Starting phenix.real_space_refine on Wed Apr 10 03:49:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9x_10740/04_2024/6y9x_10740.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9x_10740/04_2024/6y9x_10740.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9x_10740/04_2024/6y9x_10740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9x_10740/04_2024/6y9x_10740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9x_10740/04_2024/6y9x_10740.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9x_10740/04_2024/6y9x_10740.pdb" } resolution = 4.4 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-5288/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: 9.63, per 1000 atoms: 0.52 Number of scatterers: 18418 At special positions: 0 Unit cell: (136.74, 179.14, 106, 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: 7.24 Conformation dependent library (CDL) restraints added in 3.8 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: 2.05 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: 3.527A 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: 3.791A 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: 3.596A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.804A 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: 4.006A 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: 3.537A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.962A 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: 3.870A 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: 4.765A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.877A 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: 3.897A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU G 190 " --> pdb=" O THR G 186 " (cutoff:3.500A) removed outlier: 4.892A 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: 4.892A 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: 4.122A 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: 3.791A 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: 3.593A 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: 3.675A 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: 3.699A pdb=" N GLN Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.601A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.674A 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: 3.603A 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: 4.877A 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: 3.906A 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: 3.904A 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: 3.524A 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: 3.580A 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: 3.923A 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: 4.395A 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: 6.542A pdb=" N VAL J 128 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N SER J 21 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.100A 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: 3.510A pdb=" N ASP J 160 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ALA J 11 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 5.522A 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: 3.764A 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: 3.540A 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: 5.08 Time building geometry restraints manager: 7.69 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: 7785 1.44 - 1.67: 10784 1.67 - 1.90: 252 1.90 - 2.14: 0 2.14 - 2.37: 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 -0.906 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 2.366 -0.844 1.37e-02 5.33e+03 3.80e+03 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.456 2.274 -0.818 1.33e-02 5.65e+03 3.78e+03 bond pdb=" C HIS e 84 " pdb=" N PRO e 85 " ideal model delta sigma weight residual 1.330 1.514 -0.184 1.22e-02 6.72e+03 2.28e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.296 0.078 1.10e-02 8.26e+03 5.06e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 64.16 - 80.44: 1 80.44 - 96.72: 2 96.72 - 113.00: 10875 113.00 - 129.28: 14534 129.28 - 145.56: 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 64.16 49.07 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 118.21 145.56 -27.35 1.36e+00 5.41e-01 4.04e+02 angle pdb=" O PRO C 147 " pdb=" C PRO C 147 " pdb=" N THR C 148 " ideal model delta sigma weight residual 122.30 108.80 13.50 1.36e+00 5.41e-01 9.85e+01 angle pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta sigma weight residual 111.30 133.23 -21.93 2.23e+00 2.01e-01 9.67e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 10634 17.94 - 35.87: 713 35.87 - 53.81: 180 53.81 - 71.75: 19 71.75 - 89.69: 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 -163.07 40.47 0 2.50e+00 1.60e-01 2.62e+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 122.80 158.61 -35.81 0 2.50e+00 1.60e-01 2.05e+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 96.01 26.79 0 2.50e+00 1.60e-01 1.15e+02 ... (remaining 11556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.947: 2846 0.947 - 1.893: 1 1.893 - 2.839: 0 2.839 - 3.786: 0 3.786 - 4.732: 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 7.24 -4.73 2.00e-01 2.50e+01 5.60e+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 6.54e+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 0.42 2.00e-01 2.50e+01 4.49e+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 7.90e-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 " -0.064 2.00e-02 2.50e+03 9.94e-02 9.89e+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 7.89e-02 6.23e+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: 1.34 - 2.06: 6 2.06 - 2.77: 3418 2.77 - 3.48: 26032 3.48 - 4.19: 40619 4.19 - 4.90: 71418 Nonbonded interactions: 141493 Sorted by model distance: nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.344 2.520 nonbonded pdb=" OE1 GLN D 192 " pdb=" CD1 LEU H 151 " model vdw 1.514 3.460 nonbonded pdb=" CG2 VAL G 181 " pdb=" OE1 GLU d 180 " model vdw 1.586 3.460 nonbonded pdb=" OE1 GLN G 192 " pdb=" CD1 LEU d 151 " model vdw 1.748 3.460 nonbonded pdb=" CD GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.920 3.350 ... (remaining 141488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 0.110 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: 1.860 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 48.860 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 0.906 18824 Z= 0.832 Angle : 1.068 49.068 25567 Z= 0.726 Chirality : 0.108 4.732 2848 Planarity : 0.007 0.099 3345 Dihedral : 13.054 89.686 7127 Min Nonbonded Distance : 1.344 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % 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 0.100 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 1148 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1139 time to evaluate : 2.198 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: A 51 ASP cc_start: 0.9407 (m-30) cc_final: 0.9091 (m-30) REVERT: A 56 LEU cc_start: 0.9588 (mt) cc_final: 0.9325 (mt) REVERT: A 96 MET cc_start: -0.1411 (mpp) cc_final: -0.1634 (mmt) REVERT: B 2 ILE cc_start: 0.7623 (pt) cc_final: 0.7366 (tt) REVERT: B 24 VAL cc_start: 0.9458 (t) cc_final: 0.9226 (p) REVERT: B 25 LYS cc_start: 0.9575 (mttt) cc_final: 0.9080 (ttmt) REVERT: B 35 GLU cc_start: 0.9493 (pm20) cc_final: 0.9099 (mp0) REVERT: B 39 MET cc_start: 0.9295 (tpp) cc_final: 0.9067 (tpp) REVERT: B 66 MET cc_start: 0.8800 (mmt) cc_final: 0.8172 (mmm) REVERT: B 67 GLN cc_start: 0.8821 (tp40) cc_final: 0.8398 (mm-40) REVERT: B 68 MET cc_start: 0.9518 (mtp) cc_final: 0.9023 (mtt) REVERT: B 75 GLU cc_start: 0.9166 (tt0) cc_final: 0.8956 (tt0) REVERT: B 114 GLN cc_start: 0.8780 (mt0) cc_final: 0.8516 (mt0) REVERT: B 118 MET cc_start: 0.8863 (mtm) cc_final: 0.8467 (ptp) REVERT: B 131 LYS cc_start: 0.9563 (ttmt) cc_final: 0.9147 (mmmt) REVERT: C 113 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8806 (tt0) REVERT: C 129 ILE cc_start: 0.9095 (mt) cc_final: 0.8043 (mt) REVERT: C 131 LYS cc_start: 0.8605 (ttmt) cc_final: 0.8117 (mtpt) REVERT: C 187 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8897 (mp0) REVERT: C 189 LEU cc_start: 0.9100 (mm) cc_final: 0.8739 (mp) REVERT: D 27 VAL cc_start: 0.9377 (p) cc_final: 0.8620 (m) REVERT: D 35 GLU cc_start: 0.9093 (pm20) cc_final: 0.8539 (pm20) REVERT: D 55 MET cc_start: 0.9194 (mtp) cc_final: 0.8977 (ttm) REVERT: D 56 LEU cc_start: 0.9715 (mt) cc_final: 0.9316 (mt) REVERT: D 118 MET cc_start: 0.9032 (mtm) cc_final: 0.8543 (ppp) REVERT: D 130 TYR cc_start: 0.9155 (t80) cc_final: 0.8813 (t80) REVERT: D 140 LYS cc_start: 0.9600 (mttt) cc_final: 0.9301 (tptp) REVERT: D 141 ILE cc_start: 0.9212 (mt) cc_final: 0.8795 (mt) REVERT: G 23 TRP cc_start: 0.9468 (t-100) cc_final: 0.8839 (t-100) REVERT: G 35 GLU cc_start: 0.9512 (pm20) cc_final: 0.9205 (pm20) REVERT: G 39 MET cc_start: 0.9541 (ttm) cc_final: 0.9291 (ttm) REVERT: G 57 ASN cc_start: 0.9590 (m-40) cc_final: 0.9367 (m110) REVERT: G 58 THR cc_start: 0.9434 (p) cc_final: 0.9125 (p) REVERT: G 96 MET cc_start: 0.0872 (mpp) cc_final: -0.1168 (mtt) REVERT: G 111 LEU cc_start: 0.8486 (tp) cc_final: 0.8217 (mp) REVERT: G 141 ILE cc_start: 0.9550 (mt) cc_final: 0.9316 (mt) REVERT: G 152 ASP cc_start: 0.8923 (m-30) cc_final: 0.8632 (p0) REVERT: G 186 THR cc_start: 0.7960 (t) cc_final: 0.7708 (t) REVERT: G 199 LYS cc_start: 0.8953 (tttp) cc_final: 0.8696 (ttmt) REVERT: G 214 MET cc_start: 0.9364 (mtm) cc_final: 0.8335 (tpt) REVERT: H 39 MET cc_start: 0.8553 (ttm) cc_final: 0.8118 (tpt) REVERT: H 70 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8591 (ptpp) REVERT: H 135 ILE cc_start: 0.9569 (mt) cc_final: 0.9140 (pt) REVERT: H 139 ASN cc_start: 0.9158 (m-40) cc_final: 0.8824 (m-40) REVERT: J 34 GLU cc_start: 0.9506 (tp30) cc_final: 0.9115 (tp30) REVERT: J 115 CYS cc_start: 0.8642 (m) cc_final: 0.8037 (m) REVERT: J 120 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8737 (pm20) REVERT: J 129 PHE cc_start: 0.7261 (p90) cc_final: 0.5511 (p90) REVERT: J 161 CYS cc_start: 0.5318 (p) cc_final: 0.4957 (p) REVERT: N 189 LEU cc_start: 0.8913 (mm) cc_final: 0.8712 (mm) REVERT: Y 13 GLN cc_start: 0.8983 (tt0) cc_final: 0.8733 (pm20) REVERT: Y 21 ASN cc_start: 0.9541 (t0) cc_final: 0.9122 (t0) REVERT: Y 25 LYS cc_start: 0.9585 (tttt) cc_final: 0.9328 (mtpp) REVERT: Y 49 PRO cc_start: 0.9450 (Cg_exo) cc_final: 0.9213 (Cg_endo) REVERT: Y 52 LEU cc_start: 0.9691 (mt) cc_final: 0.9263 (mp) REVERT: Y 104 ILE cc_start: 0.7685 (tt) cc_final: 0.7202 (pt) REVERT: Y 110 THR cc_start: 0.9234 (t) cc_final: 0.8948 (t) REVERT: Y 114 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8663 (mm-40) REVERT: Y 117 TRP cc_start: 0.7666 (m-10) cc_final: 0.6995 (m-10) REVERT: Y 131 LYS cc_start: 0.9040 (ttmt) cc_final: 0.8727 (tptt) REVERT: Y 139 ASN cc_start: 0.9600 (m-40) cc_final: 0.9222 (m110) REVERT: d 39 MET cc_start: 0.7384 (ttm) cc_final: 0.7071 (tpt) REVERT: d 67 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8875 (mt0) REVERT: d 68 MET cc_start: 0.8221 (mtp) cc_final: 0.8001 (mtp) REVERT: d 130 TYR cc_start: 0.6904 (t80) cc_final: 0.6532 (t80) REVERT: d 139 ASN cc_start: 0.9541 (m-40) cc_final: 0.9254 (m-40) REVERT: d 140 LYS cc_start: 0.9348 (mttt) cc_final: 0.9100 (tptp) REVERT: d 162 ARG cc_start: 0.8611 (mtt180) cc_final: 0.8375 (tpt-90) REVERT: