Starting phenix.real_space_refine on Wed Apr 10 03:49:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9w_10739/04_2024/6y9w_10739.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9w_10739/04_2024/6y9w_10739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9w_10739/04_2024/6y9w_10739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9w_10739/04_2024/6y9w_10739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9w_10739/04_2024/6y9w_10739.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y9w_10739/04_2024/6y9w_10739.pdb" } resolution = 4.1 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 "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: 0.04s 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: 9.66, per 1000 atoms: 0.52 Number of scatterers: 18418 At special positions: 0 Unit cell: (136.74, 184.44, 104.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 3466 8.00 N 3207 7.00 C 11607 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 218 " distance=2.04 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 218 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 218 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 218 " distance=2.03 Simple disulfide: pdb=" SG CYS H 198 " - pdb=" SG CYS H 218 " distance=2.03 Simple disulfide: pdb=" SG CYS N 198 " - pdb=" SG CYS N 218 " distance=2.04 Simple disulfide: pdb=" SG CYS d 198 " - pdb=" SG CYS d 218 " distance=2.03 Simple disulfide: pdb=" SG CYS e 198 " - pdb=" SG CYS e 218 " distance=2.03 Simple disulfide: pdb=" SG CYS j 198 " - pdb=" SG CYS j 218 " distance=2.03 Simple disulfide: pdb=" SG CYS k 198 " - pdb=" SG CYS k 218 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.79 Conformation dependent library (CDL) restraints added in 3.5 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: 3.526A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 190 removed outlier: 3.791A 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: 3.595A pdb=" N LEU B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.805A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 31 Processing helix chain 'C' and resid 33 through 35 No H-bonds generated for 'chain 'C' and resid 33 through 35' Processing helix chain 'C' and resid 36 through 44 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 100 through 105 removed outlier: 4.008A pdb=" N ALA C 105 " --> pdb=" O GLY C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 119 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'C' and resid 160 through 174 Processing helix chain 'C' and resid 179 through 193 removed outlier: 3.537A pdb=" N GLU C 187 " --> pdb=" O ASN C 183 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N VAL C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'C' and resid 210 through 219 removed outlier: 3.872A pdb=" N CYS C 218 " --> pdb=" O MET C 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 30 removed outlier: 3.675A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 48 through 58 Processing helix chain 'D' and resid 62 through 83 Processing helix chain 'D' and resid 100 through 105 Processing helix chain 'D' and resid 110 through 118 removed outlier: 3.701A 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: 3.895A pdb=" N TRP G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) removed outlier: 4.380A 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: 3.894A pdb=" N TRP H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 Processing helix chain 'H' and resid 210 through 218 Processing helix chain 'J' and resid 29 through 42 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 135 through 144 removed outlier: 4.121A pdb=" N ARG J 144 " --> pdb=" O GLU J 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 153 removed outlier: 3.525A 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: 3.790A 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: 3.801A pdb=" N CYS N 218 " --> pdb=" O MET N 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 30 removed outlier: 3.676A pdb=" N LEU Y 20 " --> pdb=" O SER Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 44 Processing helix chain 'Y' and resid 48 through 58 Processing helix chain 'Y' and resid 62 through 83 Processing helix chain 'Y' and resid 100 through 105 Processing helix chain 'Y' and resid 110 through 118 removed outlier: 3.700A pdb=" N GLN Y 114 " --> pdb=" O THR Y 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 126 through 146 removed outlier: 3.601A pdb=" N ARG Y 132 " --> pdb=" O GLU Y 128 " (cutoff:3.500A) Processing helix chain 'd' and resid 16 through 30 removed outlier: 3.673A 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 'e' and resid 16 through 31 Processing helix chain 'e' and resid 35 through 44 Processing helix chain 'e' and resid 48 through 58 Processing helix chain 'e' and resid 62 through 84 Processing helix chain 'e' and resid 100 through 105 Processing helix chain 'e' and resid 110 through 120 Processing helix chain 'e' and resid 125 through 145 Processing helix chain 'e' and resid 149 through 153 Processing helix chain 'e' and resid 160 through 175 Processing helix chain 'e' and resid 178 through 189 removed outlier: 3.692A pdb=" N GLU e 187 " --> pdb=" O ASN e 183 " (cutoff:3.500A) Processing helix chain 'e' and resid 195 through 206 removed outlier: 3.905A pdb=" N ILE e 201 " --> pdb=" O ASP e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 210 through 218 removed outlier: 3.510A pdb=" N MET e 214 " --> pdb=" O THR e 210 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 153 Processing helix chain 'j' and resid 160 through 175 Processing helix chain 'j' and resid 178 through 189 removed outlier: 3.690A pdb=" N GLU j 187 " --> pdb=" O ASN j 183 " (cutoff:3.500A) Processing helix chain 'j' and resid 195 through 206 removed outlier: 3.904A 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: 4.360A 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: 3.921A 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: 3.669A pdb=" N VAL B 3 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 11 " --> pdb=" O VAL B 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 4 removed outlier: 3.600A pdb=" N VAL C 3 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 11 " --> pdb=" O VAL C 3 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 2 through 4 Processing sheet with