.9591 (mttt) cc_final: 0.9288 (tptp) REVERT: D 215 MET cc_start: 0.8262 (mtm) cc_final: 0.7348 (mtm) REVERT: G 18 ARG cc_start: 0.9539 (mmm-85) cc_final: 0.9289 (mpt180) REVERT: G 23 TRP cc_start: 0.9454 (t60) cc_final: 0.9122 (t60) REVERT: G 68 MET cc_start: 0.8904 (mtt) cc_final: 0.8682 (mtp) REVERT: G 140 LYS cc_start: 0.9611 (mtpp) cc_final: 0.9328 (mtpp) REVERT: G 149 SER cc_start: 0.8608 (p) cc_final: 0.7479 (p) REVERT: G 152 ASP cc_start: 0.8816 (t0) cc_final: 0.8413 (m-30) REVERT: G 159 GLU cc_start: 0.8214 (tt0) cc_final: 0.7972 (tt0) REVERT: G 168 PHE cc_start: 0.9308 (t80) cc_final: 0.9003 (t80) REVERT: G 213 GLU cc_start: 0.9168 (pt0) cc_final: 0.8934 (pt0) REVERT: H 13 GLN cc_start: 0.9521 (pp30) cc_final: 0.9221 (pm20) REVERT: H 25 LYS cc_start: 0.9452 (tttt) cc_final: 0.9051 (tppt) REVERT: H 32 PHE cc_start: 0.7353 (m-10) cc_final: 0.7036 (m-10) REVERT: H 39 MET cc_start: 0.9428 (mtm) cc_final: 0.8923 (mtt) REVERT: H 53 ASN cc_start: 0.9593 (m-40) cc_final: 0.9312 (m110) REVERT: H 55 MET cc_start: 0.9169 (mmp) cc_final: 0.8848 (mmp) REVERT: H 66 MET cc_start: 0.9553 (mmp) cc_final: 0.9209 (mmm) REVERT: H 67 GLN cc_start: 0.9287 (tp40) cc_final: 0.8943 (mt0) REVERT: H 68 MET cc_start: 0.9297 (mmt) cc_final: 0.8964 (mmm) REVERT: H 81 ASP cc_start: 0.9481 (m-30) cc_final: 0.9275 (m-30) REVERT: H 96 MET cc_start: 0.6210 (ptt) cc_final: 0.5872 (ptt) REVERT: H 102 SER cc_start: 0.9355 (m) cc_final: 0.8993 (t) REVERT: H 108 THR cc_start: 0.9425 (p) cc_final: 0.9097 (p) REVERT: H 118 MET cc_start: 0.8504 (mmm) cc_final: 0.8130 (mmt) REVERT: H 128 GLU cc_start: 0.9746 (mm-30) cc_final: 0.9362 (mp0) REVERT: H 130 TYR cc_start: 0.9218 (t80) cc_final: 0.8974 (t80) REVERT: H 145 TYR cc_start: 0.9147 (m-80) cc_final: 0.8920 (m-10) REVERT: H 152 ASP cc_start: 0.9602 (m-30) cc_final: 0.9333 (m-30) REVERT: H 162 ARG cc_start: 0.9305 (mmp-170) cc_final: 0.8821 (mmp80) REVERT: H 167 ARG cc_start: 0.9175 (ptt180) cc_final: 0.8861 (ptt90) REVERT: H 215 MET cc_start: 0.6675 (mtp) cc_final: 0.6216 (mmm) REVERT: J 24 LEU cc_start: 0.9668 (mt) cc_final: 0.9439 (mt) REVERT: J 40 SER cc_start: 0.8686 (m) cc_final: 0.8010 (p) REVERT: J 48 TYR cc_start: 0.8527 (m-80) cc_final: 0.8123 (m-80) REVERT: J 60 PHE cc_start: 0.7715 (t80) cc_final: 0.7307 (t80) REVERT: J 78 ILE cc_start: 0.9239 (pt) cc_final: 0.8978 (pt) REVERT: J 119 THR cc_start: 0.7134 (p) cc_final: 0.5671 (m) REVERT: J 122 LEU cc_start: 0.8677 (mt) cc_final: 0.8105 (mt) REVERT: J 142 MET cc_start: 0.9172 (mtt) cc_final: 0.8808 (mtp) REVERT: J 158 ILE cc_start: 0.9127 (mt) cc_final: 0.8873 (mt) REVERT: N 162 ARG cc_start: 0.9429 (mmm-85) cc_final: 0.9078 (mmm160) REVERT: N 178 SER cc_start: 0.8976 (p) cc_final: 0.8415 (t) REVERT: N 180 GLU cc_start: 0.9310 (pm20) cc_final: 0.9055 (pm20) REVERT: N 203 LYS cc_start: 0.7846 (pttt) cc_final: 0.7503 (pttt) REVERT: Y 32 PHE cc_start: 0.7773 (m-10) cc_final: 0.7567 (m-10) REVERT: Y 53 ASN cc_start: 0.9609 (m-40) cc_final: 0.9259 (m-40) REVERT: Y 63 GLN cc_start: 0.8739 (mp10) cc_final: 0.8283 (mp10) REVERT: Y 66 MET cc_start: 0.9168 (ptp) cc_final: 0.8732 (ptt) REVERT: Y 67 GLN cc_start: 0.9749 (mm-40) cc_final: 0.9418 (mt0) REVERT: Y 68 MET cc_start: 0.9277 (mtt) cc_final: 0.9008 (mtp) REVERT: Y 71 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9025 (mt-10) REVERT: Y 129 ILE cc_start: 0.9529 (mt) cc_final: 0.9280 (tt) REVERT: d 10 MET cc_start: 0.6898 (tpp) cc_final: 0.6593 (tpp) REVERT: d 23 TRP cc_start: 0.9457 (t-100) cc_final: 0.8856 (t-100) REVERT: d 25 LYS cc_start: 0.9222 (tttt) cc_final: 0.8945 (tptp) REVERT: d 30 LYS cc_start: 0.8467 (mttm) cc_final: 0.8247 (tttt) REVERT: d 39 MET cc_start: 0.9061 (mtm) cc_final: 0.8123 (mtt) REVERT: d 55 MET cc_start: 0.9367 (ppp) cc_final: 0.8908 (ppp) REVERT: d 67 GLN cc_start: 0.9079 (tp-100) cc_final: 0.8629 (tp40) REVERT: d 132 ARG cc_start: 0.9399 (ttm110) cc_final: 0.9078 (ttp-110) REVERT: d 133 TRP cc_start: 0.9459 (m-10) cc_final: 0.8742 (m-10) REVERT: d 143 ARG cc_start: 0.8675 (tpt170) cc_final: 0.8325 (tpt90) REVERT: d 168 PHE cc_start: 0.9413 (t80) cc_final: 0.9213 (t80) REVERT: d 215 MET cc_start: 0.4871 (mmt) cc_final: 0.4362 (mtp) REVERT: e 10 MET cc_start: 0.8610 (tpp) cc_final: 0.8169 (tpp) REVERT: e 39 MET cc_start: 0.9569 (mtm) cc_final: 0.9102 (mtm) REVERT: e 50 GLN cc_start: 0.9333 (mt0) cc_final: 0.8863 (mt0) REVERT: e 55 MET cc_start: 0.9159 (tpp) cc_final: 0.8907 (tpp) REVERT: e 68 MET cc_start: 0.9261 (mtp) cc_final: 0.8909 (mtp) REVERT: e 76 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9290 (mm-30) REVERT: e 104 ILE cc_start: 0.8204 (mt) cc_final: 0.7995 (mt) REVERT: e 114 GLN cc_start: 0.9411 (pt0) cc_final: 0.9021 (pt0) REVERT: e 118 MET cc_start: 0.9435 (mmt) cc_final: 0.9223 (mtt) REVERT: e 185 MET cc_start: 0.9844 (ptp) cc_final: 0.9499 (ptt) REVERT: e 203 LYS cc_start: 0.7780 (ptpt) cc_final: 0.7038 (tttt) REVERT: e 211 LEU cc_start: 0.9368 (tp) cc_final: 0.8882 (tp) REVERT: j 150 ILE cc_start: 0.9329 (tp) cc_final: 0.9097 (tp) REVERT: j 153 ILE cc_start: 0.8841 (tp) cc_final: 0.8621 (tp) REVERT: j 172 LEU cc_start: 0.9643 (tp) cc_final: 0.9312 (mm) REVERT: j 182 LYS cc_start: 0.9332 (mmtt) cc_final: 0.8895 (mmtt) REVERT: j 188 THR cc_start: 0.8221 (m) cc_final: 0.7795 (m) REVERT: k 39 MET cc_start: 0.9716 (tpt) cc_final: 0.9402 (tpt) REVERT: k 55 MET cc_start: 0.9755 (ttt) cc_final: 0.9330 (ttt) REVERT: k 76 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9283 (mm-30) REVERT: k 113 GLU cc_start: 0.9282 (tp30) cc_final: 0.8975 (tp30) REVERT: k 131 LYS cc_start: 0.9455 (tttp) cc_final: 0.8980 (tptt) REVERT: k 154 ARG cc_start: 0.9613 (ttm110) cc_final: 