d 163 ASP cc_start: 0.8555 (m-30) cc_final: 0.8347 (t0) REVERT: e 35 GLU cc_start: 0.9478 (pm20) cc_final: 0.8983 (pp20) REVERT: e 39 MET cc_start: 0.9551 (tpp) cc_final: 0.9287 (tpp) REVERT: e 51 ASP cc_start: 0.9267 (m-30) cc_final: 0.8866 (m-30) REVERT: e 66 MET cc_start: 0.8748 (mmm) cc_final: 0.8494 (mmm) REVERT: e 74 ASN cc_start: 0.9583 (m-40) cc_final: 0.9269 (m110) REVERT: e 79 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8492 (pp20) REVERT: e 104 ILE cc_start: 0.8898 (mt) cc_final: 0.8620 (mt) REVERT: e 114 GLN cc_start: 0.8259 (mt0) cc_final: 0.8051 (mt0) REVERT: e 173 ARG cc_start: 0.8552 (ttt180) cc_final: 0.8320 (tpm170) REVERT: e 178 SER cc_start: 0.8082 (p) cc_final: 0.6969 (t) REVERT: j 213 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9179 (mt-10) REVERT: k 21 ASN cc_start: 0.9536 (m110) cc_final: 0.9325 (t0) REVERT: k 52 LEU cc_start: 0.9680 (mt) cc_final: 0.9367 (mt) REVERT: k 67 GLN cc_start: 0.9276 (tp40) cc_final: 0.9035 (tp-100) REVERT: k 68 MET cc_start: 0.9334 (mtp) cc_final: 0.9133 (mtt) REVERT: k 83 VAL cc_start: 0.9195 (p) cc_final: 0.8798 (p) REVERT: k 96 MET cc_start: 0.5134 (ttm) cc_final: 0.4393 (ptp) REVERT: k 129 ILE cc_start: 0.9525 (mt) cc_final: 0.8870 (tt) REVERT: k 159 GLU cc_start: 0.8064 (tt0) cc_final: 0.7829 (tt0) REVERT: k 173 ARG cc_start: 0.9376 (ttt180) cc_final: 0.8935 (ttm170) outliers start: 9 outliers final: 2 residues processed: 1144 average time/residue: 0.3304 time to fit residues: 532.3420 Evaluate side-chains 699 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 696 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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: 7.9990 chunk 177 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 183 optimal weight: 30.0000 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 50.0000 chunk 136 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 overall best weight: 7.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 67 GLN B 53 ASN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 GLN C 53 ASN C 219 GLN D 4 GLN D 95 GLN D 179 GLN G 4 GLN G 53 ASN H 4 GLN ** H 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 ASN J 163 GLN Y 4 GLN ** Y 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 67 GLN Y 114 GLN d 4 GLN d 95 GLN e 53 ASN j 219 GLN ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 21 ASN k 53 ASN k 74 ASN ** k 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18824 Z= 0.293 Angle : 0.690 7.269 25567 Z= 0.365 Chirality : 0.046 0.225 2848 Planarity : 0.005 0.047 3345 Dihedral : 4.206 26.234 2500 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.20 % Allowed : 6.24 % Favored : 93.56 % 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: -0.17 (0.17), residues: 2338 helix: 0.33 (0.13), residues: 1444 sheet: -1.38 (0.65), residues: 62 loop : -0.61 (0.21), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP H 23 HIS 0.007 0.001 HIS B 62 PHE 0.031 0.002 PHE B 161 TYR 0.016 0.002 TYR Y 130 ARG 0.011 0.001 ARG e 143 *********************** 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 855 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 851 time to evaluate : 2.169 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: A 23 TRP cc_start: 0.9534 (t-100) cc_final: 0.9298 (t-100) REVERT: A 27 VAL cc_start: 0.9601 (t) cc_final: 0.9385 (t) REVERT: A 40 PHE cc_start: 0.9676 (t80) cc_final: 0.9300 (t80) REVERT: A 41 SER cc_start: 0.9436 (m) cc_final: 0.9076 (t) REVERT: A 45 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8093 (mm-30) REVERT: A 50 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8912 (tm-30) REVERT: A 51 ASP cc_start: 0.9348 (m-30) cc_final: 0.9143 (m-30) REVERT: A 57 ASN cc_start: 0.9647 (m110) cc_final: 0.9423 (m110) REVERT: A 71 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8888 (tm-30) REVERT: A 103 ASP cc_start: 0.6930 (m-30) cc_final: 0.5587 (m-30) REVERT: A 113 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8904 (mt-10) REVERT: B 21 ASN cc_start: 0.9529 (t0) cc_final: 0.9314 (t0) REVERT: B 24 VAL cc_start: 0.9657 (t) cc_final: 0.9221 (p) REVERT: B 25 LYS cc_start: 0.9629 (mttt) cc_final: 0.9260 (ttmt) REVERT: B 68 MET cc_start: 0.9443 (mtp) cc_final: 0.9121 (mtt) REVERT: B 74 ASN cc_start: 0.9430 (m-40) cc_final: 0.9113 (m110) REVERT: B 87 HIS cc_start: 0.8607 (p90) cc_final: 0.8211 (p-80) REVERT: B 104 ILE cc_start: 0.9224 (mt) cc_final: 0.8963 (mt) REVERT: B 114 GLN cc_start: 0.9060 (mt0) cc_final: 0.8831 (mt0) REVERT: B 118 MET cc_start: 0.8865 (mtm) cc_final: 0.8572 (ptp) REVERT: B 129 ILE cc_start: 0.9397 (pt) cc_final: 0.8543 (pt) REVERT: C 62 HIS cc_start: 0.8964 (m-70) cc_final: 0.8537 (m90) REVERT: C 131 LYS cc_start: 0.8643 (ttmt) cc_final: 0.8306 (mtpt) REVERT: C 139 ASN cc_start: 0.9202 (t0) cc_final: 0.8556 (t0) REVERT: C 187 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9009 (mp0) REVERT: C 189 LEU cc_start: 0.9168 (mm) cc_final: 0.8880 (mp) REVERT: C 215 MET cc_start: 0.9104 (mtm) cc_final: 0.8680 (mtm) REVERT: D 23 TRP cc_start: 0.9498 (t-100) cc_final: 0.9236 (t-100) REVERT: D 56 LEU cc_start: 0.9609 (mt) cc_final: 0.9347 (mt) REVERT: D 117 TRP cc_start: 0.8408 (m-10) cc_final: 0.8051 (m-10) REVERT: D 130 TYR cc_start: 0.9365 (t80) cc_final: 0.8990 (t80) REVERT: D 131 LYS cc_start: 0.9025 (tttt) cc_final: 0.8602 (tttt) REVERT: D 140 LYS cc_start: 0.9561 (mttt) cc_final: 0.9323 (tptp) REVERT: D 141 ILE cc_start: 0.8958 (mt) cc_final: 0.8739 (mt) REVERT: D 184 TRP cc_start: 0.8355 (t60) cc_final: 0.8110 (t60) REVERT: D 215 MET cc_start: 0.7895 (ttt) cc_final: 0.7569 (ttm) REVERT: G 23 TRP cc_start: 0.9562 (t-100) cc_final: 0.8485 (t-100) REVERT: G 39 MET cc_start: 0.9546 (ttm) cc_final: 0.9325 (ttm) REVERT: G 40 PHE cc_start: 0.9223 (t80) cc_final: 0.8966 (t80) REVERT: G 55 MET cc_start: 0.9446 (ttt) cc_final: 0.9100 (tmm) REVERT: G 57 ASN cc_start: 0.9584 (m-40) cc_final: 0.9345 (m110) REVERT: G 96 MET cc_start: 0.1459 (mpp) cc_final: -0.0613 (mtt) REVERT: G 152 ASP cc_start: 0.9039 (m-30) cc_final: 0.8733 (p0) REVERT: G 164 TYR cc_start: 0.8756 (t80) cc_final: 0.8446 (t80) REVERT: G 199 LYS cc_start: 0.8990 (tttp) cc_final: 0.8777 (ttmt) REVERT: G 214 MET cc_start: 0.9328 (mtm) cc_final: 0.9110 (mtm) REVERT: G 215 MET cc_start: 0.9059 (mmt) cc_final: 0.8569 (mmm) REVERT: H 39 MET cc_start: 0.8660 (ttm) cc_final: 0.8178 (tpt) REVERT: H 55 MET cc_start: 0.9522 (mmp) cc_final: 0.9284 (mmm) REVERT: H 129 ILE cc_start: 0.8855 (tt) cc_final: 0.8192 (tt) REVERT: H 133 TRP cc_start: 0.8769 (m-10) cc_final: 0.8030 (m-10) REVERT: H 161 PHE cc_start: 0.7979 (t80) cc_final: 0.7609 (t80) REVERT: H 185 MET cc_start: 0.9210 (mtm) cc_final: 0.9007 (mtm) REVERT: J 6 VAL cc_start: 0.9015 (t) cc_final: 0.8722 (t) REVERT: J 10 ILE cc_start: 0.9191 (tp) cc_final: 0.8559 (tp) REVERT: J 36 PHE cc_start: 0.8362 (t80) cc_final: 0.8038 (t80) REVERT: J 100 MET cc_start: 0.5289 (mmm) cc_final: 0.4720 (tpt) REVERT: J 122 LEU cc_start: 0.8155 (mt) cc_final: 0.7905 (mp) REVERT: J 123 ASP cc_start: 0.8878 (m-30) cc_final: 0.8618 (m-30) REVERT: J 161 CYS cc_start: 0.3861 (p) cc_final: 0.3610 (p) REVERT: N 150 ILE cc_start: 0.7863 (tp) cc_final: 0.7580 (tp) REVERT: N 153 ILE cc_start: 0.8696 (mt) cc_final: 0.8479 (mp) REVERT: Y 21 ASN cc_start: 0.9604 (t0) cc_final: 0.9103 (t0) REVERT: Y 25 LYS cc_start: 0.9578 (tttt) cc_final: 0.9368 (mtpp) REVERT: Y 45 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8398 (mm-30) REVERT: Y 49 PRO cc_start: 0.9448 (Cg_exo) cc_final: 0.9239 (Cg_endo) REVERT: Y 55 MET cc_start: 0.9469 (ttm) cc_final: 0.9218 (ttm) REVERT: Y 56 LEU cc_start: 0.9467 (mt) cc_final: 0.9100 (mt) REVERT: Y 63 GLN cc_start: 0.9077 (mm-40) cc_final: 0.8791 (mm-40) REVERT: Y 131 LYS cc_start: 0.9095 (ttmt) cc_final: 0.8333 (tptt) REVERT: Y 139 ASN cc_start: 0.9567 (m-40) cc_final: 0.9281 (m-40) REVERT: d 23 TRP cc_start: 0.8829 (t-100) cc_final: 0.8549 (t-100) REVERT: d 39 MET cc_start: 0.7839 (ttm) cc_final: 0.7435 (tpt) REVERT: d 63 GLN cc_start: 0.6911 (tt0) cc_final: 0.5737 (tt0) REVERT: d 67 GLN cc_start: 0.9151 (tp-100) cc_final: 0.8800 (mt0) REVERT: d 133 TRP cc_start: 0.8595 (m-10) cc_final: 0.7757 (m-10) REVERT: d 139 ASN cc_start: 0.9580 (m-40) cc_final: 0.9305 (m-40) REVERT: d 140 LYS cc_start: 0.9490 (mttt) cc_final: 0.9132 (tptp) REVERT: d 162 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8517 (tpt-90) REVERT: e 10 MET cc_start: 0.7944 (mmp) cc_final: 0.7658 (mmp) REVERT: e 35 GLU cc_start: 0.9568 (pm20) cc_final: 0.9292 (pm20) REVERT: e 39 MET cc_start: 0.9581 (tpp) cc_final: 0.9165 (tpp) REVERT: e 57 ASN cc_start: 0.9414 (m-40) cc_final: 0.9101 (m110) REVERT: e 66 MET cc_start: 0.9097 (mmm) cc_final: 0.8701 (mmm) REVERT: e 74 ASN cc_start: 0.9599 (m-40) cc_final: 0.9329 (m-40) REVERT: e 79 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8586 (pp20) REVERT: e 104 ILE cc_start: 0.9075 (mt) cc_final: 0.8813 (mt) REVERT: e 118 MET cc_start: 0.8653 (mtt) cc_final: 0.8382 (mtt) REVERT: e 138 LEU cc_start: 0.9621 (mt) cc_final: 0.9416 (mt) REVERT: e 163 ASP cc_start: 0.9531 (m-30) cc_final: 0.9230 (m-30) REVERT: e 166 ASP cc_start: 0.8351 (t0) cc_final: 0.8126 (t70) REVERT: e 167 ARG cc_start: 0.8662 (ttt-90) cc_final: 0.8442 (mtm110) REVERT: j 169 TYR cc_start: 0.9276 (m-10) cc_final: 0.8610 (m-10) REVERT: k 21 ASN cc_start: 0.9534 (m-40) cc_final: 0.9066 (t0) REVERT: k 25 LYS cc_start: 0.9692 (ptmt) cc_final: 0.9172 (pttm) REVERT: k 96 MET cc_start: 0.5225 (ttm) cc_final: 0.4303 (ptp) REVERT: k 132 ARG cc_start: 0.9269 (ttp-110) cc_final: 0.8943 (ptp-110) REVERT: k 144 MET cc_start: 0.8961 (ttt) cc_final: 0.8707 (ttt) REVERT: k 173 ARG cc_start: 0.9096 (ttt180) cc_final: 0.8754 (ttp80) outliers start: 4 outliers final: 2 residues processed: 853 average time/residue: 0.3588 time to fit residues: 434.2271 Evaluate side-chains 654 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 652 time to evaluate : 2.137 ------------------------------------------------------------------------------- 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: 20.0000 chunk 65 optimal weight: 8.9990 chunk 176 optimal weight: 0.4980 chunk 144 optimal weight: 30.0000 chunk 58 optimal weight: 50.0000 chunk 212 optimal weight: 4.9990 chunk 229 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 chunk 211 optimal weight: 0.5980 chunk 72 optimal weight: 8.9990 chunk 170 optimal weight: 30.