id=AA5, first strand: chain 'H' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'J' and resid 53 through 57 removed outlier: 4.394A pdb=" N ILE J 97 " --> pdb=" O CYS J 115 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N MET J 100 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL J 128 " --> pdb=" O MET J 100 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N SER J 21 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL J 12 " --> pdb=" O PRO J 16 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY J 18 " --> pdb=" O ILE J 10 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP J 160 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA J 11 " --> pdb=" O ILE J 158 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE J 158 " --> pdb=" O ALA J 11 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'e' and resid 2 through 3 removed outlier: 3.665A pdb=" N VAL e 3 " --> pdb=" O VAL e 11 " (cutoff:3.500A) removed outlier: 3.765A 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: 3.531A 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: 5.65 Time building geometry restraints manager: 7.32 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: 7782 1.44 - 1.67: 10787 1.67 - 1.90: 252 1.90 - 2.13: 0 2.13 - 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 2.238 -0.907 1.23e-02 6.61e+03 5.44e+03 bond pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 1.522 2.365 -0.844 1.37e-02 5.33e+03 3.79e+03 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.456 2.273 -0.817 1.33e-02 5.65e+03 3.77e+03 bond pdb=" C HIS e 84 " pdb=" N PRO e 85 " ideal model delta sigma weight residual 1.330 1.513 -0.183 1.22e-02 6.72e+03 2.24e+02 bond pdb=" CD2 HIS J 54 " pdb=" NE2 HIS J 54 " ideal model delta sigma weight residual 1.374 1.293 0.081 1.10e-02 8.26e+03 5.41e+01 ... (remaining 18819 not shown) Histogram of bond angle deviations from ideal: 64.14 - 80.42: 1 80.42 - 96.71: 2 96.71 - 112.99: 10873 112.99 - 129.27: 14536 129.27 - 145.55: 155 Bond angle restraints: 25567 Sorted by residual: angle pdb=" N ARG C 18 " pdb=" CA ARG C 18 " pdb=" C ARG C 18 " ideal model delta sigma weight residual 113.23 64.14 49.09 1.24e+00 6.50e-01 1.57e+03 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" O ARG C 18 " ideal model delta sigma weight residual 119.27 91.99 27.28 1.17e+00 7.31e-01 5.44e+02 angle pdb=" CA ARG C 18 " pdb=" C ARG C 18 " pdb=" N THR C 19 " ideal model delta sigma weight residual 118.21 145.55 -27.34 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 122.30 108.79 13.51 1.36e+00 5.41e-01 9.87e+01 angle pdb=" C HIS e 84 " pdb=" N PRO e 85 " pdb=" CA PRO e 85 " ideal model delta sigma weight residual 120.03 129.85 -9.82 9.90e-01 1.02e+00 9.84e+01 ... (remaining 25562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10637 17.99 - 35.99: 711 35.99 - 53.98: 179 53.98 - 71.97: 19 71.97 - 89.97: 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 -163.12 40.52 0 2.50e+00 1.60e-01 2.63e+02 dihedral pdb=" N ARG e 97 " pdb=" C ARG e 97 " pdb=" CA ARG e 97 " pdb=" CB ARG e 97 " ideal model delta harmonic sigma weight residual 122.80 158.65 -35.85 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" N ARG C 18 " pdb=" C ARG C 18 " pdb=" CA ARG C 18 " pdb=" CB ARG C 18 " ideal model delta harmonic sigma weight residual 122.80 96.10 26.70 0 2.50e+00 1.60e-01 1.14e+02 ... (remaining 11556 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.946: 2846 0.946 - 1.891: 1 1.891 - 2.837: 0 2.837 - 3.782: 0 3.782 - 4.728: 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 5.59e+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 6.56e+01 chirality pdb=" CA PRO J 30 " pdb=" N PRO J 30 " pdb=" C PRO J 30 " pdb=" CB PRO J 30 " both_signs ideal model delta sigma weight residual False 2.72 2.29 0.43 2.00e-01 2.50e+01 4.57e+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 7.92e-02 1.10e+02 pdb=" CG PHE J 60 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE J 60 " -0.094 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 9.96e-02 9.93e+01 pdb=" C PRO C 147 " 0.171 2.00e-02 2.50e+03 pdb=" O PRO C 147 " -0.068 2.00e-02 2.50e+03 pdb=" N THR C 148 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG e 97 " 0.039 2.00e-02 2.50e+03 7.86e-02 6.18e+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: 1.91 - 2.51: 80 2.51 - 3.11: 13700 3.11 - 3.70: 28195 3.70 - 4.30: 37715 4.30 - 4.90: 61472 Nonbonded interactions: 141162 Sorted by model distance: nonbonded pdb=" OE1 GLN G 7 " pdb=" NE2 GLN k 9 " model vdw 1.911 2.520 nonbonded pdb=" OE1 GLU D 180 " pdb=" CG2 VAL H 181 " model vdw 2.020 3.460 nonbonded pdb=" CD1 LEU G 151 " pdb=" OE1 GLN d 192 " model vdw 2.028 3.460 nonbonded pdb=" CD1 LEU D 151 " pdb=" OE1 GLN H 192 " model vdw 2.094 3.460 nonbonded pdb=" NH2 ARG C 143 " pdb=" O GLN C 176 " model vdw 2.125 2.520 ... (remaining 141157 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: 0.120 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: 1.790 Check model and map are aligned: 0.240 Set scattering table: 0.150 Process input model: 47.990 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.140 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: 0.000 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: 54.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.907 18824 Z= 0.831 Angle : 1.068 49.088 25567 Z= 0.726 Chirality : 0.108 4.728 2848 Planarity : 0.007 0.100 3345 Dihedral : 13.054 89.965 7127 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.97 % Favored : 97.99 % Rotamer: Outliers : 0.45 % Allowed : 3.05 % Favored : 96.50 % 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 1243 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1234 time to evaluate : 2.103 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: A 43 LEU cc_start: 0.8944 (mt) cc_final: 0.8665 (mp) REVERT: A 51 ASP cc_start: 0.9119 (m-30) cc_final: 0.8898 (m-30) REVERT: A 67 GLN cc_start: 0.9135 (tp40) cc_final: 0.8882 (tt0) REVERT: A 76 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9220 (mm-30) REVERT: A 86 VAL cc_start: 0.6828 (t) cc_final: 0.6094 (m) REVERT: A 145 TYR cc_start: 0.8844 (m-80) cc_final: 0.8527 (m-80) REVERT: B 21 ASN cc_start: 0.9511 (m-40) cc_final: 0.9238 (m110) REVERT: B 35 GLU cc_start: 0.9263 (pm20) cc_final: 0.8975 (mp0) REVERT: B 43 LEU cc_start: 0.8827 (mt) cc_final: 0.8558 (mt) REVERT: B 51 ASP cc_start: 0.9034 (m-30) cc_final: 0.8683 (m-30) REVERT: B 71 GLU cc_start: 0.9175 (tt0) cc_final: 0.8270 (tt0) REVERT: B 74 ASN cc_start: 0.9412 (m-40) cc_final: 0.9153 (m110) REVERT: B 75 GLU cc_start: 0.9243 (tt0) cc_final: 0.8975 (mt-10) REVERT: B 131 LYS cc_start: 0.9634 (ttmt) cc_final: 0.9366 (mttt) REVERT: B 144 MET cc_start: 0.9488 (ttt) cc_final: 0.9204 (ttt) REVERT: B 153 ILE cc_start: 0.9140 (mm) cc_final: 0.8535 (mt) REVERT: B 163 ASP cc_start: 0.9225 (m-30) cc_final: 0.8348 (t70) REVERT: B 173 ARG cc_start: 0.9095 (ttt180) cc_final: 0.8696 (ptm160) REVERT: B 180 GLU cc_start: 0.9453 (mp0) cc_final: 0.9250 (pm20) REVERT: B 181 VAL cc_start: 0.9815 (t) cc_final: 0.9345 (p) REVERT: B 182 LYS cc_start: 0.9638 (mttt) cc_final: 0.9207 (mtpt) REVERT: B 205 LEU cc_start: 0.7703 (mp) cc_final: 0.4867 (mp) REVERT: B 214 MET cc_start: 0.9407 (mtt) cc_final: 0.9169 (mmp) REVERT: C 25 LYS cc_start: 0.9498 (mttt) cc_final: 0.9204 (ptmm) REVERT: C 35 GLU cc_start: 0.9231 (pm20) cc_final: 0.8127 (pp20) REVERT: C 56 LEU cc_start: 0.9613 (mt) cc_final: 0.9341 (mt) REVERT: C 59 VAL cc_start: 0.9050 (t) cc_final: 0.8150 (p) REVERT: C 72 THR cc_start: 0.9308 (m) cc_final: 0.8968 (m) REVERT: C 75 GLU cc_start: 0.9266 (mm-30) cc_final: 0.8598 (pp20) REVERT: C 103 ASP cc_start: 0.8892 (m-30) cc_final: 0.8343 (m-30) REVERT: C 140 LYS cc_start: 0.9762 (mttt) cc_final: 0.9459 (tptp) REVERT: C 153 ILE cc_start: 0.8213 (mt) cc_final: 0.7918 (mm) REVERT: C 178 SER cc_start: 0.7626 (m) cc_final: 0.7042 (t) REVERT: C 182 LYS cc_start: 0.9072 (ttmm) cc_final: 0.8816 (mttm) REVERT: C 192 GLN cc_start: 0.9056 (mt0) cc_final: 0.8753 (mm-40) REVERT: C 215 MET cc_start: 0.9063 (mtm) cc_final: 0.8301 (mtm) REVERT: D 28 GLU cc_start: 0.9240 (tt0) cc_final: 0.9032 (pt0) REVERT: D 41 SER cc_start: 0.9571 (t) cc_final: 0.9071 (p) REVERT: D 53 ASN cc_start: 0.9427 (m-40) cc_final: 0.9079 (m110) REVERT: D 57 ASN cc_start: 0.9432 (m-40) cc_final: 0.9173 (m-40) REVERT: D 62 HIS cc_start: 0.8439 (m-70) cc_final: 0.8186 (m90) REVERT: D 66 MET cc_start: 0.9035 (mmm) cc_final: 0.8780 (ptp) REVERT: D 103 ASP cc_start: 0.8455 (t0) cc_final: 0.8049 (m-30) REVERT: D 128 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8530 (tm-30) REVERT: D 129 ILE cc_start: 0.9557 (mt) cc_final: 0.8479 (tt) REVERT: D 164 TYR cc_start: 0.7810 (t80) cc_final: 0.7308 (t80) REVERT: D 168 PHE cc_start: 0.8613 (t80) cc_final: 0.8377 (t80) REVERT: D 172 LEU cc_start: 0.9186 (tp) cc_final: 0.8718 (tp) REVERT: D 182 LYS cc_start: 0.8603 (mtpt) cc_final: 0.8115 (mttm) REVERT: D 190 LEU cc_start: 0.9523 (tp) cc_final: 0.9174 (tp) REVERT: D 215 MET cc_start: 0.8777 (mtm) cc_final: 0.8255 (mmm) REVERT: G 16 SER cc_start: 0.8882 (m) cc_final: 0.8341 (p) REVERT: G 55 MET cc_start: 0.9395 (mtp) cc_final: 0.9158 (mtm) REVERT: G 57 ASN cc_start: 0.9284 (m-40) cc_final: 0.9000 (m110) REVERT: G 59 VAL cc_start: 0.7983 (t) cc_final: 0.7766 (p) REVERT: G 62 HIS cc_start: 0.7960 (m-70) cc_final: 0.7395 (m90) REVERT: G 79 GLU cc_start: 0.9318 (tm-30) cc_final: 0.8962 (tm-30) REVERT: G 96 MET cc_start: 0.4939 (mpp) cc_final: 0.4174 (mpp) REVERT: G 166 ASP cc_start: 0.8751 (m-30) cc_final: 0.8316 (m-30) REVERT: G 170 LYS cc_start: 0.8995 (tttt) cc_final: 0.8794 (mptt) REVERT: G 171 THR cc_start: 0.8807 (m) cc_final: 0.8006 (p) REVERT: G 187 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9098 (mp0) REVERT: G 197 ASP cc_start: 0.9376 (m-30) cc_final: 0.9164 (p0) REVERT: G 214 MET cc_start: 0.9382 (mtm) cc_final: 0.9011 (mtt) REVERT: G 215 MET cc_start: 0.8112 (mtm) cc_final: 0.7672 (mtm) REVERT: H 23 TRP cc_start: 0.9057 (t-100) cc_final: 0.8585 (t-100) REVERT: H 68 MET cc_start: 0.9358 (mtp) cc_final: 0.8985 (ttm) REVERT: H 80 TRP cc_start: 0.9125 (t-100) cc_final: 0.8305 (t60) REVERT: H 102 SER cc_start: 0.8754 (m) cc_final: 0.8466 (t) REVERT: J 5 THR cc_start: 0.7169 (m) cc_final: 0.6471 (p) REVERT: J 22 PHE cc_start: 0.8817 (m-80) cc_final: 0.8135 (m-10) REVERT: J 29 VAL cc_start: 0.6639 (OUTLIER) cc_final: 0.5557 (p) REVERT: J 31 LYS cc_start: 0.9002 (tttm) cc_final: 0.8559 (mmmt) REVERT: J 53 PHE cc_start: 0.9016 (m-80) cc_final: 0.8560 (m-10) REVERT: J 61 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6779 (pp-130) REVERT: J 84 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6263 (pm20) REVERT: J 100 MET cc_start: 0.8964 (mmt) cc_final: 0.8739 (tpt) REVERT: J 108 ASN cc_start: 0.8442 (m-40) cc_final: 0.8034 (m110) REVERT: J 119 THR cc_start: 0.8478 (p) cc_final: 0.8259 (m) REVERT: J 122 LEU cc_start: 0.8582 (mt) cc_final: 0.8247 (mt) REVERT: J 138 ILE cc_start: 0.7739 (mm) cc_final: 0.7360 (mt) REVERT: J 160 ASP cc_start: 0.8409 (t0) cc_final: 0.8108 (t0) REVERT: J 164 LEU cc_start: 0.7098 (mt) cc_final: 0.6711 (mp) REVERT: J 165 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: N 153 ILE cc_start: 0.9210 (mm) cc_final: 0.8656 (mm) REVERT: N 163 ASP cc_start: 0.8834 (m-30) cc_final: 0.7690 (t0) REVERT: N 182 LYS cc_start: 0.9557 (mttt) cc_final: 0.8938 (mmmt) REVERT: N 212 GLU cc_start: 0.9304 (pt0) cc_final: 0.9074 (pm20) REVERT: Y 13 GLN cc_start: 0.9034 (tt0) cc_final: 0.8604 (tm-30) REVERT: Y 33 SER cc_start: 0.8036 (m) cc_final: 0.7718 (p) REVERT: Y 41 SER cc_start: 0.9617 (t) cc_final: 0.9347 (p) REVERT: Y 43 LEU cc_start: 0.9364 (mt) cc_final: 0.8973 (mt) REVERT: Y 49 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.9222 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9328 (m-30) cc_final: 0.8577 (m-30) REVERT: Y 52 LEU cc_start: 0.9537 (mt) cc_final: 0.9155 (mp) REVERT: Y 53 ASN cc_start: 0.9527 (m-40) cc_final: 0.9271 (m-40) REVERT: Y 67 GLN cc_start: 0.9041 (tp-100) cc_final: 0.8353 (mt0) REVERT: Y 68 MET cc_start: 0.9189 (mtp) cc_final: 0.8615 (mmt) REVERT: Y 69 LEU cc_start: 0.9588 (tp) cc_final: 0.9319 (tp) REVERT: Y 71 GLU cc_start: 0.9393 (tm-30) cc_final: 0.9103 (mt-10) REVERT: Y 72 THR cc_start: 0.9599 (m) cc_final: 0.9054 (p) REVERT: Y 75 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8830 (pt0) REVERT: Y 96 MET cc_start: 0.3438 (mpp) cc_final: 0.2625 (mtp) REVERT: Y 104 ILE cc_start: 0.8590 (tt) cc_final: 0.8295 (pt) REVERT: Y 113 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8289 (mp0) REVERT: Y 117 TRP cc_start: 0.8273 (m-10) cc_final: 0.7768 (m-10) REVERT: Y 129 ILE cc_start: 0.9487 (mt) cc_final: 0.9264 (pt) REVERT: d 2 ILE cc_start: 