0.9147 (tpp80) REVERT: k 168 PHE cc_start: 0.9513 (t80) cc_final: 0.9250 (t80) REVERT: k 179 GLN cc_start: 0.9546 (tp-100) cc_final: 0.9279 (tp-100) REVERT: k 185 MET cc_start: 0.9314 (mtm) cc_final: 0.8967 (mtm) REVERT: k 193 ASN cc_start: 0.9295 (m110) cc_final: 0.8806 (m-40) outliers start: 0 outliers final: 0 residues processed: 824 average time/residue: 0.3489 time to fit residues: 405.7354 Evaluate side-chains 661 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 661 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.8881 > 50: distance: 37 - 57: 12.643 distance: 41 - 66: 12.151 distance: 45 - 74: 16.131 distance: 51 - 57: 13.038 distance: 52 - 81: 3.242 distance: 57 - 58: 11.648 distance: 58 - 59: 3.275 distance: 58 - 61: 19.981 distance: 59 - 60: 5.343 distance: 59 - 66: 8.603 distance: 60 - 92: 15.148 distance: 61 - 62: 20.563 distance: 62 - 63: 3.186 distance: 63 - 64: 10.997 distance: 64 - 65: 4.361 distance: 66 - 67: 6.606 distance: 67 - 68: 7.392 distance: 67 - 70: 12.707 distance: 68 - 69: 6.105 distance: 68 - 74: 5.199 distance: 69 - 100: 28.148 distance: 70 - 71: 8.350 distance: 70 - 72: 17.031 distance: 71 - 73: 15.925 distance: 74 - 75: 7.174 distance: 75 - 78: 15.031 distance: 76 - 77: 16.833 distance: 76 - 81: 7.634 distance: 78 - 79: 11.787 distance: 78 - 80: 17.902 distance: 81 - 82: 7.116 distance: 82 - 83: 6.744 distance: 82 - 85: 6.770 distance: 83 - 84: 9.245 distance: 83 - 92: 4.540 distance: 85 - 86: 6.975 distance: 86 - 87: 5.012 distance: 87 - 88: 8.307 distance: 88 - 89: 4.045 distance: 89 - 90: 11.253 distance: 92 - 93: 8.598 distance: 93 - 94: 10.577 distance: 93 - 96: 20.707 distance: 94 - 95: 16.188 distance: 94 - 100: 26.186 distance: 96 - 97: 15.127 distance: 97 - 98: 15.127 distance: 98 - 99: 7.164 distance: 100 - 101: 22.783 distance: 101 - 102: 17.547 distance: 101 - 104: 10.283 distance: 102 - 103: 9.877 distance: 102 - 112: 6.576 distance: 104 - 105: 7.223 distance: 105 - 106: 17.457 distance: 105 - 107: 9.323 distance: 106 - 108: 9.833 distance: 107 - 109: 6.835 distance: 108 - 110: 7.530 distance: 109 - 110: 15.065 distance: 110 - 111: 14.671 distance: 112 - 113: 6.826 distance: 113 - 114: 22.315 distance: 113 - 116: 40.809 distance: 114 - 115: 14.901 distance: 114 - 118: 27.517 distance: 118 - 119: 13.604 distance: 118 - 124: 28.091 distance: 119 - 120: 19.273 distance: 119 - 122: 7.903 distance: 120 - 121: 20.450 distance: 120 - 125: 11.062 distance: 122 - 123: 30.920 distance: 125 - 126: 20.876 distance: 126 - 127: 6.942 distance: 126 - 129: 26.076 distance: 127 - 128: 12.143 distance: 127 - 132: 20.040 distance: 129 - 130: 22.563 distance: 129 - 131: 22.388 distance: 132 - 133: 15.731 distance: 133 - 134: 29.007 distance: 133 - 136: 22.729 distance: 134 - 135: 25.657 distance: 134 - 138: 7.860 distance: 135 - 151: 28.726