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 ASN B 179 GLN B 183 ASN C 53 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 183 ASN H 67 GLN J 92 HIS J 163 GLN ** N 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 ASN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN k 74 ASN ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5779 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 : 0.645 9.337 25567 Z= 0.334 Chirality : 0.045 0.208 2848 Planarity : 0.005 0.053 3345 Dihedral : 4.319 22.535 2500 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.05 % Allowed : 4.40 % Favored : 95.55 % 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: 0.07 (0.17), residues: 2338 helix: 0.48 (0.13), residues: 1436 sheet: -1.34 (0.60), residues: 75 loop : -0.38 (0.21), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP H 80 HIS 0.008 0.001 HIS J 54 PHE 0.014 0.001 PHE N 168 TYR 0.027 0.002 TYR e 130 ARG 0.010 0.001 ARG k 162 *********************** 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 835 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 834 time to evaluate : 2.110 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: A 40 PHE cc_start: 0.9702 (t80) cc_final: 0.9155 (t80) REVERT: A 41 SER cc_start: 0.9370 (m) cc_final: 0.8901 (t) REVERT: A 45 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7890 (mm-30) REVERT: A 50 GLN cc_start: 0.9261 (tm-30) cc_final: 0.8942 (tm-30) REVERT: A 51 ASP cc_start: 0.9452 (m-30) cc_final: 0.9033 (m-30) REVERT: A 52 LEU cc_start: 0.9764 (mm) cc_final: 0.9453 (mm) REVERT: A 55 MET cc_start: 0.9158 (ttt) cc_final: 0.8920 (tmm) REVERT: A 56 LEU cc_start: 0.9551 (mt) cc_final: 0.9264 (mt) REVERT: A 96 MET cc_start: -0.0694 (mpp) cc_final: -0.0918 (mmt) REVERT: A 113 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8844 (mt-10) REVERT: B 21 ASN cc_start: 0.9546 (t0) cc_final: 0.9339 (t0) REVERT: B 24 VAL cc_start: 0.9599 (t) cc_final: 0.9338 (p) REVERT: B 25 LYS cc_start: 0.9632 (mttt) cc_final: 0.9282 (ttmt) REVERT: B 30 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8750 (mmmt) REVERT: B 51 ASP cc_start: 0.9232 (m-30) cc_final: 0.9027 (m-30) REVERT: B 55 MET cc_start: 0.9273 (ttm) cc_final: 0.9023 (ttt) REVERT: B 68 MET cc_start: 0.9453 (mtp) cc_final: 0.9225 (mtt) REVERT: B 74 ASN cc_start: 0.9456 (m-40) cc_final: 0.9007 (m110) REVERT: B 118 MET cc_start: 0.9087 (mtm) cc_final: 0.8647 (ptp) REVERT: B 131 LYS cc_start: 0.9582 (ttmt) cc_final: 0.9227 (tttt) REVERT: C 55 MET cc_start: 0.9110 (ttm) cc_final: 0.8514 (ttp) REVERT: C 62 HIS cc_start: 0.8761 (m-70) cc_final: 0.8273 (m170) REVERT: C 74 ASN cc_start: 0.9441 (m110) cc_final: 0.9238 (m110) REVERT: C 100 ARG cc_start: 0.8138 (mpp-170) cc_final: 0.6759 (mpp-170) REVERT: C 131 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8327 (mtpt) REVERT: C 132 ARG cc_start: 0.9006 (ptt-90) cc_final: 0.8679 (ptp90) REVERT: C 170 LYS cc_start: 0.9355 (pttp) cc_final: 0.9122 (ptpp) REVERT: C 187 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9041 (mp0) REVERT: C 189 LEU cc_start: 0.9186 (mm) cc_final: 0.8931 (mp) REVERT: C 215 MET cc_start: 0.9345 (mtm) cc_final: 0.7963 (mtm) REVERT: D 56 LEU cc_start: 0.9647 (mt) cc_final: 0.9406 (mt) REVERT: D 57 ASN cc_start: 0.9629 (m110) cc_final: 0.9347 (m110) REVERT: D 117 TRP cc_start: 0.8300 (m-10) cc_final: 0.8028 (m-10) REVERT: D 130 TYR cc_start: 0.9370 (t80) cc_final: 0.8998 (t80) REVERT: D 131 LYS cc_start: 0.9090 (tttt) cc_final: 0.8833 (tttt) REVERT: D 140 LYS cc_start: 0.9545 (mttt) cc_final: 0.9318 (tptp) REVERT: D 141 ILE cc_start: 0.8968 (mt) cc_final: 0.8701 (mt) REVERT: D 215 MET cc_start: 0.7873 (ttt) cc_final: 0.7426 (ttm) REVERT: G 23 TRP cc_start: 0.9483 (t-100) cc_final: 0.8794 (t-100) REVERT: G 57 ASN cc_start: 0.9577 (m-40) cc_final: 0.9341 (m110) REVERT: G 96 MET cc_start: 0.1556 (mpp) cc_final: -0.0148 (mtp) REVERT: G 139 ASN cc_start: 0.9632 (m110) cc_final: 0.9432 (m110) REVERT: G 152 ASP cc_start: 0.9124 (m-30) cc_final: 0.8680 (p0) REVERT: G 164 TYR cc_start: 0.8743 (t80) cc_final: 0.8364 (t80) REVERT: G 185 MET cc_start: 0.9153 (mtt) cc_final: 0.8440 (mtt) REVERT: G 193 ASN cc_start: 0.9302 (m-40) cc_final: 0.9080 (m-40) REVERT: G 214 MET cc_start: 0.9305 (mtm) cc_final: 0.9095 (mtt) REVERT: G 215 MET cc_start: 0.8679 (mmt) cc_final: 0.8298 (mmm) REVERT: H 39 MET cc_start: 0.8523 (ttm) cc_final: 0.8105 (tpt) REVERT: H 132 ARG cc_start: 0.9228 (mmp80) cc_final: 0.8998 (mmm160) REVERT: H 161 PHE cc_start: 0.8301 (t80) cc_final: 0.7447 (t80) REVERT: H 185 MET cc_start: 0.9172 (mtm) cc_final: 0.8835 (mtm) REVERT: H 215 MET cc_start: 0.9038 (tpt) cc_final: 0.8629 (tpt) REVERT: J 10 ILE cc_start: 0.9267 (tp) cc_final: 0.8863 (tp) REVERT: J 25 PHE cc_start: 0.8216 (m-80) cc_final: 0.7635 (m-80) REVERT: J 48 TYR cc_start: 0.7251 (m-10) cc_final: 0.6795 (m-10) REVERT: J 92 HIS cc_start: 0.7354 (m90) cc_final: 0.7087 (m-70) REVERT: J 100 MET cc_start: 0.5653 (mmm) cc_final: 0.4706 (tpp) REVERT: J 123 ASP cc_start: 0.8886 (m-30) cc_final: 0.8591 (m-30) REVERT: J 129 PHE cc_start: 0.7138 (p90) cc_final: 0.6697 (p90) REVERT: J 143 GLU cc_start: 0.7383 (tp30) cc_final: 0.7168 (tp30) REVERT: N 150 ILE cc_start: 0.7677 (tp) cc_final: 0.7455 (tp) REVERT: N 153 ILE cc_start: 0.8800 (mt) cc_final: 0.8561 (mp) REVERT: N 179 GLN cc_start: 0.9118 (pp30) cc_final: 0.8360 (pm20) REVERT: N 185 MET cc_start: 0.8686 (ptp) cc_final: 0.8283 (ptp) REVERT: Y 20 LEU cc_start: 0.9628 (pp) cc_final: 0.9324 (pp) REVERT: Y 23 TRP cc_start: 0.9199 (t-100) cc_final: 0.8934 (t-100) REVERT: Y 52 LEU cc_start: 0.9724 (mm) cc_final: 0.9342 (mp) REVERT: Y 55 MET cc_start: 0.9480 (ttm) cc_final: 0.9191 (tpp) REVERT: Y 56 LEU cc_start: 0.9477 (mt) cc_final: 0.9113 (mt) REVERT: Y 63 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8828 (mm110) REVERT: Y 130 TYR cc_start: 0.9219 (t80) cc_final: 0.8721 (t80) REVERT: Y 131 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8486 (tptt) REVERT: Y 139 ASN cc_start: 0.9531 (m-40) cc_final: 0.9221 (m110) REVERT: d 39 MET cc_start: 0.7777 (ttm) cc_final: 0.7496 (tpt) REVERT: d 63 GLN cc_start: 0.6778 (tt0) cc_final: 0.5740 (tt0) REVERT: d 129 ILE cc_start: 0.9598 (tp) cc_final: 0.9321 (tp) REVERT: d 133 TRP cc_start: 0.8579 (m-10) cc_final: 0.7553 (m-10) REVERT: d 139 ASN cc_start: 0.9575 (m-40) cc_final: 0.9311 (m-40) REVERT: d 140 LYS cc_start: 0.9509 (mttt) cc_final: 0.9041 (tptp) REVERT: e 10 MET cc_start: 0.8265 (mmp) cc_final: 0.8026 (mmp) REVERT: e 39 MET cc_start: 0.9543 (tpp) cc_final: 0.9203 (tpp) REVERT: e 57 ASN cc_start: 0.9422 (m-40) cc_final: 0.9090 (m110) REVERT: e 66 MET cc_start: 0.8971 (mmm) cc_final: 0.8737 (mmm) REVERT: e 70 LYS cc_start: 0.9228 (ptpp) cc_final: 0.9024 (ptpt) REVERT: e 79 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8581 (pp20) REVERT: e 82 ARG cc_start: 0.9037 (tmm160) cc_final: 0.8826 (ttp80) REVERT: e 96 MET cc_start: 0.6967 (mtp) cc_final: 0.6343 (mmm) REVERT: e 100 ARG cc_start: 0.7136 (mmm160) cc_final: 0.6751 (mmm-85) REVERT: e 114 GLN cc_start: 0.8509 (mt0) cc_final: 0.8284 (mt0) REVERT: e 117 TRP cc_start: 0.8314 (m-10) cc_final: 0.7941 (m-10) REVERT: e 118 MET cc_start: 0.8668 (mtt) cc_final: 0.8429 (mtt) REVERT: e 128 GLU cc_start: 0.9226 (mp0) cc_final: 0.8905 (mp0) REVERT: e 163 ASP cc_start: 0.9565 (m-30) cc_final: 0.9356 (m-30) REVERT: e 166 ASP cc_start: 0.8330 (t0) cc_final: 0.8108 (t70) REVERT: e 168 PHE cc_start: 0.9592 (t80) cc_final: 0.9350 (t80) REVERT: e 215 MET cc_start: 0.8187 (ptm) cc_final: 0.7909 (ptp) REVERT: j 155 GLN cc_start: 0.6441 (mt0) cc_final: 0.5488 (pm20) REVERT: k 25 LYS cc_start: 0.9607 (ptmt) cc_final: 0.9333 (ptmm) REVERT: k 96 MET cc_start: 0.5265 (ttm) cc_final: 0.4125 (mpp) REVERT: k 104 ILE cc_start: 0.8422 (mm) cc_final: 0.7979 (mm) REVERT: k 131 LYS cc_start: 0.9437 (ttmt) cc_final: 0.9116 (mtpt) REVERT: k 132 ARG cc_start: 0.9300 (ttp-110) cc_final: 0.8990 (ttp-110) REVERT: k 153 ILE cc_start: 0.9315 (mm) cc_final: 0.8770 (mt) REVERT: k 173 ARG cc_start: 0.9115 (ttt180) cc_final: 0.8713 (ttp80) REVERT: k 182 LYS cc_start: 0.9271 (ptpp) cc_final: 0.9019 (pttm) REVERT: k 211 LEU cc_start: 0.9312 (tp) cc_final: 0.8926 (tt) REVERT: k 214 MET cc_start: 0.9170 (tpp) cc_final: 0.8576 (tmm) REVERT: k 215 MET cc_start: 0.8868 (ttt) cc_final: 0.8299 (ttp) outliers start: 1 outliers final: 0 residues processed: 835 average time/residue: 0.3567 time to fit residues: 425.2222 Evaluate side-chains 646 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 646 time to evaluate : 1.952 ------------------------------------------------------------------------------- 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: 5.9990 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 101 optimal weight: 0.9990 chunk 142 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 226 optimal weight: 0.0770 chunk 111 optimal weight: 40.0000 chunk 202 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN G 114 GLN J 163 GLN N 193 ASN ** Y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 GLN k 53 ASN k 74 ASN ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18824 Z= 0.198 Angle : 0.620 11.324 25567 Z= 0.317 Chirality : 0.044 0.249 2848 Planarity : 0.005 0.060 3345 Dihedral : 4.350 25.769 2500 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.05 % 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: 0.29 (0.17), residues: 2338 helix: 0.64 (0.14), residues: 1433 sheet: -1.21 (0.63), residues: 66 loop : -0.29 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 184 HIS 0.007 0.001 HIS J 54 PHE 0.021 0.002 PHE G 40 TYR 0.021 0.002 TYR N 164 ARG 0.006 0.001 ARG A 97 *********************** 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 814 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 813 time to evaluate : 2.226 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 29 GLU cc_start: 0.9329 (pm20) cc_final: 0.9024 (pm20) REVERT: A 40 PHE cc_start: 0.9674 (t80) cc_final: 0.9214 (t80) REVERT: A 50 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9019 (tm-30) REVERT: A 51 ASP cc_start: 0.9489 (m-30) cc_final: 0.9067 (m-30) REVERT: A 52 LEU cc_start: 0.9754 (mm) cc_final: 0.9432 (mm) REVERT: A 56 LEU cc_start: 0.9540 (mt) cc_final: 0.9240 (mt) REVERT: A 57 ASN cc_start: 0.9660 (m110) cc_final: 0.9403 (m110) REVERT: A 68 MET cc_start: 0.8870 (mtt) cc_final: 0.8575 (mtt) REVERT: A 71 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8869 (tm-30) REVERT: A 86 VAL cc_start: 0.6820 (t) cc_final: 0.4937 (t) REVERT: A 113 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8808 (mt-10) REVERT: A 118 MET cc_start: 0.9221 (mmp) cc_final: 0.8973 (tmm) REVERT: A 119 THR cc_start: 0.8486 (t) cc_final: 0.7931 (t) REVERT: B 21 ASN cc_start: 0.9535 (t0) cc_final: 0.9315 (t0) REVERT: B 24 VAL cc_start: 0.9700 (t) cc_final: 0.9311 (p) REVERT: B 25 LYS cc_start: 0.9641 (mttt) cc_final: 0.9282 (ttmt) REVERT: B 30 LYS cc_start: 0.9154 (mmpt) cc_final: 0.8742 (mmmt) REVERT: B 51 ASP cc_start: 0.9260 (m-30) cc_final: 0.9057 (m-30) REVERT: B 68 MET cc_start: 0.9474 (mtp) cc_final: 0.9126 (mtt) REVERT: B 74 ASN cc_start: 0.9389 (m-40) cc_final: 0.8991 (m110) REVERT: B 118 MET cc_start: 0.9148 (mtm) cc_final: 0.8807 (ptp) REVERT: C 18 ARG cc_start: 0.9260 (mtm-85) cc_final: 0.9000 (mtt90) REVERT: C 53 ASN cc_start: 0.9362 (m-40) cc_final: 0.9134 (m110) REVERT: C 55 MET cc_start: 0.9216 (ttm) cc_final: 0.8990 (ttt) REVERT: C 74 ASN cc_start: 0.9446 (m110) cc_final: 0.9218 (m110) REVERT: C 100 ARG cc_start: 0.8265 (mpp-170) cc_final: 0.7105 (mpp-170) REVERT: C 131 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8498 (mttt) REVERT: C 187 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9076 (mp0) REVERT: C 189 LEU cc_start: 0.9218 (mm) cc_final: 0.8959 (mp) REVERT: C 215 MET cc_start: 0.8807 (mtm) cc_final: 0.8201 (mtm) REVERT: D 45 GLU cc_start: 0.8260 (mm-30) cc_final: 0.7710 (mm-30) REVERT: D 56 LEU cc_start: 0.9752 (mt) cc_final: 0.9368 (mt) REVERT: D 117 TRP cc_start: 0.8174 (m-10) cc_final: 0.7409 (m-90) REVERT: D 130 TYR cc_start: 0.9378 (t80) cc_final: 0.8998 (t80) REVERT: D 131 LYS cc_start: 0.9237 (tttt) cc_final: 0.8872 (tttt) REVERT: D 144 MET cc_start: 0.7783 (ttt) cc_final: 0.7572 (ttm) REVERT: D 215 MET cc_start: 0.7817 (ttt) cc_final: 0.7274 (ptm) REVERT: G 23 TRP cc_start: 0.9436 (t-100) cc_final: 