0.6151 (mt) cc_final: 0.5910 (mm) REVERT: d 23 TRP cc_start: 0.9256 (t-100) cc_final: 0.9012 (t-100) REVERT: d 67 GLN cc_start: 0.9521 (tp-100) cc_final: 0.9087 (tt0) REVERT: d 74 ASN cc_start: 0.9373 (m-40) cc_final: 0.9148 (m110) REVERT: d 91 ILE cc_start: 0.3991 (mm) cc_final: 0.3741 (tt) REVERT: d 103 ASP cc_start: 0.8717 (t0) cc_final: 0.8150 (t0) REVERT: d 128 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9266 (mp0) REVERT: d 129 ILE cc_start: 0.9416 (mt) cc_final: 0.9107 (tp) REVERT: d 130 TYR cc_start: 0.8506 (t80) cc_final: 0.8199 (t80) REVERT: d 139 ASN cc_start: 0.9663 (m-40) cc_final: 0.9446 (m-40) REVERT: d 143 ARG cc_start: 0.9047 (mtt180) cc_final: 0.8841 (ttm-80) REVERT: d 183 ASN cc_start: 0.9572 (m-40) cc_final: 0.9323 (m110) REVERT: d 193 ASN cc_start: 0.8314 (m-40) cc_final: 0.7859 (t0) REVERT: e 6 ILE cc_start: 0.9062 (mt) cc_final: 0.8799 (tp) REVERT: e 41 SER cc_start: 0.9237 (m) cc_final: 0.8835 (p) REVERT: e 58 THR cc_start: 0.9169 (p) cc_final: 0.8937 (p) REVERT: e 59 VAL cc_start: 0.9281 (p) cc_final: 0.9038 (m) REVERT: e 74 ASN cc_start: 0.9693 (m-40) cc_final: 0.9358 (m110) REVERT: e 76 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8663 (mm-30) REVERT: e 79 GLU cc_start: 0.8688 (mt-10) cc_final: 0.8177 (pp20) REVERT: e 96 MET cc_start: 0.5059 (mpp) cc_final: 0.4718 (mpp) REVERT: e 104 ILE cc_start: 0.8661 (mt) cc_final: 0.8243 (mt) REVERT: e 124 ILE cc_start: 0.8634 (mm) cc_final: 0.8127 (mm) REVERT: e 128 GLU cc_start: 0.9289 (mp0) cc_final: 0.8827 (mp0) REVERT: e 129 ILE cc_start: 0.9564 (mt) cc_final: 0.9303 (mm) REVERT: e 153 ILE cc_start: 0.8813 (mm) cc_final: 0.8602 (mm) REVERT: e 158 LYS cc_start: 0.8367 (tptt) cc_final: 0.8126 (tppt) REVERT: e 181 VAL cc_start: 0.9677 (t) cc_final: 0.9465 (t) REVERT: e 183 ASN cc_start: 0.9595 (m-40) cc_final: 0.9163 (m-40) REVERT: e 186 THR cc_start: 0.9548 (t) cc_final: 0.9171 (p) REVERT: j 153 ILE cc_start: 0.8793 (mm) cc_final: 0.8414 (mm) REVERT: j 189 LEU cc_start: 0.8917 (tp) cc_final: 0.8648 (tp) REVERT: j 199 LYS cc_start: 0.9212 (tttt) cc_final: 0.8892 (ttmm) REVERT: k 25 LYS cc_start: 0.9489 (mttt) cc_final: 0.9176 (ptmm) REVERT: k 32 PHE cc_start: 0.8459 (m-80) cc_final: 0.8191 (m-80) REVERT: k 40 PHE cc_start: 0.9421 (t80) cc_final: 0.9164 (t80) REVERT: k 43 LEU cc_start: 0.9337 (mt) cc_final: 0.9091 (mp) REVERT: k 55 MET cc_start: 0.9576 (mtp) cc_final: 0.9012 (ttm) REVERT: k 72 THR cc_start: 0.9014 (m) cc_final: 0.8530 (m) REVERT: k 76 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8912 (mm-30) REVERT: k 79 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8832 (tp30) REVERT: k 82 ARG cc_start: 0.8573 (ttp80) cc_final: 0.8265 (ttp80) REVERT: k 103 ASP cc_start: 0.8836 (m-30) cc_final: 0.8599 (m-30) REVERT: k 111 LEU cc_start: 0.8269 (tp) cc_final: 0.7919 (tt) REVERT: k 128 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8958 (mm-30) REVERT: k 129 ILE cc_start: 0.9334 (mt) cc_final: 0.8572 (pt) REVERT: k 131 LYS cc_start: 0.9505 (ttmt) cc_final: 0.9086 (ttmt) REVERT: k 136 LEU cc_start: 0.9762 (tt) cc_final: 0.9459 (mt) REVERT: k 139 ASN cc_start: 0.9109 (m-40) cc_final: 0.8887 (m110) REVERT: k 164 TYR cc_start: 0.8749 (t80) cc_final: 0.8202 (t80) REVERT: k 173 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8465 (ttp80) REVERT: k 180 GLU cc_start: 0.8944 (mp0) cc_final: 0.8685 (mp0) REVERT: k 185 MET cc_start: 0.9539 (mtm) cc_final: 0.9241 (mtm) REVERT: k 215 MET cc_start: 0.8615 (mtm) cc_final: 0.8295 (mtp) outliers start: 9 outliers final: 0 residues processed: 1237 average time/residue: 0.3180 time to fit residues: 555.7473 Evaluate side-chains 837 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 833 time to evaluate : 1.403 ------------------------------------------------------------------------------- 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: 5.9990 chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 183 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 212 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 4 GLN A 53 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 GLN B 12 HIS B 53 ASN B 219 GLN C 53 ASN C 112 GLN ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 GLN D 95 GLN G 4 GLN G 183 ASN H 4 GLN H 84 HIS N 219 GLN ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 95 GLN d 4 GLN d 95 GLN d 112 GLN ** e 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 53 ASN e 120 ASN e 219 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 62 HIS k 63 GLN ** k 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 95 GLN ** k 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 18824 Z= 0.342 Angle : 0.700 9.068 25567 Z= 0.366 Chirality : 0.046 0.217 2848 Planarity : 0.006 0.073 3345 Dihedral : 4.116 21.522 2500 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.80 % Favored : 98.16 % Rotamer: Outliers : 0.10 % Allowed : 5.54 % Favored : 94.36 % 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: -0.16 (0.17), residues: 2338 helix: 0.32 (0.13), residues: 1442 sheet: -1.25 (0.70), residues: 56 loop : -0.56 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP e 117 HIS 0.008 0.001 HIS C 84 PHE 0.021 0.002 PHE J 113 TYR 0.023 0.002 TYR e 130 ARG 0.006 0.001 ARG C 18 *********************** 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 976 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 974 time to evaluate : 2.285 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: A 25 LYS cc_start: 0.9812 (tttt) cc_final: 0.9407 (ttmm) REVERT: A 51 ASP cc_start: 0.8886 (m-30) cc_final: 0.8275 (m-30) REVERT: A 52 LEU cc_start: 0.9667 (mt) cc_final: 0.9396 (mt) REVERT: A 53 ASN cc_start: 0.9305 (m-40) cc_final: 0.9099 (m110) REVERT: A 67 GLN cc_start: 0.9211 (tp40) cc_final: 0.8263 (tm-30) REVERT: A 68 MET cc_start: 0.9114 (mtt) cc_final: 0.8369 (mtp) REVERT: A 76 GLU cc_start: 0.9566 (mm-30) cc_final: 0.9144 (mm-30) REVERT: A 96 MET cc_start: 0.6888 (mpp) cc_final: 0.6621 (mpp) REVERT: A 100 ARG cc_start: 0.8734 (mpp80) cc_final: 0.8500 (mtt90) REVERT: A 103 ASP cc_start: 0.8527 (m-30) cc_final: 0.8254 (m-30) REVERT: B 21 ASN cc_start: 0.9533 (m-40) cc_final: 0.9298 (m110) REVERT: B 39 MET cc_start: 0.9610 (tpp) cc_final: 0.9169 (tpt) REVERT: B 43 LEU cc_start: 0.8635 (mt) cc_final: 0.8097 (mt) REVERT: B 50 GLN cc_start: 0.8397 (mt0) cc_final: 0.8090 (mt0) REVERT: B 74 ASN cc_start: 0.9542 (m-40) cc_final: 0.9233 (m110) REVERT: B 96 MET cc_start: 0.7915 (mpp) cc_final: 0.7523 (mpp) REVERT: B 173 ARG cc_start: 0.9229 (ttt180) cc_final: 0.8819 (ptm160) REVERT: B 182 LYS cc_start: 0.9567 (mttt) cc_final: 0.9229 (mttt) REVERT: B 205 LEU cc_start: 0.6155 (mp) cc_final: 0.4887 (mp) REVERT: B 214 MET cc_start: 0.9588 (mtt) cc_final: 0.9281 (mmp) REVERT: C 43 LEU cc_start: 0.9287 (mt) cc_final: 0.9015 (mt) REVERT: C 59 VAL cc_start: 0.9004 (t) cc_final: 0.8690 (p) REVERT: C 76 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8671 (mm-30) REVERT: C 103 ASP cc_start: 0.8978 (m-30) cc_final: 0.8722 (m-30) REVERT: C 132 ARG cc_start: 0.9444 (ttp-110) cc_final: 0.9120 (ttm110) REVERT: C 139 ASN cc_start: 0.9299 (m110) cc_final: 0.9046 (m-40) REVERT: C 140 LYS cc_start: 0.9751 (mttt) cc_final: 0.9441 (tptp) REVERT: C 178 SER cc_start: 0.8012 (m) cc_final: 0.7681 (t) REVERT: C 182 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8854 (mttm) REVERT: C 192 GLN cc_start: 0.9189 (mt0) cc_final: 0.8682 (tm-30) REVERT: C 215 MET cc_start: 0.9044 (mtm) cc_final: 0.8354 (mtm) REVERT: D 53 ASN cc_start: 0.9294 (m-40) cc_final: 0.9073 (m-40) REVERT: D 62 HIS cc_start: 0.8332 (m-70) cc_final: 0.7937 (m90) REVERT: D 103 ASP cc_start: 0.8892 (t0) cc_final: 0.8511 (t0) REVERT: D 114 GLN cc_start: 0.9362 (mm-40) cc_final: 0.8608 (mp10) REVERT: D 143 ARG cc_start: 0.8821 (mtt90) cc_final: 0.8245 (tpm170) REVERT: D 146 SER cc_start: 0.8810 (p) cc_final: 0.8536 (t) REVERT: D 167 ARG cc_start: 0.8631 (ptm160) cc_final: 0.8363 (ptm-80) REVERT: D 182 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8118 (mttp) REVERT: D 203 LYS cc_start: 0.8612 (ptmt) cc_final: 0.8319 (pttm) REVERT: D 215 MET cc_start: 0.8879 (mtm) cc_final: 0.8433 (mmt) REVERT: G 23 TRP cc_start: 0.9214 (t60) cc_final: 0.8899 (t60) REVERT: G 62 HIS cc_start: 0.7896 (m-70) cc_final: 0.7474 (m90) REVERT: G 166 ASP cc_start: 0.8782 (m-30) cc_final: 0.8482 (m-30) REVERT: G 187 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9147 (mm-30) REVERT: G 197 ASP cc_start: 0.9348 (m-30) cc_final: 0.9148 (p0) REVERT: G 203 LYS cc_start: 0.9372 (mttp) cc_final: 0.9126 (mttp) REVERT: H 23 TRP cc_start: 0.9039 (t-100) cc_final: 0.8488 (t-100) REVERT: H 51 ASP cc_start: 0.9262 (m-30) cc_final: 0.8934 (m-30) REVERT: H 68 MET cc_start: 0.9307 (mtp) cc_final: 0.9081 (ttm) REVERT: H 80 TRP cc_start: 0.9351 (t-100) cc_final: 0.8641 (t60) REVERT: H 102 SER cc_start: 0.8655 (m) cc_final: 0.8147 (t) REVERT: H 113 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9219 (mt-10) REVERT: H 139 ASN cc_start: 0.9148 (m-40) cc_final: 0.8868 (m-40) REVERT: H 143 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8923 (mtt-85) REVERT: H 149 SER cc_start: 0.8245 (t) cc_final: 0.7801 (t) REVERT: J 22 PHE cc_start: 0.8613 (m-80) cc_final: 0.8177 (m-80) REVERT: J 35 ASN cc_start: 0.9485 (t0) cc_final: 0.9274 (t0) REVERT: J 37 ARG cc_start: 0.9163 (ttt-90) cc_final: 0.8843 (ptm-80) REVERT: J 84 GLU cc_start: 0.8439 (pm20) cc_final: 0.7973 (pm20) REVERT: J 100 MET cc_start: 0.8992 (mmt) cc_final: 0.8753 (tpt) REVERT: J 108 ASN cc_start: 0.8473 (m-40) cc_final: 0.8084 (m110) REVERT: J 138 ILE cc_start: 0.8342 (mm) cc_final: 0.7722 (mt) REVERT: J 140 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8968 (tp30) REVERT: J 142 MET cc_start: 0.8905 (mtm) cc_final: 0.8374 (mtm) REVERT: J 143 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7707 (mm-30) REVERT: J 164 LEU cc_start: 0.7597 (mt) cc_final: 0.7241 (mp) REVERT: N 163 ASP cc_start: 0.8873 (m-30) cc_final: 0.8085 (t0) REVERT: N 181 VAL cc_start: 0.9377 (p) cc_final: 0.9167 (p) REVERT: N 203 LYS cc_start: 0.9148 (mtpt) cc_final: 0.8905 (ptmt) REVERT: Y 15 ILE cc_start: 0.9202 (mm) cc_final: 0.8999 (mm) REVERT: Y 48 THR cc_start: 0.9115 (t) cc_final: 0.8731 (t) REVERT: Y 49 PRO cc_start: 0.9331 (Cg_exo) cc_final: 0.8971 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9228 (m-30) cc_final: 0.8804 (m-30) REVERT: Y 53 ASN cc_start: 0.9532 (m-40) cc_final: 0.9249 (m-40) REVERT: Y 55 MET cc_start: 0.8597 (tmm) cc_final: 0.8330 (tmm) REVERT: Y 67 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8570 (mt0) REVERT: Y 69 LEU cc_start: 0.9649 (tp) cc_final: 0.9381 (tp) REVERT: Y 71 GLU cc_start: 0.9444 (tm-30) cc_final: 0.8970 (mt-10) REVERT: Y 72 THR cc_start: 0.9488 (m) cc_final: 0.9216 (p) REVERT: Y 74 ASN cc_start: 0.9031 (m-40) cc_final: 0.8720 (m110) REVERT: Y 96 MET cc_start: 0.3490 (mpp) cc_final: 0.2638 (mtp) REVERT: Y 103 ASP cc_start: 0.8977 (t0) cc_final: 0.8699 (t0) REVERT: Y 104 ILE cc_start: 0.8706 (tt) cc_final: 0.8234 (pt) REVERT: Y 117 TRP cc_start: 0.8791 (m-10) cc_final: 0.8185 (m-90) REVERT: Y 128 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8521 (tm-30) REVERT: Y 136 LEU cc_start: 0.9560 (mt) cc_final: 0.9307 (mt) REVERT: Y 141 ILE cc_start: 0.9610 (mt) cc_final: 0.9388 (mt) REVERT: d 23 TRP cc_start: 0.9228 (t-100) cc_final: 0.8937 (t-100) REVERT: d 103 ASP cc_start: 0.8794 (t0) cc_final: 0.8477 (t0) REVERT: d 128 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9266 (mp0) REVERT: d 130 TYR cc_start: 0.8769 (t80) cc_final: 0.8362 (t80) REVERT: d 135 ILE cc_start: 0.9611 (mt) cc_final: 0.9347 (mt) REVERT: d 141 ILE cc_start: 0.9627 (mt) cc_final: 0.9391 (mt) REVERT: d 166 ASP cc_start: 0.8909 (t0) cc_final: 0.8546 (t0) REVERT: d 215 MET cc_start: 0.4272 (mtp) cc_final: 0.3561 (tpt) REVERT: e 35 GLU cc_start: 0.9349 (pm20) cc_final: 0.9036 (pm20) REVERT: e 66 MET cc_start: 0.9255 (ptp) cc_final: 0.8718 (ptp) REVERT: e 74 ASN cc_start: 0.9737 (m-40) cc_final: 0.9401 (m-40) REVERT: e 76 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8772 (mm-30) REVERT: e 104 ILE cc_start: 0.8644 (mt) cc_final: 0.8429 (mt) REVERT: e 129 ILE cc_start: 0.9599 (mt) cc_final: 0.9317 (tp) REVERT: e 154 ARG cc_start: 0.9468 (ttm110) cc_final: 0.9153 (ttm110) REVERT: e 158 LYS cc_start: 0.8444 (tptt) cc_final: 0.8235 (tppt) REVERT: e 167 ARG cc_start: 0.9024 (ptm160) cc_final: 0.8735 (ptt180) REVERT: j 189 LEU cc_start: 0.9010 (tp) cc_final: 0.8733 (tp) REVERT: j 199 LYS cc_start: 0.9414 (tttt) cc_final: 0.8935 (mtpt) REVERT: j 212 GLU cc_start: 0.9442 (pt0) cc_final: 0.9023 (pm20) REVERT: k 13 GLN cc_start: 0.9548 (tp40) cc_final: 0.9030 (mm110) REVERT: k 25 LYS cc_start: 0.9616 (mttt) cc_final: 0.9244 (ttpp) REVERT: k 26 