0.8308 (t60) REVERT: G 57 ASN cc_start: 0.9547 (m-40) cc_final: 0.9307 (m110) REVERT: G 96 MET cc_start: 0.1730 (mpp) cc_final: -0.0643 (mtt) REVERT: G 139 ASN cc_start: 0.9648 (m110) cc_final: 0.9381 (m110) REVERT: G 152 ASP cc_start: 0.9213 (m-30) cc_final: 0.8505 (p0) REVERT: G 168 PHE cc_start: 0.9390 (t80) cc_final: 0.9189 (t80) REVERT: G 181 VAL cc_start: 0.9268 (t) cc_final: 0.9057 (p) REVERT: G 185 MET cc_start: 0.9080 (mtt) cc_final: 0.8411 (mtt) REVERT: G 193 ASN cc_start: 0.9470 (m-40) cc_final: 0.9001 (t0) REVERT: G 215 MET cc_start: 0.8685 (mmt) cc_final: 0.8467 (mmm) REVERT: H 39 MET cc_start: 0.8548 (ttm) cc_final: 0.8242 (tpt) REVERT: H 161 PHE cc_start: 0.8163 (t80) cc_final: 0.7233 (t80) REVERT: H 185 MET cc_start: 0.9267 (mtm) cc_final: 0.9065 (mtm) REVERT: H 215 MET cc_start: 0.8993 (tpt) cc_final: 0.8556 (tpt) REVERT: J 6 VAL cc_start: 0.8987 (t) cc_final: 0.8279 (p) REVERT: J 10 ILE cc_start: 0.9271 (tp) cc_final: 0.8956 (tp) REVERT: J 25 PHE cc_start: 0.8361 (m-80) cc_final: 0.7738 (m-80) REVERT: J 29 VAL cc_start: 0.5818 (m) cc_final: 0.5544 (t) REVERT: J 31 LYS cc_start: 0.8506 (ttmt) cc_final: 0.8247 (ttmt) REVERT: J 32 THR cc_start: 0.8933 (t) cc_final: 0.8651 (t) REVERT: J 35 ASN cc_start: 0.9106 (t0) cc_final: 0.8798 (m-40) REVERT: J 48 TYR cc_start: 0.7550 (m-10) cc_final: 0.7120 (m-10) REVERT: J 100 MET cc_start: 0.5711 (mmm) cc_final: 0.5120 (tpp) REVERT: J 123 ASP cc_start: 0.8973 (m-30) cc_final: 0.8715 (m-30) REVERT: J 143 GLU cc_start: 0.7450 (tp30) cc_final: 0.6826 (tp30) REVERT: J 148 ARG cc_start: 0.8852 (ttt-90) cc_final: 0.8559 (mmm-85) REVERT: N 150 ILE cc_start: 0.7517 (tp) cc_final: 0.7191 (tp) REVERT: N 153 ILE cc_start: 0.8709 (mt) cc_final: 0.8444 (mp) REVERT: N 179 GLN cc_start: 0.9136 (pp30) cc_final: 0.8380 (pm20) REVERT: N 181 VAL cc_start: 0.8902 (p) cc_final: 0.8624 (p) REVERT: N 185 MET cc_start: 0.8648 (ptp) cc_final: 0.8174 (ptp) REVERT: N 191 VAL cc_start: 0.9198 (m) cc_final: 0.8898 (m) REVERT: Y 5 ASN cc_start: 0.8273 (t0) cc_final: 0.7977 (t0) REVERT: Y 20 LEU cc_start: 0.9628 (pp) cc_final: 0.9343 (pp) REVERT: Y 23 TRP cc_start: 0.9246 (t-100) cc_final: 0.8936 (t-100) REVERT: Y 52 LEU cc_start: 0.9746 (mm) cc_final: 0.9294 (mp) REVERT: Y 55 MET cc_start: 0.9510 (ttm) cc_final: 0.9218 (tpp) REVERT: Y 56 LEU cc_start: 0.9482 (mt) cc_final: 0.9110 (mt) REVERT: Y 70 LYS cc_start: 0.9557 (mtmm) cc_final: 0.9271 (mttm) REVERT: Y 117 TRP cc_start: 0.8262 (m-10) cc_final: 0.7498 (m-90) REVERT: Y 130 TYR cc_start: 0.9281 (t80) cc_final: 0.8737 (t80) REVERT: Y 139 ASN cc_start: 0.9534 (m-40) cc_final: 0.9214 (m110) REVERT: d 72 THR cc_start: 0.9496 (p) cc_final: 0.9051 (p) REVERT: d 129 ILE cc_start: 0.9599 (tp) cc_final: 0.8796 (tp) REVERT: d 130 TYR cc_start: 0.7516 (t80) cc_final: 0.6937 (t80) REVERT: d 133 TRP cc_start: 0.8542 (m-10) cc_final: 0.6932 (m-10) REVERT: d 136 LEU cc_start: 0.9752 (tp) cc_final: 0.9530 (tp) REVERT: d 139 ASN cc_start: 0.9600 (m-40) cc_final: 0.9340 (m-40) REVERT: d 152 ASP cc_start: 0.8287 (m-30) cc_final: 0.8054 (m-30) REVERT: d 167 ARG cc_start: 0.8561 (mmp-170) cc_final: 0.8156 (mmp80) REVERT: e 10 MET cc_start: 0.8199 (mmp) cc_final: 0.7981 (mmp) REVERT: e 39 MET cc_start: 0.9533 (tpp) cc_final: 0.9264 (tpp) REVERT: e 57 ASN cc_start: 0.9431 (m-40) cc_final: 0.9116 (m110) REVERT: e 66 MET cc_start: 0.9035 (mmm) cc_final: 0.8647 (mmm) REVERT: e 70 LYS cc_start: 0.9243 (ptpp) cc_final: 0.9031 (ptpt) REVERT: e 79 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8637 (pp20) REVERT: e 82 ARG cc_start: 0.9034 (tmm160) cc_final: 0.8825 (ttp80) REVERT: e 96 MET cc_start: 0.7236 (mtp) cc_final: 0.6706 (mmm) REVERT: e 100 ARG cc_start: 0.7296 (mmm160) cc_final: 0.6975 (mmm-85) REVERT: e 114 GLN cc_start: 0.8563 (mt0) cc_final: 0.8355 (mt0) REVERT: e 117 TRP cc_start: 0.8429 (m-10) cc_final: 0.8052 (m-10) REVERT: e 118 MET cc_start: 0.8827 (mtt) cc_final: 0.8517 (mtt) REVERT: e 128 GLU cc_start: 0.9269 (mp0) cc_final: 0.8933 (mp0) REVERT: e 168 PHE cc_start: 0.9606 (t80) cc_final: 0.9282 (t80) REVERT: e 215 MET cc_start: 0.8055 (ptm) cc_final: 0.7746 (ptt) REVERT: j 155 GLN cc_start: 0.6544 (mt0) cc_final: 0.5548 (pm20) REVERT: j 215 MET cc_start: 0.8305 (ppp) cc_final: 0.8024 (ppp) REVERT: k 21 ASN cc_start: 0.9317 (t0) cc_final: 0.8859 (t0) REVERT: k 43 LEU cc_start: 0.9645 (mm) cc_final: 0.9442 (mp) REVERT: k 68 MET cc_start: 0.9288 (mtp) cc_final: 0.8784 (mtt) REVERT: k 96 MET cc_start: 0.5273 (ttm) cc_final: 0.4152 (mpp) REVERT: k 104 ILE cc_start: 0.8474 (mm) cc_final: 0.8001 (mm) REVERT: k 153 ILE cc_start: 0.9244 (mm) cc_final: 0.8881 (mt) REVERT: k 173 ARG cc_start: 0.9114 (ttt180) cc_final: 0.8697 (ttp80) REVERT: k 182 LYS cc_start: 0.9234 (ptpp) cc_final: 0.8944 (pttm) REVERT: k 211 LEU cc_start: 0.9392 (tp) cc_final: 0.8923 (tt) REVERT: k 214 MET cc_start: 0.9162 (tpp) cc_final: 0.8827 (tmm) REVERT: k 215 MET cc_start: 0.8900 (ttt) cc_final: 0.8509 (ttp) outliers start: 1 outliers final: 0 residues processed: 813 average time/residue: 0.3904 time to fit residues: 461.3635 Evaluate side-chains 636 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 636 time to evaluate : 2.292 ------------------------------------------------------------------------------- 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: 5.9990 chunk 128 optimal weight: 40.0000 chunk 3 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 93 optimal weight: 20.0000 chunk 193 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 115 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 57 optimal weight: 3.9990 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 63 GLN A 139 ASN B 53 ASN ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 179 GLN C 183 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN H 67 GLN J 163 GLN Y 95 GLN ** Y 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 GLN k 74 ASN ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18824 Z= 0.205 Angle : 0.637 9.046 25567 Z= 0.328 Chirality : 0.044 0.183 2848 Planarity : 0.005 0.059 3345 Dihedral : 4.332 29.015 2500 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.05 % Allowed : 3.35 % Favored : 96.60 % 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: 0.35 (0.17), residues: 2338 helix: 0.68 (0.14), residues: 1440 sheet: -1.34 (0.55), residues: 75 loop : -0.22 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 184 HIS 0.007 0.001 HIS J 54 PHE 0.012 0.001 PHE A 40 TYR 0.025 0.002 TYR e 130 ARG 0.010 0.001 ARG A 100 *********************** 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 787 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 786 time to evaluate : 2.200 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: A 50 GLN cc_start: 0.9345 (tm-30) cc_final: 0.8994 (tm-30) REVERT: A 51 ASP cc_start: 0.9469 (m-30) cc_final: 0.9019 (m-30) REVERT: A 52 LEU cc_start: 0.9712 (mm) cc_final: 0.9434 (mm) REVERT: A 55 MET cc_start: 0.9008 (tmm) cc_final: 0.8767 (tmm) REVERT: A 57 ASN cc_start: 0.9654 (m110) cc_final: 0.9376 (m110) REVERT: A 103 ASP cc_start: 0.6862 (m-30) cc_final: 0.6046 (m-30) REVERT: A 113 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8798 (mt-10) REVERT: A 118 MET cc_start: 0.9258 (mmp) cc_final: 0.8938 (tmm) REVERT: A 119 THR cc_start: 0.8396 (t) cc_final: 0.7949 (t) REVERT: B 21 ASN cc_start: 0.9538 (t0) cc_final: 0.9287 (t0) REVERT: B 25 LYS cc_start: 0.9666 (mttt) cc_final: 0.9304 (ttmt) REVERT: B 30 LYS cc_start: 0.9183 (mmpt) cc_final: 0.8718 (mmmm) REVERT: B 74 ASN cc_start: 0.9481 (m-40) cc_final: 0.9155 (m110) REVERT: B 118 MET cc_start: 0.9238 (mtm) cc_final: 0.8877 (ptp) REVERT: B 131 LYS cc_start: 0.9573 (ttmt) cc_final: 0.9234 (tttt) REVERT: B 132 ARG cc_start: 0.9263 (ttp-110) cc_final: 0.8997 (ttp-110) REVERT: B 143 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8732 (mtm110) REVERT: B 167 ARG cc_start: 0.9336 (ptp-170) cc_final: 0.8788 (ptt180) REVERT: C 18 ARG cc_start: 0.9262 (mtm-85) cc_final: 0.9021 (mtt90) REVERT: C 55 MET cc_start: 0.9202 (ttm) cc_final: 0.8566 (ttp) REVERT: C 67 GLN cc_start: 0.7720 (pm20) cc_final: 0.7460 (pm20) REVERT: C 170 LYS cc_start: 0.9590 (ptmm) cc_final: 0.9138 (ptpp) REVERT: C 187 GLU cc_start: 0.9314 (mt-10) cc_final: 0.9023 (mm-30) REVERT: C 189 LEU cc_start: 0.9247 (mm) cc_final: 0.9011 (mp) REVERT: C 215 MET cc_start: 0.8819 (mtm) cc_final: 0.8407 (mtm) REVERT: D 57 ASN cc_start: 0.9603 (m110) cc_final: 0.9375 (m110) REVERT: D 117 TRP cc_start: 0.8136 (m-10) cc_final: 0.7391 (m-90) REVERT: D 131 LYS cc_start: 0.9223 (tttt) cc_final: 0.8842 (tttt) REVERT: D 141 ILE cc_start: 0.8941 (mt) cc_final: 0.8719 (mt) REVERT: D 143 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7944 (mmm160) REVERT: D 144 MET cc_start: 0.7784 (ttt) cc_final: 0.7424 (ttm) REVERT: D 203 LYS cc_start: 0.9034 (mptt) cc_final: 0.8659 (mmtm) REVERT: D 215 MET cc_start: 0.7839 (ttt) cc_final: 0.7462 (ttm) REVERT: G 23 TRP cc_start: 0.9383 (t-100) cc_final: 0.8833 (t-100) REVERT: G 39 MET cc_start: 0.9309 (ttp) cc_final: 0.8806 (tmm) REVERT: G 40 PHE cc_start: 0.9214 (t80) cc_final: 0.8841 (t80) REVERT: G 43 LEU cc_start: 0.9751 (mm) cc_final: 0.9391 (mm) REVERT: G 57 ASN cc_start: 0.9472 (m-40) cc_final: 0.9224 (m-40) REVERT: G 58 THR cc_start: 0.9557 (p) cc_final: 0.9244 (p) REVERT: G 96 MET cc_start: 0.1679 (mpp) cc_final: -0.0761 (mtt) REVERT: G 139 ASN cc_start: 0.9665 (m110) cc_final: 0.9396 (m110) REVERT: G 143 ARG cc_start: 0.9082 (mmt-90) cc_final: 0.8676 (mmt-90) REVERT: G 152 ASP cc_start: 0.9209 (m-30) cc_final: 0.8502 (p0) REVERT: G 168 PHE cc_start: 0.9413 (t80) cc_final: 0.9194 (t80) REVERT: G 170 LYS cc_start: 0.9315 (mtpt) cc_final: 0.8624 (mptt) REVERT: G 181 VAL cc_start: 0.9299 (t) cc_final: 0.9054 (p) REVERT: G 185 MET cc_start: 0.9038 (mtt) cc_final: 0.8440 (mtt) REVERT: G 193 ASN cc_start: 0.9469 (m-40) cc_final: 0.8956 (t0) REVERT: G 214 MET cc_start: 0.9338 (mtm) cc_final: 0.9117 (ptp) REVERT: G 215 MET cc_start: 0.8611 (mmt) cc_final: 0.8404 (mmm) REVERT: H 39 MET cc_start: 0.8519 (ttm) cc_final: 0.8166 (tpt) REVERT: H 130 TYR cc_start: 0.5848 (t80) cc_final: 0.5333 (t80) REVERT: H 161 PHE cc_start: 0.8173 (t80) cc_final: 0.7422 (t80) REVERT: H 176 GLN cc_start: 0.7790 (pt0) cc_final: 0.7519 (pp30) REVERT: H 215 MET cc_start: 0.9047 (tpt) cc_final: 0.8684 (tpt) REVERT: J 6 VAL cc_start: 0.9020 (t) cc_final: 0.8524 (p) REVERT: J 10 ILE cc_start: 0.9210 (tp) cc_final: 0.8792 (tp) REVERT: J 25 PHE cc_start: 0.8358 (m-80) cc_final: 0.7687 (m-80) REVERT: J 48 TYR cc_start: 0.7693 (m-10) cc_final: 0.7139 (m-10) REVERT: J 100 MET cc_start: 0.5618 (mmm) cc_final: 0.4727 (tpt) REVERT: J 123 ASP cc_start: 0.8872 (m-30) cc_final: 0.8605 (m-30) REVERT: J 129 PHE cc_start: 0.7303 (p90) cc_final: 0.6777 (p90) REVERT: J 143 GLU cc_start: 0.7658 (tp30) cc_final: 0.7126 (tp30) REVERT: N 181 VAL cc_start: 0.8935 (p) cc_final: 0.8664 (p) REVERT: N 185 MET cc_start: 0.8659 (ptp) cc_final: 0.8126 (ptp) REVERT: Y 5 ASN cc_start: 0.8272 (t0) cc_final: 0.7838 (t0) REVERT: Y 20 LEU cc_start: 0.9633 (pp) cc_final: 0.9310 (pp) REVERT: Y 40 PHE cc_start: 0.9154 (t80) cc_final: 0.8603 (t80) REVERT: Y 52 LEU cc_start: 0.9740 (mm) cc_final: 0.9378 (mp) REVERT: Y 55 MET cc_start: 0.9512 (ttm) cc_final: 0.9307 (ttm) REVERT: Y 56 LEU cc_start: 0.9507 (mt) cc_final: 0.9222 (mt) REVERT: Y 70 LYS cc_start: 0.9484 (mtmm) cc_final: 0.9240 (mttm) REVERT: Y 117 TRP cc_start: 0.8276 (m-10) cc_final: 0.8053 (m-90) REVERT: Y 139 ASN cc_start: 0.9539 (m-40) cc_final: 0.9226 (m110) REVERT: d 23 TRP cc_start: 0.8707 (t-100) cc_final: 0.8295 (t-100) REVERT: d 39 MET cc_start: 0.7549 (tpp) cc_final: 0.7293 (tpp) REVERT: d 55 MET cc_start: 0.9417 (mmp) cc_final: 0.9129 (mmm) REVERT: d 130 TYR cc_start: 0.7542 (t80) cc_final: 0.7119 (t80) REVERT: d 135 ILE cc_start: 0.9744 (mt) cc_final: 0.9538 (mm) REVERT: d 139 ASN cc_start: 0.9592 (m-40) cc_final: 0.9325 (m-40) REVERT: d 152 ASP cc_start: 0.8357 (m-30) cc_final: 0.8105 (m-30) REVERT: d 167 ARG cc_start: 0.8540 (mmp-170) cc_final: 0.8118 (mmp80) REVERT: e 10 MET cc_start: 0.8224 (mmp) cc_final: 0.8017 (mmp) REVERT: e 39 MET cc_start: 0.9532 (tpp) cc_final: 0.9291 (tpp) REVERT: e 51 ASP cc_start: 0.9401 (m-30) cc_final: 0.9189 (m-30) REVERT: e 52 LEU cc_start: 0.9557 (mp) cc_final: 0.9317 (mp) REVERT: e 57 ASN cc_start: 0.9490 (m-40) cc_final: 0.9168 (m110) REVERT: e 70 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9053 (ptpt) REVERT: e 79 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8648 (pp20) REVERT: e 82 ARG cc_start: 0.9069 (tmm160) cc_final: 0.8840 (ttp80) REVERT: e 96 MET cc_start: 0.7412 (mtp) cc_final: 0.6962 (tpp) REVERT: e 117 TRP cc_start: 0.8559 (m-10) cc_final: 0.8245 (m-10) REVERT: e 118 MET cc_start: 0.9004 (mtt) cc_final: 0.8715 (mtt) REVERT: e 128 GLU cc_start: 0.9300 (mp0) cc_final: 0.8963 (mp0) REVERT: e 131 LYS cc_start: 0.9133 (mtpp) cc_final: 0.8907 (mmtt) REVERT: e 168 PHE cc_start: 0.9622 (t80) cc_final: 0.9037 (t80) REVERT: k 21 ASN cc_start: 0.9272 (t0) cc_final: 0.9019 (t0) REVERT: k 55 MET cc_start: 0.9255 (tpt) cc_final: 0.8675 (tpp) REVERT: k 68 MET cc_start: 0.9373 (mtp) cc_final: 0.9019 (mtm) REVERT: k 70 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8728 (mtmm) REVERT: k 76 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9110 (mm-30) REVERT: k 96 MET cc_start: 0.4818 (ttm) cc_final: 0.3792 (mpp) REVERT: k 104 ILE cc_start: 0.8482 (mm) cc_final: 0.7979 (mm) REVERT: k 132 ARG cc_start: 0.9392 (ttp-110) cc_final: 0.8699 (ttp-110) REVERT: k 153 ILE cc_start: 0.9241 (mm) cc_final: 0.8893 (mt) REVERT: k 173 ARG cc_start: 0.9175 (ttt180) cc_final: 0.8703 (ttp80) REVERT: k 182 LYS cc_start: 0.9260 (ptpp) cc_final: 0.8665 (pttp) REVERT: k 211 LEU cc_start: 0.9376 (tp) cc_final: 0.8979 (tt) REVERT: k 214 MET cc_start: 0.9132 (tpp) cc_final: 0.8809 (tmm) REVERT: k 215 MET cc_start: 0.8905 (ttt) cc_final: 0.8598 (ttp) outliers start: 1 outliers final: 0 residues processed: 787 average time/residue: 0.3750 time to fit residues: 426.4898 Evaluate side-chains 607 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 2.346 ------------------------------------------------------------------------------- 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: 3.9990 chunk 203 optimal weight: 40.0000 chunk 44 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 55 optimal weight: 7.9990 chunk 226 optimal weight: 0.2980 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 74 optimal weight: 7.9990 chunk 118 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 53 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN H 193 ASN J 163 GLN N 179 GLN N 183 ASN ** Y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 12 HIS ** d 63 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 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18824 Z= 0.214 Angle : 0.649 8.482 25567 Z= 0.337 Chirality : 0.045 0.207 2848 Planarity : 0.005 0.059 3345 Dihedral : 4.413 30.537 2500 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: 0.76 (0.14), residues: 1443 sheet: -1.02 (0.70), residues: 57 loop : -0.14 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 23 HIS 0.006 0.001 HIS J 54 PHE 0.023 0.002 PHE B 40 TYR 0.023 0.002 TYR e 130 ARG 0.013 0.001 ARG A 97 *********************** 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 763 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 763 time to evaluate : 2.178 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 33 SER cc_start: 0.8245 (t) cc_final: 0.7939 (p) REVERT: A 50 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8890 (tm-30) REVERT: A 51 ASP cc_start: 0.9438 (m-30) cc_final: 0.8874 (m-30) REVERT: A 52 LEU cc_start: 0.9757 (mm) cc_final: 0.9466 (mm) REVERT: A 56 LEU cc_start: 0.9521 (mt) cc_final: 0.9260 (mt) REVERT: A 57 ASN cc_start: 0.9637 (m110) cc_final: 0.9334 (m110) REVERT: A 71 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8278 (tm-30) REVERT: A 86 VAL cc_start: 0.7133 (t) cc_final: 0.6850 (t) REVERT: A 103 ASP cc_start: 0.6702 (m-30) cc_final: 0.6452 (m-30) REVERT: A 113 GLU cc_start: 0.9204 (mt-10) cc_final: 0.8794 (mt-10) REVERT: A 118 MET cc_start: 0.9252 (mmp) cc_final: 0.8901 (tmm) REVERT: A 119 THR cc_start: 0.8403 (t) cc_final: 0.7935 (t) REVERT: B 21 ASN cc_start: 0.9449 (t0) cc_final: 0.9247 (t0) REVERT: B 25 LYS cc_start: 0.9627 (mttt) cc_final: 0.9389 (ttmt) REVERT: B 30 LYS cc_start: 0.9187 (mmpt) cc_final: 0.8787 (mmmm) REVERT: B 32 PHE cc_start: 0.8595 (m-80) cc_final: 0.8337 (m-80) REVERT: B 51 ASP cc_start: 0.9301 (m-30) cc_final: 0.9077 (m-30) REVERT: B 55 MET cc_start: 0.9556 (ttt) cc_final: 0.9256 (tpp) REVERT: B 66 MET cc_start: 0.8748 (mmm) cc_final: 0.8524 (mmm) REVERT: B 74 ASN cc_start: 0.9480 (m-40) cc_final: 0.9040 (m110) REVERT: B 118 MET cc_start: 0.9271 (mtm) cc_final: 0.8896 (ptp) REVERT: B 131 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9300 (mtpt) REVERT: B 132 ARG cc_start: 0.9234 (ttp-110) cc_final: 0.9025 (ttm110) REVERT: B 143 ARG cc_start: 0.9173 (mtm110) cc_final: 0.8823 (mtm110) REVERT: B 167 ARG cc_start: 0.9180 (ptp-170) cc_final: 0.8849 (ptt180) REVERT: C 18 ARG cc_start: 0.9251 (mtm-85) cc_final: 0.9047 (mtt90) REVERT: C 53 ASN cc_start: 0.9354 (m-40) cc_final: 0.9135 (m110) REVERT: C 55 MET cc_start: 0.9234 (ttm) cc_final: 0.8955 (ttt) REVERT: C 170 LYS cc_start: 0.9607 (ptmm) cc_final: 0.9150 (ptpp) REVERT: C 187 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9054 (mm-30) REVERT: C 189 LEU cc_start: 0.9263 (mm) cc_final: 0.9001 (mp) REVERT: D 40 PHE cc_start: 0.9513 (t80) cc_final: 0.9293 (t80) REVERT: D 56 LEU cc_start: 0.9738 (mt) cc_final: 0.9501 (mt) REVERT: D 57 ASN cc_start: 0.9604 (m110) cc_final: 0.9358 (m110) REVERT: D 117 TRP cc_start: 0.8183 (m-10) cc_final: 0.7442 (m-90) REVERT: D 131 LYS cc_start: 0.9222 (tttt) cc_final: 0.8959 (tttt) REVERT: D 141 ILE cc_start: 0.8893 (mt) cc_final: 0.8680 (mt) REVERT: D 215 MET cc_start: 0.7972 (ttt) cc_final: 0.7490 (ttm) REVERT: G 13 GLN cc_start: 0.9437 (mm-40) cc_final: 0.9189 (mp10) REVERT: G 23 TRP cc_start: 0.9349 (t-100) cc_final: 0.8727 (t-100) REVERT: G 96 MET cc_start: 0.1820 (mpp) cc_final: 0.0345 (mmm) REVERT: G 139 ASN cc_start: 0.9657 (m110) cc_final: 0.9383 (m110) REVERT: G 152 ASP cc_start: 0.9226 (m-30) cc_final: 0.8499 (p0) REVERT: G 168 PHE cc_start: 0.9434 (t80) cc_final: 0.9158 (t80) REVERT: G 170 LYS cc_start: 0.9351 (mtpt) cc_final: 0.8627 (mmtt) REVERT: G 181 VAL cc_start: 0.9306 (t) cc_final: 0.9062 (p) REVERT: G 185 MET cc_start: 0.9018 (mtt) cc_final: 0.8427 (mtt) REVERT: G 193 ASN cc_start: 0.9443 (m-40) cc_final: 0.8895 (t0) REVERT: G 214 MET cc_start: 0.9364 (mtm) cc_final: 0.9054 (ptp) REVERT: G 215 MET cc_start: 0.8664 (mmt) cc_final: 0.8453 (mmm) REVERT: H 10 MET cc_start: 0.5452 (ttt) cc_final: 0.5108 (ttt) REVERT: H 39 MET cc_start: 0.8593 (ttm) cc_final: 0.8312 (tpt) REVERT: H 130 TYR cc_start: 0.5860 (t80) cc_final: 0.5421 (t80) REVERT: H 161 PHE cc_start: 0.8069 (t80) cc_final: 0.7308 (t80) REVERT: H 167 ARG cc_start: 0.9221 (mmm160) cc_final: 0.8507 (mmm160) REVERT: H 203 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8621 (mtmt) REVERT: H 215 MET cc_start: 0.9010 (tpt) cc_final: 0.8609 (tpt) REVERT: J 6 VAL cc_start: 0.9022 (t) cc_final: 0.8594 (p) REVERT: J 10 ILE cc_start: 0.9191 (tp) cc_final: 0.8741 (tp) REVERT: J 25 PHE cc_start: 0.8391 (m-80) cc_final: 0.7746 (m-80) REVERT: J 48 TYR cc_start: 0.7838 (m-10) cc_final: 0.7364 (m-10) REVERT: J 78 ILE cc_start: 0.7807 (pt) cc_final: 0.7247 (pt) REVERT: J 100 MET cc_start: 0.5543 (mmm) cc_final: 0.4864 (tpt) REVERT: J 123 ASP cc_start: 0.8886 (m-30) cc_final: 0.8595 (m-30) REVERT: J 129 PHE cc_start: 0.7297 (p90) cc_final: 0.7003 (p90) REVERT: J 143 GLU cc_start: 0.7945 (tp30) cc_final: 0.7418 (tp30) REVERT: N 153 ILE cc_start: 0.8821 (mt) cc_final: 0.8606 (mt) REVERT: N 181 VAL cc_start: 0.8962 (p) cc_final: 0.8692 (p) REVERT: N 185 MET cc_start: 0.8687 (ptp) cc_final: 0.8168 (ptp) REVERT: Y 13 GLN cc_start: 0.9197 (tt0) cc_final: 0.8898 (pm20) REVERT: Y 20 LEU cc_start: 0.9669 (pp) cc_final: 0.9367 (pp) REVERT: Y 51 ASP cc_start: 0.9373 (m-30) cc_final: 0.9100 (m-30) REVERT: Y 56 LEU cc_start: 0.9508 (mt) cc_final: 0.9229 (mt) REVERT: Y 63 GLN cc_start: 0.9131 (mm110) cc_final: 0.8878 (mm-40) REVERT: Y 117 TRP cc_start: 0.8531 (m-10) cc_final: 0.7911 (m-90) REVERT: Y 139 ASN cc_start: 0.9508 (m-40) cc_final: 0.9174 (m110) REVERT: d 23 TRP cc_start: 0.8777 (t-100) cc_final: 0.8404 (t-100) REVERT: d 55 MET cc_start: 0.9473 (mmp) cc_final: 0.9182 (mmm) REVERT: d 130 TYR cc_start: 0.7574 (t80) cc_final: 0.7085 (t80) REVERT: d 135 ILE cc_start: 0.9711 (mt) cc_final: 0.9508 (mt) REVERT: d 139 ASN cc_start: 0.9633 (m-40) cc_final: 0.9264 (m-40) REVERT: d 140 LYS cc_start: 0.9480 (mtmt) cc_final: 0.9165 (mtmt) REVERT: d 143 ARG cc_start: 0.9186 (mtt180) cc_final: 0.8709 (mtm-85) REVERT: d 152 ASP cc_start: 0.8357 (m-30) cc_final: 0.8151 (m-30) REVERT: d 167 ARG cc_start: 0.8576 (mmp-170) cc_final: 0.8169 (mmp80) REVERT: e 10 MET cc_start: 0.8167 (mmp) cc_final: 0.7944 (mmp) REVERT: e 51 ASP cc_start: 0.9458 (m-30) cc_final: 0.8860 (m-30) REVERT: e 57 ASN cc_start: 0.9480 (m-40) cc_final: 0.9178 (m110) REVERT: e 66 MET cc_start: 0.9300 (mmp) cc_final: 0.8865 (mmm) REVERT: e 70 LYS cc_start: 0.9351 (ptpp) cc_final: 0.8925 (ptpt) REVERT: e 79 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8672 (pp20) REVERT: e 82 ARG cc_start: 0.9121 (tmm160) cc_final: 0.8870 (ttp80) REVERT: e 97 ARG cc_start: 0.5724 (mpp-170) cc_final: 0.5355 (mmm160) REVERT: e 117 TRP cc_start: 0.8674 (m-10) cc_final: 0.8439 (m-10) REVERT: e 118 MET cc_start: 0.9069 (mtt) cc_final: 0.8781 (mtt) REVERT: e 128 GLU cc_start: 0.9275 (mp0) cc_final: 0.8956 (mp0) REVERT: e 168 PHE cc_start: 0.9619 (t80) cc_final: 0.9254 (t80) REVERT: e 215 MET cc_start: 0.7991 (ptm) cc_final: 0.7646 (ptt) REVERT: j 215 MET cc_start: 0.8382 (ppp) cc_final: 0.8148 (ppp) REVERT: k 25 LYS cc_start: 0.9509 (ptmm) cc_final: 0.9262 (ptmm) REVERT: k 55 MET cc_start: 0.9469 (tpt) cc_final: 0.9029 (tpp) REVERT: k 68 MET cc_start: 0.9381 (mtp) cc_final: 0.9045 (mtm) REVERT: k 96 MET cc_start: 0.4597 (ttm) cc_final: 0.3866 (mtt) REVERT: k 104 ILE cc_start: 0.8376 (mm) cc_final: 0.7836 (mm) REVERT: k 132 ARG cc_start: 0.9382 (ttp-110) cc_final: 0.8948 (ttp-110) REVERT: k 153 ILE cc_start: 0.9314 (mm) cc_final: 0.8944 (mt) REVERT: k 173 ARG cc_start: 0.9222 (ttt180) cc_final: 0.8774 (ttp80) REVERT: k 211 LEU cc_start: 0.9347 (tp) cc_final: 0.8837 (tt) outliers start: 0 outliers final: 0 residues processed: 763 average time/residue: 0.3552 time to fit residues: 386.2601 Evaluate side-chains 607 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 2.021 ------------------------------------------------------------------------------- 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: 20.0000 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 165 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 104 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN A 74 ASN A 139 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 163 GLN ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 ASN ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.7511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18824 Z= 0.245 Angle : 0.688 8.227 25567 Z= 0.358 Chirality : 0.046 0.248 2848 Planarity : 0.005 0.059 3345 Dihedral : 4.548 33.441 2500 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: 0.35 (0.17), residues: 2338 helix: 0.63 (0.14), residues: 1452 sheet: -1.12 (0.68), residues: 57 loop : -0.19 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 184 HIS 0.007 0.001 HIS H 84 PHE 0.027 0.002 PHE Y 40 TYR 0.028 0.002 TYR D 169 ARG 0.018 0.001 ARG N 162 *********************** 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 751 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 751 time to evaluate : 2.340 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: A 50 GLN cc_start: 0.9374 (tm-30) cc_final: 0.8934 (tm-30) REVERT: A 51 ASP cc_start: 0.9509 (m-30) cc_final: 0.9047 (m-30) REVERT: A 52 LEU cc_start: 0.9721 (mm) cc_final: 0.9484 (mm) REVERT: A 57 ASN cc_start: 0.9629 (m110) cc_final: 0.9328 (m110) REVERT: A 71 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8824 (tm-30) REVERT: A 86 VAL cc_start: 0.7103 (t) cc_final: 0.5388 (t) REVERT: A 113 GLU cc_start: 0.9179 (mt-10) cc_final: 0.8770 (mt-10) REVERT: A 118 MET cc_start: 0.9246 (mmp) cc_final: 0.8887 (tmm) REVERT: A 119 THR cc_start: 0.8397 (t) cc_final: 0.7994 (t) REVERT: A 124 ILE cc_start: 0.9001 (mm) cc_final: 0.8780 (pt) REVERT: B 10 MET cc_start: 0.9000 (mmp) cc_final: 0.8629 (mmp) REVERT: B 21 ASN cc_start: 0.9480 (t0) cc_final: 0.9126 (t0) REVERT: B 25 LYS cc_start: 0.9657 (mttt) cc_final: 0.9295 (ttmt) REVERT: B 30 LYS cc_start: 0.9085 (mmpt) cc_final: 0.8693 (mmmm) REVERT: B 32 PHE cc_start: 0.8645 (m-80) cc_final: 0.8440 (m-80) REVERT: B 74 ASN cc_start: 0.9470 (m-40) cc_final: 0.9080 (m110) REVERT: B 82 ARG cc_start: 0.9088 (ttp80) cc_final: 0.8653 (ttp80) REVERT: B 118 MET cc_start: 0.9334 (mtm) cc_final: 0.8924 (ptp) REVERT: B 131 LYS cc_start: 0.9598 (ttmt) cc_final: 0.9290 (tttt) REVERT: B 143 ARG cc_start: 0.9149 (mtm110) cc_final: 0.8911 (mtm110) REVERT: B 167 ARG cc_start: 0.9236 (ptp-170) cc_final: 0.8923 (ptt180) REVERT: C 55 MET cc_start: 0.9187 (ttm) cc_final: 0.8577 (ttp) REVERT: C 67 GLN cc_start: 0.8206 (pm20) cc_final: 0.7836 (pm20) REVERT: C 131 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8448 (mtpt) REVERT: C 132 ARG cc_start: 0.9089 (ptp90) cc_final: 0.8701 (ptt90) REVERT: C 187 GLU cc_start: 0.9353 (mt-10) cc_final: 0.9096 (mm-30) REVERT: C 189 LEU cc_start: 0.9272 (mm) cc_final: 0.9012 (mp) REVERT: D 40 PHE cc_start: 0.9480 (t80) cc_final: 0.9225 (t80) REVERT: D 56 LEU cc_start: 0.9751 (mt) cc_final: 0.9442 (mt) REVERT: D 57 ASN cc_start: 0.9628 (m110) cc_final: 0.9362 (m110) REVERT: D 117 TRP cc_start: 0.8214 (m-10) cc_final: 0.7370 (m-90) REVERT: D 130 TYR cc_start: 0.9524 (t80) cc_final: 0.9159 (t80) REVERT: D 131 LYS cc_start: 0.9322 (tttt) cc_final: 0.8903 (mttt) REVERT: D 143 ARG cc_start: 0.9100 (mmm160) cc_final: 0.8759 (mmm160) REVERT: D 145 TYR cc_start: 0.8859 (t80) cc_final: 0.8581 (t80) REVERT: D 163 ASP cc_start: 0.8866 (m-30) cc_final: 0.8649 (m-30) REVERT: D 169 TYR cc_start: 0.8870 (m-80) cc_final: 0.8531 (m-80) REVERT: D 215 MET cc_start: 0.8019 (ttt) cc_final: 0.7568 (ttm) REVERT: G 23 TRP cc_start: 0.9296 (t-100) cc_final: 0.8784 (t-100) REVERT: G 39 MET cc_start: 0.9246 (ttp) cc_final: 0.8919 (tmm) REVERT: G 43 LEU cc_start: 0.9714 (mm) cc_final: 0.9419 (mm) REVERT: G 96 MET cc_start: 0.2109 (mpp) cc_final: 0.0916 (mmm) REVERT: G 139 ASN cc_start: 0.9661 (m110) cc_final: 0.9373 (m110) REVERT: G 152 ASP cc_start: 0.9252 (m-30) cc_final: 0.8501 (p0) REVERT: G 168 PHE cc_start: 0.9441 (t80) cc_final: 0.9082 (t80) REVERT: G 170 LYS cc_start: 0.9354 (mtpt) cc_final: 0.8640 (mmtt) REVERT: G 181 VAL cc_start: 0.9336 (t) cc_final: 0.9113 (p) REVERT: G 185 MET cc_start: 0.9024 (mtt) cc_final: 0.8441 (mtt) REVERT: G 193 ASN cc_start: 0.9459 (m-40) cc_final: 0.8983 (m-40) REVERT: G 214 MET cc_start: 0.9367 (mtm) cc_final: 0.9105 (ptp) REVERT: H 10 MET cc_start: 0.5479 (ttt) cc_final: 0.5060 (ttt) REVERT: H 39 MET cc_start: 0.8555 (ttm) cc_final: 0.8232 (tpt) REVERT: H 161 PHE cc_start: 0.8138 (t80) cc_final: 0.7344 (t80) REVERT: H 167 ARG cc_start: 0.9249 (mmm160) cc_final: 0.8546 (mmm160) REVERT: H 203 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8643 (mtmt) REVERT: H 215 MET cc_start: 0.9027 (tpt) cc_final: 0.8592 (tpt) REVERT: J 10 ILE cc_start: 0.9130 (tp) cc_final: 0.8838 (tp) REVERT: J 25 PHE cc_start: 0.8395 (m-80) cc_final: 0.7764 (m-80) REVERT: J 43 GLU cc_start: 0.8042 (pp20) cc_final: 0.7774 (pp20) REVERT: J 48 TYR cc_start: 0.8059 (m-10) cc_final: 0.7658 (m-10) REVERT: J 78 ILE cc_start: 0.7876 (pt) cc_final: 0.7395 (pt) REVERT: J 79 TYR cc_start: 0.8029 (m-80) cc_final: 0.7794 (m-10) REVERT: J 100 MET cc_start: 0.5501 (mmm) cc_final: 0.5225 (tpt) REVERT: J 123 ASP cc_start: 0.8821 (m-30) cc_final: 0.8507 (m-30) REVERT: N 181 VAL cc_start: 0.8999 (p) cc_final: 0.8705 (p) REVERT: N 185 MET cc_start: 0.8648 (ptp) cc_final: 0.8061 (ptp) REVERT: N 215 MET cc_start: 0.8776 (ttt) cc_final: 0.8451 (ttp) REVERT: Y 51 ASP cc_start: 0.9316 (m-30) cc_final: 0.9093 (m-30) REVERT: Y 56 LEU cc_start: 0.9511 (mt) cc_final: 0.9263 (mt) REVERT: Y 63 GLN cc_start: 0.9070 (mm110) cc_final: 0.8863 (mm110) REVERT: Y 117 TRP cc_start: 0.8546 (m-10) cc_final: 0.7958 (m-90) REVERT: Y 139 ASN cc_start: 0.9517 (m-40) cc_final: 0.9185 (m110) REVERT: d 23 TRP cc_start: 0.8780 (t-100) cc_final: 0.8483 (t-100) REVERT: d 129 ILE cc_start: 0.9615 (tp) cc_final: 0.9205 (tp) REVERT: d 130 TYR cc_start: 0.7590 (t80) cc_final: 0.7172 (t80) REVERT: d 139 ASN cc_start: 0.9643 (m-40) cc_final: 0.9283 (m-40) REVERT: d 140 LYS cc_start: 0.9486 (mtmt) cc_final: 0.9125 (mtmt) REVERT: d 143 ARG cc_start: 0.9249 (mtt180) cc_final: 0.8750 (mtm-85) REVERT: e 25 LYS cc_start: 0.9654 (mttt) cc_final: 0.9439 (mtmm) REVERT: e 50 GLN cc_start: 0.9315 (tm-30) cc_final: 0.9044 (tm-30) REVERT: e 51 ASP cc_start: 0.9496 (m-30) cc_final: 0.8731 (m-30) REVERT: e 55 MET cc_start: 0.8705 (ttt) cc_final: 0.7880 (tmm) REVERT: e 57 ASN cc_start: 0.9538 (m-40) cc_final: 0.9286 (m110) REVERT: e 79 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8742 (pp20) REVERT: e 82 ARG cc_start: 0.9149 (tmm160) cc_final: 0.8881 (ttp80) REVERT: e 97 ARG cc_start: 0.5931 (mpp-170) cc_final: 0.5525 (mmm160) REVERT: e 117 TRP cc_start: 0.8753 (m-10) cc_final: 0.8535 (m-10) REVERT: e 118 MET cc_start: 0.9071 (mtt) cc_final: 0.8807 (mtt) REVERT: e 128 GLU cc_start: 0.9306 (mp0) cc_final: 0.8984 (mp0) REVERT: e 168 PHE cc_start: 0.9625 (t80) cc_final: 0.9013 (t80) REVERT: e 185 MET cc_start: 0.8944 (mtm) cc_final: 0.8732 (mtp) REVERT: j 191 VAL cc_start: 0.9121 (m) cc_final: 0.8852 (p) REVERT: k 55 MET cc_start: 0.9487 (tpt) cc_final: 0.9208 (tpp) REVERT: k 68 MET cc_start: 0.9455 (mtp) cc_final: 0.9044 (mtt) REVERT: k 70 LYS cc_start: 0.9059 (mtmt) cc_final: 0.8837 (mtmm) REVERT: k 76 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9102 (mm-30) REVERT: k 96 MET cc_start: 0.4743 (ttm) cc_final: 0.4006 (mtp) REVERT: k 104 ILE cc_start: 0.8540 (mm) cc_final: 0.8058 (mm) REVERT: k 115 ILE cc_start: 0.9060 (pt) cc_final: 0.8557 (pt) REVERT: k 118 MET cc_start: 0.8924 (mmp) cc_final: 0.8279 (mtm) REVERT: k 131 LYS cc_start: 0.9384 (ttmt) cc_final: 0.9174 (mtpt) REVERT: k 132 ARG cc_start: 0.9381 (ttp-110) cc_final: 0.8724 (ptm-80) REVERT: k 173 ARG cc_start: 0.9263 (ttt180) cc_final: 0.8828 (ttp80) REVERT: k 211 LEU cc_start: 0.9325 (tp) cc_final: 0.9095 (tt) outliers start: 0 outliers final: 0 residues processed: 751 average time/residue: 0.3472 time to fit residues: 374.4735 Evaluate side-chains 568 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 568 time to evaluate : 2.156 ------------------------------------------------------------------------------- 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: 40.0000 chunk 134 optimal weight: 50.0000 chunk 67 optimal weight: 50.0000 chunk 44 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 177 optimal weight: 0.4980 chunk 205 optimal weight: 30.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN C 53 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN J 163 GLN ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** d 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 195 ASN k 9 GLN ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.7718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18824 Z= 0.205 Angle : 0.670 7.702 25567 Z= 0.347 Chirality : 0.046 0.221 2848 Planarity : 0.005 0.058 3345 Dihedral : 4.541 33.540 2500 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.05 % Allowed : 0.80 % Favored : 99.15 % 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: 0.44 (0.17), residues: 2338 helix: 0.70 (0.14), residues: 1444 sheet: -1.06 (0.67), residues: 57 loop : -0.13 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 184 HIS 0.007 0.001 HIS J 54 PHE 0.016 0.001 PHE A 40 TYR 0.025 0.002 TYR D 169 ARG 0.013 0.001 ARG N 162 *********************** 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 759 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 758 time to evaluate : 2.060 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: A 52 LEU cc_start: 0.9685 (mm) cc_final: 0.9423 (mm) REVERT: A 57 ASN cc_start: 0.9596 (m110) cc_final: 0.9274 (m110) REVERT: A 86 VAL cc_start: 0.7100 (t) cc_final: 0.4932 (t) REVERT: A 113 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 118 MET cc_start: 0.9251 (mmp) cc_final: 0.8900 (tmm) REVERT: A 124 ILE cc_start: 0.9003 (mm) cc_final: 0.8774 (pt) REVERT: B 10 MET cc_start: 0.9078 (mmp) cc_final: 0.8769 (mmp) REVERT: B 30 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8704 (mmmm) REVERT: B 32 PHE cc_start: 0.8646 (m-80) cc_final: 0.8431 (m-80) REVERT: B 51 ASP cc_start: 0.9318 (m-30) cc_final: 0.9106 (m-30) REVERT: B 74 ASN cc_start: 0.9431 (m-40) cc_final: 0.9016 (m110) REVERT: B 82 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8640 (ttp80) REVERT: B 118 MET cc_start: 0.9373 (mtm) cc_final: 0.8979 (ptp) REVERT: B 131 LYS cc_start: 0.9564 (ttmt) cc_final: 0.9302 (tttt) REVERT: B 143 ARG cc_start: 0.9138 (mtm110) cc_final: 0.8893 (mtm110) REVERT: B 144 MET cc_start: 0.9229 (ttt) cc_final: 0.8905 (ttt) REVERT: C 48 THR cc_start: 0.9319 (p) cc_final: 0.8994 (p) REVERT: C 53 ASN cc_start: 0.9254 (m-40) cc_final: 0.8976 (m110) REVERT: C 55 MET cc_start: 0.9188 (ttm) cc_final: 0.8689 (ttp) REVERT: C 130 TYR cc_start: 0.9068 (t80) cc_final: 0.8805 (t80) REVERT: C 131 LYS cc_start: 0.8807 (ttmt) cc_final: 0.8508 (mtpt) REVERT: C 182 LYS cc_start: 0.9614 (mtmm) cc_final: 0.9184 (mtmt) REVERT: C 187 GLU cc_start: 0.9352 (mt-10) cc_final: 0.9064 (mm-30) REVERT: C 189 LEU cc_start: 0.9259 (mm) cc_final: 0.8965 (mp) REVERT: D 23 TRP cc_start: 0.9376 (t-100) cc_final: 0.9136 (t-100) REVERT: D 56 