VAL cc_start: 0.9540 (p) cc_final: 0.9332 (m) REVERT: k 32 PHE cc_start: 0.8696 (m-80) cc_final: 0.8353 (m-80) REVERT: k 40 PHE cc_start: 0.9409 (t80) cc_final: 0.9087 (t80) REVERT: k 55 MET cc_start: 0.9634 (mtp) cc_final: 0.9007 (ttm) REVERT: k 71 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8634 (mt-10) REVERT: k 72 THR cc_start: 0.9018 (m) cc_final: 0.8532 (m) REVERT: k 76 GLU cc_start: 0.9295 (mm-30) cc_final: 0.8943 (mm-30) REVERT: k 79 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8833 (tp30) REVERT: k 82 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8257 (ttp80) REVERT: k 129 ILE cc_start: 0.9284 (mt) cc_final: 0.8899 (mt) REVERT: k 131 LYS cc_start: 0.9462 (ttmt) cc_final: 0.9190 (ttmt) REVERT: k 132 ARG cc_start: 0.9043 (ptp90) cc_final: 0.8232 (ptp-170) REVERT: k 136 LEU cc_start: 0.9712 (tt) cc_final: 0.9453 (mt) REVERT: k 139 ASN cc_start: 0.9444 (m-40) cc_final: 0.8960 (m110) REVERT: k 164 TYR cc_start: 0.8767 (t80) cc_final: 0.8206 (t80) REVERT: k 175 GLU cc_start: 0.8972 (tp30) cc_final: 0.8726 (tp30) REVERT: k 176 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8309 (tm-30) REVERT: k 187 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8996 (tm-30) REVERT: k 192 GLN cc_start: 0.9339 (mt0) cc_final: 0.8908 (mt0) REVERT: k 214 MET cc_start: 0.9462 (mtt) cc_final: 0.9237 (mtt) REVERT: k 215 MET cc_start: 0.8606 (mtm) cc_final: 0.8140 (mtm) outliers start: 2 outliers final: 0 residues processed: 975 average time/residue: 0.3750 time to fit residues: 512.8669 Evaluate side-chains 778 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 778 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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: 20.0000 chunk 176 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 58 optimal weight: 30.0000 chunk 212 optimal weight: 0.0980 chunk 229 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 211 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 170 optimal weight: 50.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 4 GLN B 53 ASN B 84 HIS C 53 ASN C 112 GLN G 63 GLN G 179 GLN G 183 ASN ** H 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 139 ASN J 111 GLN N 193 ASN Y 4 GLN ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 84 HIS e 67 GLN j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 18824 Z= 0.266 Angle : 0.662 8.080 25567 Z= 0.345 Chirality : 0.045 0.247 2848 Planarity : 0.005 0.060 3345 Dihedral : 4.332 24.040 2500 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.25 % Allowed : 4.15 % Favored : 95.60 % 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: 0.01 (0.17), residues: 2338 helix: 0.39 (0.13), residues: 1445 sheet: -1.12 (0.68), residues: 55 loop : -0.37 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP J 121 HIS 0.005 0.001 HIS k 62 PHE 0.016 0.002 PHE D 168 TYR 0.026 0.002 TYR A 130 ARG 0.013 0.001 ARG e 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 937 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 932 time to evaluate : 2.273 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: A 21 ASN cc_start: 0.9528 (t0) cc_final: 0.9317 (t0) REVERT: A 25 LYS cc_start: 0.9774 (tttt) cc_final: 0.9394 (ttmm) REVERT: A 45 GLU cc_start: 0.9498 (tm-30) cc_final: 0.9170 (tm-30) REVERT: A 51 ASP cc_start: 0.8951 (m-30) cc_final: 0.8581 (m-30) REVERT: A 74 ASN cc_start: 0.9359 (m110) cc_final: 0.9074 (m-40) REVERT: A 76 GLU cc_start: 0.9527 (mm-30) cc_final: 0.9157 (mm-30) REVERT: A 96 MET cc_start: 0.6904 (mpp) cc_final: 0.6639 (mpp) REVERT: A 103 ASP cc_start: 0.8621 (m-30) cc_final: 0.8357 (m-30) REVERT: B 18 ARG cc_start: 0.9469 (mtm-85) cc_final: 0.9148 (mtm-85) REVERT: B 21 ASN cc_start: 0.9540 (m-40) cc_final: 0.9217 (m-40) REVERT: B 25 LYS cc_start: 0.9678 (mttt) cc_final: 0.9415 (mtmm) REVERT: B 28 GLU cc_start: 0.9350 (tt0) cc_final: 0.9103 (tt0) REVERT: B 39 MET cc_start: 0.9611 (tpp) cc_final: 0.9220 (tpt) REVERT: B 43 LEU cc_start: 0.8835 (mt) cc_final: 0.8349 (mt) REVERT: B 50 GLN cc_start: 0.8768 (mt0) cc_final: 0.8501 (mt0) REVERT: B 51 ASP cc_start: 0.9044 (m-30) cc_final: 0.8786 (m-30) REVERT: B 52 LEU cc_start: 0.9635 (mp) cc_final: 0.9399 (mp) REVERT: B 63 GLN cc_start: 0.8826 (mp10) cc_final: 0.8547 (mp10) REVERT: B 74 ASN cc_start: 0.9552 (m-40) cc_final: 0.9273 (m110) REVERT: B 96 MET cc_start: 0.7802 (mpp) cc_final: 0.7426 (mpp) REVERT: B 131 LYS cc_start: 0.9674 (mttt) cc_final: 0.9345 (mttt) REVERT: B 173 ARG cc_start: 0.9121 (ttt180) cc_final: 0.8836 (ptm160) REVERT: B 182 LYS cc_start: 0.9575 (mttt) cc_final: 0.9253 (mttt) REVERT: B 205 LEU cc_start: 0.6674 (mp) cc_final: 0.4937 (mp) REVERT: B 213 GLU cc_start: 0.9626 (tp30) cc_final: 0.9377 (tp30) REVERT: B 214 MET cc_start: 0.9619 (mtt) cc_final: 0.9290 (mmp) REVERT: C 25 LYS cc_start: 0.9442 (ptmm) cc_final: 0.9125 (ptpp) REVERT: C 43 LEU cc_start: 0.9408 (mt) cc_final: 0.9169 (mp) REVERT: C 51 ASP cc_start: 0.9173 (m-30) cc_final: 0.8954 (m-30) REVERT: C 76 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8627 (mm-30) REVERT: C 103 ASP cc_start: 0.8942 (m-30) cc_final: 0.8670 (m-30) REVERT: C 139 ASN cc_start: 0.9388 (m110) cc_final: 0.9121 (m110) REVERT: C 140 LYS cc_start: 0.9764 (mttt) cc_final: 0.9428 (tptp) REVERT: C 154 ARG cc_start: 0.9230 (mtp85) cc_final: 0.8571 (mmm160) REVERT: C 178 SER cc_start: 0.8451 (m) cc_final: 0.8037 (t) REVERT: D 103 ASP cc_start: 0.8968 (t0) cc_final: 0.8748 (t0) REVERT: D 114 GLN cc_start: 0.9388 (mm-40) cc_final: 0.8749 (mp10) REVERT: D 172 LEU cc_start: 0.9201 (tt) cc_final: 0.8933 (tt) REVERT: D 182 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8209 (mttt) REVERT: G 45 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8126 (mt-10) REVERT: G 57 ASN cc_start: 0.9260 (m-40) cc_final: 0.9016 (m110) REVERT: G 62 HIS cc_start: 0.7939 (m-70) cc_final: 0.7491 (m170) REVERT: G 79 GLU cc_start: 0.9268 (tm-30) cc_final: 0.8971 (tm-30) REVERT: G 82 ARG cc_start: 0.9463 (tmm-80) cc_final: 0.9145 (tmm-80) REVERT: G 128 GLU cc_start: 0.9351 (pm20) cc_final: 0.9110 (pp20) REVERT: G 132 ARG cc_start: 0.9401 (mtm110) cc_final: 0.9193 (mtm110) REVERT: G 159 GLU cc_start: 0.8429 (tt0) cc_final: 0.8183 (tt0) REVERT: G 179 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8962 (pp30) REVERT: G 187 GLU cc_start: 0.9418 (mt-10) cc_final: 0.9122 (mp0) REVERT: G 197 ASP cc_start: 0.9306 (m-30) cc_final: 0.9056 (p0) REVERT: H 23 TRP cc_start: 0.8988 (t-100) cc_final: 0.8424 (t-100) REVERT: H 50 GLN cc_start: 0.9330 (tt0) cc_final: 0.8973 (pt0) REVERT: H 51 ASP cc_start: 0.9101 (m-30) cc_final: 0.8482 (m-30) REVERT: H 102 SER cc_start: 0.8588 (m) cc_final: 0.8211 (t) REVERT: H 139 ASN cc_start: 0.9127 (m110) cc_final: 0.8858 (m-40) REVERT: H 149 SER cc_start: 0.8570 (t) cc_final: 0.8185 (t) REVERT: J 22 PHE cc_start: 0.8673 (m-80) cc_final: 0.8280 (m-80) REVERT: J 35 ASN cc_start: 0.9549 (t0) cc_final: 0.9279 (t0) REVERT: J 39 LEU cc_start: 0.9308 (mt) cc_final: 0.9031 (mt) REVERT: J 48 TYR cc_start: 0.8469 (m-80) cc_final: 0.8032 (m-80) REVERT: J 57 ILE cc_start: 0.8718 (mp) cc_final: 0.8453 (mp) REVERT: J 100 MET cc_start: 0.8987 (mmt) cc_final: 0.8712 (tpt) REVERT: J 108 ASN cc_start: 0.8438 (m-40) cc_final: 0.8089 (m110) REVERT: J 138 ILE cc_start: 0.8416 (mm) cc_final: 0.8039 (mt) REVERT: J 140 GLU cc_start: 0.9233 (mm-30) cc_final: 0.8884 (tp30) REVERT: J 142 MET cc_start: 0.8918 (mtm) cc_final: 0.8378 (mtm) REVERT: J 163 GLN cc_start: 0.8087 (tt0) cc_final: 0.7866 (tt0) REVERT: N 163 ASP cc_start: 0.9052 (m-30) cc_final: 0.8279 (t0) REVERT: N 167 ARG cc_start: 0.7046 (ptt-90) cc_final: 0.6674 (ptt-90) REVERT: N 181 VAL cc_start: 0.9470 (p) cc_final: 0.9180 (p) REVERT: N 183 ASN cc_start: 0.9360 (m-40) cc_final: 0.9160 (m-40) REVERT: N 203 LYS cc_start: 0.9153 (mtpt) cc_final: 0.8821 (ptmt) REVERT: Y 28 GLU cc_start: 0.9239 (mm-30) cc_final: 0.9021 (pt0) REVERT: Y 48 THR cc_start: 0.9097 (t) cc_final: 0.8896 (t) REVERT: Y 49 PRO cc_start: 0.9256 (Cg_exo) cc_final: 0.8910 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9298 (m-30) cc_final: 0.8887 (m-30) REVERT: Y 53 ASN cc_start: 0.9524 (m-40) cc_final: 0.9225 (m-40) REVERT: Y 55 MET cc_start: 0.8444 (tmm) cc_final: 0.8177 (tmm) REVERT: Y 67 GLN cc_start: 0.9086 (tp-100) cc_final: 0.8811 (mt0) REVERT: Y 69 LEU cc_start: 0.9648 (tp) cc_final: 0.9376 (tp) REVERT: Y 75 GLU cc_start: 0.8729 (pt0) cc_final: 0.8370 (pp20) REVERT: Y 96 MET cc_start: 0.3572 (mpp) cc_final: 0.2630 (mtp) REVERT: Y 118 MET cc_start: 0.8936 (mmp) cc_final: 0.8713 (mmm) REVERT: Y 128 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8467 (tm-30) REVERT: Y 132 ARG cc_start: 0.8916 (mtm-85) cc_final: 0.8572 (mtm-85) REVERT: Y 139 ASN cc_start: 0.9382 (m-40) cc_final: 0.9158 (m110) REVERT: d 51 ASP cc_start: 0.9094 (m-30) cc_final: 0.8889 (m-30) REVERT: d 67 GLN cc_start: 0.9515 (tp40) cc_final: 0.9247 (tt0) REVERT: d 74 ASN cc_start: 0.9115 (m110) cc_final: 0.8888 (m110) REVERT: d 103 ASP cc_start: 0.8873 (t0) cc_final: 0.8539 (t0) REVERT: d 126 VAL cc_start: 0.8840 (m) cc_final: 0.8549 (m) REVERT: d 128 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9164 (mp0) REVERT: d 132 ARG cc_start: 0.9315 (ttp-110) cc_final: 0.8689 (mtp-110) REVERT: d 214 MET cc_start: 0.8741 (mtm) cc_final: 0.8479 (mpp) REVERT: d 215 MET cc_start: 0.3890 (mtp) cc_final: 0.3645 (tpt) REVERT: e 30 LYS cc_start: 0.9154 (mttm) cc_final: 0.8935 (mtpp) REVERT: e 66 MET cc_start: 0.9349 (ptp) cc_final: 0.8886 (ptp) REVERT: e 74 ASN cc_start: 0.9734 (m-40) cc_final: 0.9433 (m110) REVERT: e 76 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8580 (mm-30) REVERT: e 111 LEU cc_start: 0.8655 (tp) cc_final: 0.8357 (tp) REVERT: e 128 GLU cc_start: 0.8939 (pm20) cc_final: 0.8570 (pm20) REVERT: e 129 ILE cc_start: 0.9616 (mt) cc_final: 0.9381 (mm) REVERT: e 167 ARG cc_start: 0.9099 (ptm160) cc_final: 0.8677 (ptt180) REVERT: j 189 LEU cc_start: 0.9034 (tp) cc_final: 0.8769 (tp) REVERT: j 199 LYS cc_start: 0.9364 (tttt) cc_final: 0.8992 (ttmm) REVERT: k 3 VAL cc_start: 0.9223 (m) cc_final: 0.8768 (t) REVERT: k 13 GLN cc_start: 0.9574 (tp40) cc_final: 0.9182 (mp10) REVERT: k 25 LYS cc_start: 0.9625 (mttt) cc_final: 0.9408 (ttpp) REVERT: k 26 VAL cc_start: 0.9546 (p) cc_final: 0.9018 (m) REVERT: k 32 PHE cc_start: 0.8708 (m-80) cc_final: 0.8305 (m-80) REVERT: k 40 PHE cc_start: 0.9417 (t80) cc_final: 0.9096 (t80) REVERT: k 50 GLN cc_start: 0.9702 (tt0) cc_final: 0.9483 (tt0) REVERT: k 55 MET cc_start: 0.9602 (mtp) cc_final: 0.9058 (ttm) REVERT: k 57 ASN cc_start: 0.9384 (m-40) cc_final: 0.9082 (m110) REVERT: k 62 HIS cc_start: 0.7851 (m-70) cc_final: 0.7239 (m170) REVERT: k 71 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8786 (mt-10) REVERT: k 72 THR cc_start: 0.9034 (m) cc_final: 0.8495 (m) REVERT: k 76 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8861 (mm-30) REVERT: k 79 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8876 (tm-30) REVERT: k 111 LEU cc_start: 0.8209 (tt) cc_final: 0.7826 (tt) REVERT: k 129 ILE cc_start: 0.9264 (mt) cc_final: 0.8820 (mm) REVERT: k 131 LYS cc_start: 0.9478 (ttmt) cc_final: 0.9227 (ttmt) REVERT: k 132 ARG cc_start: 0.9133 (ptp90) cc_final: 0.8212 (ptp-170) REVERT: k 136 LEU cc_start: 0.9715 (tt) cc_final: 0.9453 (mt) REVERT: k 139 ASN cc_start: 0.9436 (m-40) cc_final: 0.8953 (m110) REVERT: k 164 TYR cc_start: 0.8836 (t80) cc_final: 0.8094 (t80) REVERT: k 176 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8584 (tm-30) REVERT: k 185 MET cc_start: 0.9422 (mtm) cc_final: 0.9138 (mtm) REVERT: k 187 GLU cc_start: 0.9286 (mt-10) cc_final: 0.9052 (tm-30) REVERT: k 212 GLU cc_start: 0.8571 (pm20) cc_final: 0.8189 (pm20) REVERT: k 213 GLU cc_start: 0.9211 (mp0) cc_final: 0.8795 (mp0) REVERT: k 214 MET cc_start: 0.9555 (mtt) cc_final: 0.9252 (mtt) REVERT: k 215 MET cc_start: 0.8469 (mtm) cc_final: 0.8205 (mtp) outliers start: 5 outliers final: 0 residues processed: 935 average time/residue: 0.3801 time to fit residues: 499.7887 Evaluate side-chains 770 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 769 time to evaluate : 2.217 ------------------------------------------------------------------------------- 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: 7.9990 chunk 160 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 101 optimal weight: 0.1980 chunk 142 optimal weight: 5.9990 chunk 213 optimal weight: 1.9990 chunk 226 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 202 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN C 112 GLN C 193 ASN D 74 ASN ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 GLN ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 18824 Z= 0.241 Angle : 0.649 8.690 25567 Z= 0.337 Chirality : 0.045 0.248 2848 Planarity : 0.005 