LEU cc_start: 0.9753 (mt) cc_final: 0.9408 (mt) REVERT: D 117 TRP cc_start: 0.8064 (m-10) cc_final: 0.7764 (m-90) REVERT: D 130 TYR cc_start: 0.9536 (t80) cc_final: 0.9150 (t80) REVERT: D 131 LYS cc_start: 0.9310 (tttt) cc_final: 0.8909 (mttt) REVERT: D 145 TYR cc_start: 0.8801 (t80) cc_final: 0.8524 (t80) REVERT: D 163 ASP cc_start: 0.8813 (m-30) cc_final: 0.8609 (m-30) REVERT: D 169 TYR cc_start: 0.8775 (m-80) cc_final: 0.8469 (m-80) REVERT: D 215 MET cc_start: 0.8170 (ttt) cc_final: 0.7636 (ttm) REVERT: G 23 TRP cc_start: 0.9272 (t-100) cc_final: 0.8755 (t-100) REVERT: G 39 MET cc_start: 0.9272 (ttp) cc_final: 0.8992 (tpt) REVERT: G 96 MET cc_start: 0.1936 (mpp) cc_final: 0.0759 (mmm) REVERT: G 139 ASN cc_start: 0.9645 (m110) cc_final: 0.9360 (m110) REVERT: G 152 ASP cc_start: 0.9237 (m-30) cc_final: 0.8482 (p0) REVERT: G 154 ARG cc_start: 0.8190 (mmm-85) cc_final: 0.7904 (mmm-85) REVERT: G 168 PHE cc_start: 0.9435 (t80) cc_final: 0.9045 (t80) REVERT: G 170 LYS cc_start: 0.9361 (mtpt) cc_final: 0.8663 (mptt) REVERT: G 181 VAL cc_start: 0.9312 (t) cc_final: 0.9087 (p) REVERT: G 185 MET cc_start: 0.8973 (mtt) cc_final: 0.8420 (mtt) REVERT: G 193 ASN cc_start: 0.9456 (m-40) cc_final: 0.8670 (m110) REVERT: G 203 LYS cc_start: 0.8837 (mmmt) cc_final: 0.8607 (mmmm) REVERT: H 10 MET cc_start: 0.5614 (ttt) cc_final: 0.5106 (ttt) REVERT: H 39 MET cc_start: 0.8560 (ttm) cc_final: 0.8300 (tpt) REVERT: H 132 ARG cc_start: 0.8934 (ttp80) cc_final: 0.8689 (tpt90) REVERT: H 161 PHE cc_start: 0.8053 (t80) cc_final: 0.7273 (t80) REVERT: H 167 ARG cc_start: 0.9262 (mmm160) cc_final: 0.8577 (mmm160) REVERT: H 215 MET cc_start: 0.9016 (tpt) cc_final: 0.8577 (tpt) REVERT: J 10 ILE cc_start: 0.9140 (tp) cc_final: 0.8841 (tp) REVERT: J 25 PHE cc_start: 0.8345 (m-80) cc_final: 0.7709 (m-80) REVERT: J 43 GLU cc_start: 0.8031 (pp20) cc_final: 0.7795 (pp20) REVERT: J 48 TYR cc_start: 0.8023 (m-10) cc_final: 0.7501 (m-10) REVERT: J 78 ILE cc_start: 0.8122 (pt) cc_final: 0.7697 (pt) REVERT: J 79 TYR cc_start: 0.8098 (m-80) cc_final: 0.7811 (m-10) REVERT: J 88 PHE cc_start: 0.7352 (m-80) cc_final: 0.6835 (m-80) REVERT: J 97 ILE cc_start: 0.7750 (mm) cc_final: 0.7450 (tp) REVERT: J 100 MET cc_start: 0.5488 (mmm) cc_final: 0.4910 (tpp) REVERT: J 143 GLU cc_start: 0.7877 (tp30) cc_final: 0.7207 (tp30) REVERT: N 179 GLN cc_start: 0.9127 (tm-30) cc_final: 0.8675 (pm20) REVERT: N 181 VAL cc_start: 0.8969 (p) cc_final: 0.8763 (p) REVERT: N 185 MET cc_start: 0.8627 (ptp) cc_final: 0.8274 (ptp) REVERT: N 213 GLU cc_start: 0.9658 (mp0) cc_final: 0.9423 (pm20) REVERT: Y 5 ASN cc_start: 0.8489 (t0) cc_final: 0.8237 (t0) REVERT: Y 20 LEU cc_start: 0.9649 (pp) cc_final: 0.9404 (pp) REVERT: Y 56 LEU cc_start: 0.9524 (mt) cc_final: 0.9275 (mt) REVERT: Y 63 GLN cc_start: 0.8993 (mm110) cc_final: 0.8747 (mm-40) REVERT: Y 112 GLN cc_start: 0.9276 (tm-30) cc_final: 0.9037 (tm-30) REVERT: Y 117 TRP cc_start: 0.8485 (m-10) cc_final: 0.7734 (m-90) REVERT: Y 139 ASN cc_start: 0.9471 (m-40) cc_final: 0.9123 (m110) REVERT: d 23 TRP cc_start: 0.8793 (t-100) cc_final: 0.8523 (t-100) REVERT: d 55 MET cc_start: 0.9497 (mmp) cc_final: 0.9228 (mmm) REVERT: d 68 MET cc_start: 0.8005 (mtp) cc_final: 0.7772 (mtp) REVERT: d 130 TYR cc_start: 0.7668 (t80) cc_final: 0.7284 (t80) REVERT: d 139 ASN cc_start: 0.9625 (m-40) cc_final: 0.9287 (m-40) REVERT: d 140 LYS cc_start: 0.9527 (mtmt) cc_final: 0.9148 (mtmt) REVERT: d 143 ARG cc_start: 0.9261 (mtt180) cc_final: 0.8787 (mtm-85) REVERT: d 152 ASP cc_start: 0.8349 (m-30) cc_final: 0.8132 (m-30) REVERT: d 167 ARG cc_start: 0.8539 (mmp-170) cc_final: 0.8312 (mmp80) REVERT: e 57 ASN cc_start: 0.9514 (m-40) cc_final: 0.9295 (m110) REVERT: e 66 MET cc_start: 0.9193 (mmp) cc_final: 0.8925 (mmm) REVERT: e 70 LYS cc_start: 0.9285 (ptpp) cc_final: 0.8966 (ptpt) REVERT: e 79 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8715 (pp20) REVERT: e 82 ARG cc_start: 0.9164 (tmm160) cc_final: 0.8886 (ttp80) REVERT: e 97 ARG cc_start: 0.6197 (mpp-170) cc_final: 0.5608 (mmm160) REVERT: e 104 ILE cc_start: 0.9013 (mp) cc_final: 0.8795 (mp) REVERT: e 117 TRP cc_start: 0.8821 (m-10) cc_final: 0.8581 (m-10) REVERT: e 118 MET cc_start: 0.9114 (mtt) cc_final: 0.8858 (mtt) REVERT: e 128 GLU cc_start: 0.9349 (mp0) cc_final: 0.9039 (mp0) REVERT: e 139 ASN cc_start: 0.9409 (m-40) cc_final: 0.9039 (m110) REVERT: e 168 PHE cc_start: 0.9620 (t80) cc_final: 0.9217 (t80) REVERT: e 185 MET cc_start: 0.8996 (mtm) cc_final: 0.8709 (mtp) REVERT: j 167 ARG cc_start: 0.8292 (mmm160) cc_final: 0.7276 (mmm160) REVERT: j 170 LYS cc_start: 0.8780 (tmtt) cc_final: 0.8456 (tmtt) REVERT: k 55 MET cc_start: 0.9498 (tpt) cc_final: 0.9129 (tpp) REVERT: k 68 MET cc_start: 0.9433 (mtp) cc_final: 0.9002 (mtt) REVERT: k 70 LYS cc_start: 0.9056 (mtmt) cc_final: 0.8849 (ptpt) REVERT: k 96 MET cc_start: 0.4558 (ttm) cc_final: 0.4031 (mtp) REVERT: k 104 ILE cc_start: 0.8552 (mm) cc_final: 0.8053 (mm) REVERT: k 115 ILE cc_start: 0.8950 (pt) cc_final: 0.8397 (pt) REVERT: k 118 MET cc_start: 0.8985 (mmp) cc_final: 0.8366 (mtm) REVERT: k 173 ARG cc_start: 0.9241 (ttt180) cc_final: 0.8773 (ttp80) REVERT: k 182 LYS cc_start: 0.9248 (ptpp) cc_final: 0.8839 (pttm) outliers start: 1 outliers final: 0 residues processed: 758 average time/residue: 0.3551 time to fit residues: 384.2302 Evaluate side-chains 589 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 589 time to evaluate : 1.945 ------------------------------------------------------------------------------- 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: 1.9990 chunk 197 optimal weight: 20.0000 chunk 210 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 165 optimal weight: 20.0000 chunk 64 optimal weight: 30.0000 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN A 63 GLN A 139 ASN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 163 GLN ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 9 GLN ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.7909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18824 Z= 0.202 Angle : 0.692 14.820 25567 Z= 0.354 Chirality : 0.046 0.288 2848 Planarity : 0.005 0.053 3345 Dihedral : 4.510 33.871 2500 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.05 % Allowed : 0.75 % Favored : 99.20 % 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: 0.44 (0.17), residues: 2338 helix: 0.67 (0.14), residues: 1442 sheet: -0.90 (0.68), residues: 57 loop : -0.06 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 184 HIS 0.006 0.001 HIS J 54 PHE 0.026 0.002 PHE Y 40 TYR 0.023 0.002 TYR D 169 ARG 0.012 0.001 ARG N 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 756 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 755 time to evaluate : 2.165 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 52 LEU cc_start: 0.9671 (mm) cc_final: 0.9437 (mm) REVERT: A 57 ASN cc_start: 0.9585 (m110) cc_final: 0.9236 (m110) REVERT: A 71 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8814 (tm-30) REVERT: A 113 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8817 (mt-10) REVERT: A 118 MET cc_start: 0.9249 (mmp) cc_final: 0.8906 (tmm) REVERT: A 124 ILE cc_start: 0.8996 (mm) cc_final: 0.8777 (pt) REVERT: B 10 MET cc_start: 0.9113 (mmp) cc_final: 0.8799 (mmp) REVERT: B 21 ASN cc_start: 0.9439 (t0) cc_final: 0.9143 (t0) REVERT: B 30 LYS cc_start: 0.8892 (mmpt) cc_final: 0.8665 (mmmm) REVERT: B 70 LYS cc_start: 0.9708 (ptmm) cc_final: 0.9375 (ptpt) REVERT: B 74 ASN cc_start: 0.9488 (m-40) cc_final: 0.9158 (m110) REVERT: B 82 ARG cc_start: 0.9124 (ttp80) cc_final: 0.8680 (ttp80) REVERT: B 118 MET cc_start: 0.9362 (mtm) cc_final: 0.8976 (ptp) REVERT: B 129 ILE cc_start: 0.9310 (pt) cc_final: 0.8749 (pt) REVERT: B 131 LYS cc_start: 0.9602 (ttmt) cc_final: 0.9375 (mtpt) REVERT: B 143 ARG cc_start: 0.9086 (mtm110) cc_final: 0.8850 (mtm110) REVERT: B 167 ARG cc_start: 0.9277 (ptp-170) cc_final: 0.8981 (ptt180) REVERT: C 48 THR cc_start: 0.9318 (p) cc_final: 0.9002 (p) REVERT: C 53 ASN cc_start: 0.9156 (m-40) cc_final: 0.8856 (m110) REVERT: C 55 MET cc_start: 0.9196 (ttm) cc_final: 0.8715 (ttp) REVERT: C 131 LYS cc_start: 0.8792 (ttmt) cc_final: 0.8441 (mtpt) REVERT: C 154 ARG cc_start: 0.9264 (mtp-110) cc_final: 0.8784 (mmm160) REVERT: C 182 LYS cc_start: 0.9608 (mtmm) cc_final: 0.9158 (mtmt) REVERT: C 187 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9040 (mm-30) REVERT: C 189 LEU cc_start: 0.9241 (mm) cc_final: 0.8941 (mp) REVERT: D 56 LEU cc_start: 0.9748 (mt) cc_final: 0.9352 (mt) REVERT: D 57 ASN cc_start: 0.9597 (m110) cc_final: 0.9315 (m-40) REVERT: D 117 TRP cc_start: 0.8532 (m-10) cc_final: 0.7931 (m-90) REVERT: D 130 TYR cc_start: 0.9485 (t80) cc_final: 0.9204 (t80) REVERT: D 131 LYS cc_start: 0.9348 (tttt) cc_final: 0.9026 (mttt) REVERT: D 141 ILE cc_start: 0.8918 (mt) cc_final: 0.8713 (mt) REVERT: D 143 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8204 (mmm160) REVERT: D 169 TYR cc_start: 0.8773 (m-80) cc_final: 0.8436 (m-80) REVERT: D 215 MET cc_start: 0.8140 (ttt) cc_final: 0.7606 (ttm) REVERT: G 23 TRP cc_start: 0.9271 (t-100) cc_final: 0.8756 (t-100) REVERT: G 39 MET cc_start: 0.9229 (ttp) cc_final: 0.9000 (tpt) REVERT: G 96 MET cc_start: 0.1954 (mpp) cc_final: 0.0865 (mmm) REVERT: G 139 ASN cc_start: 0.9589 (m110) cc_final: 0.9323 (m110) REVERT: G 154 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7933 (mmm-85) REVERT: G 168 PHE cc_start: 0.9395 (t80) cc_final: 0.9038 (t80) REVERT: G 170 LYS cc_start: 0.9372 (mtpt) cc_final: 0.8694 (mptt) REVERT: G 181 VAL cc_start: 0.9298 (t) cc_final: 0.9062 (p) REVERT: G 185 MET cc_start: 0.9015 (mtt) cc_final: 0.8422 (mtt) REVERT: G 193 ASN cc_start: 0.9444 (m-40) cc_final: 0.8621 (m110) REVERT: H 10 MET cc_start: 0.5561 (ttt) cc_final: 0.5067 (ttt) REVERT: H 39 MET cc_start: 0.8624 (ttm) cc_final: 0.8336 (tpt) REVERT: H 55 MET cc_start: 0.9340 (mmp) cc_final: 0.9130 (mmm) REVERT: H 161 PHE cc_start: 0.8041 (t80) cc_final: 0.7095 (t80) REVERT: H 167 ARG cc_start: 0.9257 (mmm160) cc_final: 0.8573 (mmm160) REVERT: H 215 MET cc_start: 0.9011 (tpt) cc_final: 0.8597 (mmm) REVERT: J 10 ILE cc_start: 0.9125 (tp) cc_final: 0.8835 (tp) REVERT: J 25 PHE cc_start: 0.8287 (m-80) cc_final: 0.7650 (m-80) REVERT: J 78 ILE cc_start: 0.8221 (pt) cc_final: 0.7802 (pt) REVERT: J 79 TYR cc_start: 0.8080 (m-80) cc_final: 0.7717 (m-10) REVERT: J 88 PHE cc_start: 0.7410 (m-80) cc_final: 0.6861 (m-80) REVERT: J 97 ILE cc_start: 0.7730 (mm) cc_final: 0.7446 (tp) REVERT: J 100 MET cc_start: 0.5356 (mmm) cc_final: 0.5019 (tpt) REVERT: N 153 ILE cc_start: 0.8830 (mt) cc_final: 0.8628 (mt) REVERT: N 185 MET cc_start: 0.8696 (ptp) cc_final: 0.8456 (ptt) REVERT: N 213 GLU cc_start: 0.9653 (mp0) cc_final: 0.9405 (pm20) REVERT: Y 5 ASN cc_start: 0.8547 (t0) cc_final: 0.8293 (t0) REVERT: Y 51 ASP cc_start: 0.9319 (m-30) cc_final: 0.9087 (m-30) REVERT: Y 56 LEU cc_start: 0.9526 (mt) cc_final: 0.9281 (mt) REVERT: Y 63 GLN cc_start: 0.9014 (mm110) cc_final: 0.8747 (mm-40) REVERT: Y 117 TRP cc_start: 0.8421 (m-10) cc_final: 0.7760 (m-90) REVERT: Y 139 ASN cc_start: 0.9469 (m-40) cc_final: 0.9119 (m110) REVERT: d 23 TRP cc_start: 0.8814 (t-100) cc_final: 0.8514 (t-100) REVERT: d 130 TYR cc_start: 0.7637 (t80) cc_final: 0.7357 (t80) REVERT: d 139 ASN cc_start: 0.9592 (m-40) cc_final: 0.9125 (m-40) REVERT: d 140 LYS cc_start: 0.9545 (mtmt) cc_final: 0.9220 (mtmt) REVERT: d 143 ARG cc_start: 0.9229 (mtt180) cc_final: 0.8780 (mtm-85) REVERT: d 152 ASP cc_start: 0.8307 (m-30) cc_final: 0.8092 (m-30) REVERT: d 167 ARG cc_start: 0.8570 (mmp-170) cc_final: 0.8182 (mmp80) REVERT: e 10 MET cc_start: 0.7973 (mmp) cc_final: 0.7709 (mmm) REVERT: e 51 ASP cc_start: 0.9538 (m-30) cc_final: 0.9306 (m-30) REVERT: e 55 MET cc_start: 0.8609 (ttt) cc_final: 0.7800 (tmm) REVERT: e 79 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8718 (pp20) REVERT: e 82 ARG cc_start: 0.9189 (tmm160) cc_final: 0.8889 (ttp80) REVERT: e 104 ILE cc_start: 0.9103 (mp) cc_final: 0.8865 (mp) REVERT: e 117 TRP cc_start: 0.8852 (m-10) cc_final: 0.8505 (m-10) REVERT: e 118 MET cc_start: 0.9177 (mtt) cc_final: 0.8873 (mtt) REVERT: e 128 GLU cc_start: 0.9316 (mp0) cc_final: 0.8993 (mp0) REVERT: e 139 ASN cc_start: 0.9404 (m-40) cc_final: 0.8997 (m110) REVERT: e 168 PHE cc_start: 0.9603 (t80) cc_final: 0.9216 (t80) REVERT: e 185 MET cc_start: 0.8865 (mtm) cc_final: 0.8640 (mtp) REVERT: j 167 ARG cc_start: 0.8321 (mmm160) cc_final: 0.7439 (mmm160) REVERT: j 170 LYS cc_start: 0.8800 (tmtt) cc_final: 0.8484 (tmtt) REVERT: k 55 MET cc_start: 0.9497 (tpt) cc_final: 0.9143 (tpp) REVERT: k 68 MET cc_start: 0.9408 (mtp) cc_final: 0.9025 (mtt) REVERT: k 70 LYS cc_start: 0.9039 (mtmt) cc_final: 0.8718 (ptpt) REVERT: k 76 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9041 (tp30) REVERT: k 96 MET cc_start: 0.4595 (ttm) cc_final: 0.4085 (mtp) REVERT: k 104 ILE cc_start: 0.8521 (mm) cc_final: 0.8019 (mm) REVERT: k 173 ARG cc_start: 0.9225 (ttt180) cc_final: 0.8738 (ttp80) REVERT: k 182 LYS cc_start: 0.9235 (ptpp) cc_final: 0.8904 (pttm) outliers start: 1 outliers final: 0 residues processed: 755 average time/residue: 0.3503 time to fit residues: 377.2757 Evaluate side-chains 581 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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: 7.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 9.9990 chunk 154 optimal weight: 20.0000 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 147 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 114 GLN ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 163 GLN ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 139 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.8156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18824 Z= 0.221 Angle : 0.701 13.081 25567 Z= 0.362 Chirality : 0.046 0.275 2848 Planarity : 0.005 0.051 3345 Dihedral : 4.611 32.921 2500 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.05 % Allowed : 0.45 % Favored : 99.50 % 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: 0.70 (0.14), residues: 1431 sheet: -0.78 (0.69), residues: 57 loop : -0.00 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 184 HIS 0.006 0.001 HIS J 54 PHE 0.020 0.002 PHE G 161 TYR 0.032 0.002 TYR D 145 ARG 0.011 0.001 ARG d 82 ********************** 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 740 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 739 time to evaluate : 2.185 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: A 32 PHE cc_start: 0.8245 (m-80) cc_final: 0.7989 (m-80) REVERT: A 52 LEU cc_start: 0.9703 (mm) cc_final: 0.9483 (mm) REVERT: A 57 ASN cc_start: 0.9565 (m110) cc_final: 0.9320 (m-40) REVERT: A 63 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8209 (mp10) REVERT: A 96 MET cc_start: 0.0654 (mtt) cc_final: 0.0416 (mtt) REVERT: A 113 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8802 (mt-10) REVERT: A 118 MET cc_start: 0.9258 (mmp) cc_final: 0.8878 (tmm) REVERT: A 119 THR cc_start: 0.8204 (t) cc_final: 0.7901 (t) REVERT: A 124 ILE cc_start: 0.8990 (mm) cc_final: 0.8778 (pt) REVERT: A 144 MET cc_start: 0.9076 (ttt) cc_final: 0.8847 (ttt) REVERT: B 10 MET cc_start: 0.9112 (mmp) cc_final: 0.8825 (mmp) REVERT: B 30 LYS cc_start: 0.8834 (mmpt) cc_final: 0.8586 (mmmm) REVERT: B 55 MET cc_start: 0.9156 (tpp) cc_final: 0.8871 (tpp) REVERT: B 70 LYS cc_start: 0.9729 (ptmm) cc_final: 0.9466 (ptmm) REVERT: B 74 ASN cc_start: 0.9485 (m-40) cc_final: 0.8967 (m110) REVERT: B 82 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8718 (ttp80) REVERT: B 118 MET cc_start: 0.9414 (mtm) cc_final: 0.9075 (ptp) REVERT: B 129 ILE cc_start: 0.9254 (pt) cc_final: 0.9006 (pt) REVERT: B 131 LYS cc_start: 0.9593 (ttmt) cc_final: 0.9235 (mmmt) REVERT: B 143 ARG cc_start: 0.9075 (mtm110) cc_final: 0.8828 (mtm110) REVERT: B 166 ASP cc_start: 0.9224 (t0) cc_final: 0.9012 (t70) REVERT: B 167 ARG cc_start: 0.9275 (ptp-170) cc_final: 0.8969 (ptt180) REVERT: C 48 THR cc_start: 0.9335 (p) cc_final: 0.9030 (p) REVERT: C 53 ASN cc_start: 0.9162 (m-40) cc_final: 0.8856 (m110) REVERT: C 55 MET cc_start: 0.9183 (ttm) cc_final: 0.8757 (ttp) REVERT: C 131 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8528 (mtpt) REVERT: C 182 LYS cc_start: 0.9609 (mtmm) cc_final: 0.9160 (mtmt) REVERT: C 187 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9038 (mm-30) REVERT: C 189 LEU cc_start: 0.9234 (mm) cc_final: 0.8901 (mp) REVERT: D 56 LEU cc_start: 0.9697 (mt) cc_final: 0.9488 (mt) REVERT: D 57 ASN cc_start: 0.9612 (m110) cc_final: 0.9294 (m-40) REVERT: D 117 TRP cc_start: 0.8563 (m-10) cc_final: 0.7913 (m-90) REVERT: D 130 TYR cc_start: 0.9515 (t80) cc_final: 0.9207 (t80) REVERT: D 131 LYS cc_start: 0.9327 (tttt) cc_final: 0.9070 (mttt) REVERT: D 141 ILE cc_start: 0.8897 (mt) cc_final: 0.8687 (mt) REVERT: D 143 ARG cc_start: 0.9053 (mmm160) cc_final: 0.8216 (mmm160) REVERT: D 169 TYR cc_start: 0.8801 (m-80) cc_final: 0.8433 (m-80) REVERT: D 215 MET cc_start: 0.8126 (ttt) cc_final: 0.7572 (ttm) REVERT: G 23 TRP cc_start: 0.9270 (t-100) cc_final: 0.8757 (t-100) REVERT: G 75 GLU cc_start: 0.9014 (pt0) cc_final: 0.8800 (pt0) REVERT: G 96 MET cc_start: 0.2020 (mpp) cc_final: 0.0922 (mmm) REVERT: G 139 ASN cc_start: 0.9542 (m110) cc_final: 0.9278 (m110) REVERT: G 168 PHE cc_start: 0.9399 (t80) cc_final: 0.9006 (t80) REVERT: G 170 LYS cc_start: 0.9380 (mtpt) cc_final: 0.8715 (mptt) REVERT: G 181 VAL cc_start: 0.9274 (t) cc_final: 0.9049 (p) REVERT: G 185 MET cc_start: 0.9018 (mtt) cc_final: 0.8425 (mtt) REVERT: G 193 ASN cc_start: 0.9457 (m-40) cc_final: 0.8739 (m110) REVERT: H 10 MET cc_start: 0.5594 (ttt) cc_final: 0.5111 (ttt) REVERT: H 39 MET cc_start: 0.8658 (ttm) cc_final: 0.8420 (tpt) REVERT: H 161 PHE cc_start: 0.8091 (t80) cc_final: 0.7316 (t80) REVERT: H 167 ARG cc_start: 0.9275 (mmm160) cc_final: 0.8592 (mmm160) REVERT: H 215 MET cc_start: 0.9012 (tpt) cc_final: 0.8605 (tpt) REVERT: J 10 ILE cc_start: 0.9100 (tp) cc_final: 0.8820 (tp) REVERT: J 25 PHE cc_start: 0.8280 (m-80) cc_final: 0.7589 (m-80) REVERT: J 78 ILE cc_start: 0.8229 (pt) cc_final: 0.7884 (pt) REVERT: J 79 TYR cc_start: 0.8123 (m-80) cc_final: 0.7831 (m-10) REVERT: J 97 ILE cc_start: 0.7859 (mm) cc_final: 0.7551 (tp) REVERT: J 100 MET cc_start: 0.5527 (mmm) cc_final: 0.5272 (tpt) REVERT: N 185 MET cc_start: 0.8597 (ptp) cc_final: 0.8125 (ptp) REVERT: N 213 GLU cc_start: 0.9634 (mp0) cc_final: 0.9354 (pm20) REVERT: Y 5 ASN cc_start: 0.8545 (t0) cc_final: 0.8289 (t0) REVERT: Y 13 GLN cc_start: 0.9211 (tt0) cc_final: 0.8921 (pm20) REVERT: Y 20 LEU cc_start: 0.9695 (pp) cc_final: 0.9408 (pp) REVERT: Y 45 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8105 (mm-30) REVERT: Y 51 ASP cc_start: 0.9311 (m-30) cc_final: 0.9073 (m-30) REVERT: Y 56 LEU cc_start: 0.9532 (mt) cc_final: 0.9260 (mt) REVERT: Y 63 GLN cc_start: 0.9066 (mm110) cc_final: 0.8828 (mm110) REVERT: Y 112 GLN cc_start: 0.9221 (tm-30) cc_final: 0.9010 (tm-30) REVERT: d 23 TRP cc_start: 0.8835 (t-100) cc_final: 0.8562 (t-100) REVERT: d 96 MET cc_start: 0.5725 (mtm) cc_final: 0.5521 (mpp) REVERT: d 130 TYR cc_start: 0.7837 (t80) cc_final: 0.7351 (t80) REVERT: d 139 ASN cc_start: 0.9638 (m-40) cc_final: 0.9188 (m-40) REVERT: d 140 LYS cc_start: 0.9545 (mtmt) cc_final: 0.9179 (mtmt) REVERT: d 143 ARG cc_start: 0.9229 (mtt180) cc_final: 0.8780 (mtt90) REVERT: d 152 ASP cc_start: 0.8307 (m-30) cc_final: 0.8053 (m-30) REVERT: d 167 ARG cc_start: 0.8528 (mmp-170) cc_final: 0.8153 (mmp80) REVERT: e 25 LYS cc_start: 0.9651 (mttt) cc_final: 0.9402 (mtmm) REVERT: e 51 ASP cc_start: 0.9591 (m-30) cc_final: 0.9297 (m-30) REVERT: e 55 MET cc_start: 0.8642 (ttt) cc_final: 0.7812 (tmm) REVERT: e 57 ASN cc_start: 0.9499 (m110) cc_final: 0.9287 (m-40) REVERT: e 66 MET cc_start: 0.9254 (mmp) cc_final: 0.8884 (mmm) REVERT: e 70 LYS cc_start: 0.9283 (ptpp) cc_final: 0.8932 (ptpt) REVERT: e 79 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8777 (pp20) REVERT: e 82 ARG cc_start: 0.9242 (tmm160) cc_final: 0.8924 (ttp80) REVERT: e 117 TRP cc_start: 0.8923 (m-10) cc_final: 0.8579 (m-10) REVERT: e 118 MET cc_start: 0.9187 (mtt) cc_final: 0.8890 (mtt) REVERT: e 128 GLU cc_start: 0.9299 (mp0) cc_final: 0.8991 (mp0) REVERT: e 168 PHE cc_start: 0.9612 (t80) cc_final: 0.9242 (t80) REVERT: e 215 MET cc_start: 0.7886 (ptm) cc_final: 0.7426 (ptp) REVERT: j 167 ARG cc_start: 0.8331 (mmm160) cc_final: 0.7634 (mmm160) REVERT: j 215 MET cc_start: 0.8273 (ppp) cc_final: 0.7994 (ppp) REVERT: k 55 MET cc_start: 0.9499 (tpt) cc_final: 0.9180 (tpp) REVERT: k 68 MET cc_start: 0.9245 (mtp) cc_final: 0.8917 (mtp) REVERT: k 70 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8681 (mtmm) REVERT: k 76 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9133 (mm-30) REVERT: k 96 MET cc_start: 0.4680 (ttm) cc_final: 0.4082 (mtp) REVERT: k 104 ILE cc_start: 0.8537 (mm) cc_final: 0.8094 (mm) REVERT: k 182 LYS cc_start: 0.9234 (ptpp) cc_final: 0.8776 (pttm) REVERT: k 214 MET cc_start: 0.9151 (ptp) cc_final: 0.8842 (ptp) outliers start: 1 outliers final: 0 residues processed: 739 average time/residue: 0.3568 time to fit residues: 376.2169 Evaluate side-chains 583 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 583 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 171 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 185 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 190 optimal weight: 20.0000 chunk 23 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN G 114 GLN ** G 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN J 163 GLN ** N 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 12 HIS ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 193 ASN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 74 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.098633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.075266 restraints weight = 78367.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.077315 restraints weight = 55624.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.078795 restraints weight = 43152.912| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.8476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 18824 Z= 0.270 Angle : 0.735 13.621 25567 Z= 0.384 Chirality : 0.047 0.268 2848 Planarity : 0.005 0.051 3345 Dihedral : 4.759 35.020 2500 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.13 (0.17), residues: 2338 helix: 0.40 (0.13), residues: 1446 sheet: -0.76 (0.70), residues: 57 loop : -0.17 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 23 HIS 0.007 0.001 HIS J 54 PHE 0.026 0.002 PHE Y 40 TYR 0.022 0.002 TYR D 169 ARG 0.010 0.001 ARG J 37 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6152.67 seconds wall clock time: 111 minutes 33.16 seconds (6693.16 seconds total)