0.088 3345 Dihedral : 4.411 24.530 2500 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.05 % Allowed : 3.30 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.17), residues: 2338 helix: 0.49 (0.14), residues: 1445 sheet: -1.09 (0.60), residues: 64 loop : -0.30 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP e 117 HIS 0.005 0.001 HIS G 87 PHE 0.015 0.002 PHE D 168 TYR 0.027 0.002 TYR B 145 ARG 0.008 0.001 ARG C 162 *********************** 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 913 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 912 time to evaluate : 2.041 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: A 25 LYS cc_start: 0.9805 (tttt) cc_final: 0.9500 (ttmm) REVERT: A 45 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9190 (tm-30) REVERT: A 50 GLN cc_start: 0.9376 (tm-30) cc_final: 0.9169 (tm-30) REVERT: A 51 ASP cc_start: 0.9177 (m-30) cc_final: 0.8510 (m-30) REVERT: A 52 LEU cc_start: 0.9747 (mt) cc_final: 0.9463 (mt) REVERT: A 53 ASN cc_start: 0.9339 (m-40) cc_final: 0.9129 (m110) REVERT: A 76 GLU cc_start: 0.9532 (mm-30) cc_final: 0.9179 (mm-30) REVERT: B 21 ASN cc_start: 0.9554 (m-40) cc_final: 0.9320 (m-40) REVERT: B 28 GLU cc_start: 0.9391 (tt0) cc_final: 0.9136 (tt0) REVERT: B 32 PHE cc_start: 0.8818 (m-80) cc_final: 0.8582 (m-80) REVERT: B 33 SER cc_start: 0.8627 (m) cc_final: 0.8413 (t) REVERT: B 39 MET cc_start: 0.9612 (tpp) cc_final: 0.9249 (tpt) REVERT: B 43 LEU cc_start: 0.8768 (mt) cc_final: 0.8272 (mt) REVERT: B 51 ASP cc_start: 0.9015 (m-30) cc_final: 0.8758 (m-30) REVERT: B 52 LEU cc_start: 0.9635 (mp) cc_final: 0.9383 (mp) REVERT: B 66 MET cc_start: 0.9176 (mmm) cc_final: 0.8700 (mmm) REVERT: B 74 ASN cc_start: 0.9548 (m-40) cc_final: 0.9245 (m110) REVERT: B 96 MET cc_start: 0.7772 (mpp) cc_final: 0.7439 (mpp) REVERT: B 173 ARG cc_start: 0.9118 (ttt180) cc_final: 0.8863 (ptm160) REVERT: B 182 LYS cc_start: 0.9552 (mttt) cc_final: 0.9186 (mttt) REVERT: B 205 LEU cc_start: 0.6808 (mp) cc_final: 0.6095 (mp) REVERT: C 25 LYS cc_start: 0.9425 (ptmm) cc_final: 0.9156 (pttm) REVERT: C 103 ASP cc_start: 0.8949 (m-30) cc_final: 0.8719 (m-30) REVERT: C 140 LYS cc_start: 0.9763 (mttt) cc_final: 0.9390 (tptp) REVERT: C 154 ARG cc_start: 0.9208 (mtp85) cc_final: 0.8576 (mmm160) REVERT: C 178 SER cc_start: 0.8608 (m) cc_final: 0.8317 (t) REVERT: C 189 LEU cc_start: 0.9384 (mm) cc_final: 0.9167 (mm) REVERT: C 215 MET cc_start: 0.9477 (mtp) cc_final: 0.9228 (tmm) REVERT: D 103 ASP cc_start: 0.9021 (t0) cc_final: 0.8320 (t0) REVERT: D 104 ILE cc_start: 0.7813 (tp) cc_final: 0.7587 (tp) REVERT: D 114 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8751 (mp10) REVERT: D 118 MET cc_start: 0.9053 (mmp) cc_final: 0.8836 (mmp) REVERT: D 139 ASN cc_start: 0.9437 (m110) cc_final: 0.9219 (m110) REVERT: D 172 LEU cc_start: 0.9217 (tt) cc_final: 0.8916 (tt) REVERT: G 23 TRP cc_start: 0.9069 (t60) cc_final: 0.8770 (t60) REVERT: G 27 VAL cc_start: 0.9353 (p) cc_final: 0.9066 (m) REVERT: G 57 ASN cc_start: 0.9260 (m-40) cc_final: 0.9014 (m110) REVERT: G 62 HIS cc_start: 0.7835 (m-70) cc_final: 0.7507 (m170) REVERT: G 79 GLU cc_start: 0.9279 (tm-30) cc_final: 0.8766 (tm-30) REVERT: G 81 ASP cc_start: 0.9250 (m-30) cc_final: 0.8833 (m-30) REVERT: G 82 ARG cc_start: 0.9462 (tmm-80) cc_final: 0.9255 (tmm-80) REVERT: G 132 ARG cc_start: 0.9478 (mtm110) cc_final: 0.9264 (mtm110) REVERT: G 143 ARG cc_start: 0.8556 (tpp-160) cc_final: 0.8273 (tpp-160) REVERT: G 159 GLU cc_start: 0.8463 (tt0) cc_final: 0.8228 (tt0) REVERT: G 182 LYS cc_start: 0.9109 (mtpt) cc_final: 0.8721 (mtpp) REVERT: G 187 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9131 (mp0) REVERT: G 197 ASP cc_start: 0.9314 (m-30) cc_final: 0.9011 (p0) REVERT: H 50 GLN cc_start: 0.9327 (tt0) cc_final: 0.8956 (pt0) REVERT: H 51 ASP cc_start: 0.8850 (m-30) cc_final: 0.8484 (m-30) REVERT: H 66 MET cc_start: 0.9298 (mmp) cc_final: 0.8868 (mmm) REVERT: H 79 GLU cc_start: 0.9630 (mm-30) cc_final: 0.9328 (mm-30) REVERT: H 80 TRP cc_start: 0.8877 (t60) cc_final: 0.7644 (t60) REVERT: H 132 ARG cc_start: 0.9324 (ptp-110) cc_final: 0.9077 (mtm110) REVERT: H 149 SER cc_start: 0.8598 (t) cc_final: 0.8212 (t) REVERT: J 10 ILE cc_start: 0.8261 (mp) cc_final: 0.7986 (mp) REVERT: J 22 PHE cc_start: 0.8832 (m-80) cc_final: 0.8461 (m-80) REVERT: J 37 ARG cc_start: 0.9249 (ttt-90) cc_final: 0.8929 (ptm-80) REVERT: J 39 LEU cc_start: 0.9271 (mt) cc_final: 0.8987 (mt) REVERT: J 53 PHE cc_start: 0.9102 (m-80) cc_final: 0.8430 (m-80) REVERT: J 57 ILE cc_start: 0.8625 (mp) cc_final: 0.8254 (mp) REVERT: J 100 MET cc_start: 0.8977 (mmt) cc_final: 0.8697 (tpt) REVERT: J 108 ASN cc_start: 0.8449 (m-40) cc_final: 0.7867 (m110) REVERT: J 111 GLN cc_start: 0.8164 (mt0) cc_final: 0.7859 (mm-40) REVERT: J 138 ILE cc_start: 0.8379 (mm) cc_final: 0.7960 (mm) REVERT: J 142 MET cc_start: 0.8955 (mtm) cc_final: 0.8405 (mtm) REVERT: N 163 ASP cc_start: 0.9036 (m-30) cc_final: 0.8201 (t0) REVERT: N 167 ARG cc_start: 0.6961 (ptt-90) cc_final: 0.6580 (ptt-90) REVERT: N 181 VAL cc_start: 0.9421 (p) cc_final: 0.9103 (p) REVERT: N 203 LYS cc_start: 0.9111 (mtpt) cc_final: 0.8761 (ptmt) REVERT: N 205 LEU cc_start: 0.7462 (tt) cc_final: 0.6756 (tt) REVERT: N 214 MET cc_start: 0.8434 (mtm) cc_final: 0.7976 (mmp) REVERT: Y 15 ILE cc_start: 0.9241 (mm) cc_final: 0.8984 (mm) REVERT: Y 48 THR cc_start: 0.9084 (t) cc_final: 0.8856 (t) REVERT: Y 49 PRO cc_start: 0.9335 (Cg_exo) cc_final: 0.8964 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9321 (m-30) cc_final: 0.8912 (m-30) REVERT: Y 52 LEU cc_start: 0.9436 (mt) cc_final: 0.9170 (mt) REVERT: Y 53 ASN cc_start: 0.9503 (m-40) cc_final: 0.9246 (m-40) REVERT: Y 55 MET cc_start: 0.8505 (tmm) cc_final: 0.8144 (tmm) REVERT: Y 67 GLN cc_start: 0.9145 (tp-100) cc_final: 0.8859 (mt0) REVERT: Y 74 ASN cc_start: 0.9027 (m-40) cc_final: 0.8732 (m-40) REVERT: Y 75 GLU cc_start: 0.8833 (pt0) cc_final: 0.8376 (pp20) REVERT: Y 96 MET cc_start: 0.3335 (mpp) cc_final: 0.2335 (mtp) REVERT: d 74 ASN cc_start: 0.9094 (m110) cc_final: 0.8866 (m110) REVERT: d 103 ASP cc_start: 0.8820 (t0) cc_final: 0.8479 (t0) REVERT: d 126 VAL cc_start: 0.8787 (m) cc_final: 0.8484 (m) REVERT: d 128 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9272 (mp0) REVERT: d 136 LEU cc_start: 0.9455 (tt) cc_final: 0.9197 (tt) REVERT: d 139 ASN cc_start: 0.9518 (m110) cc_final: 0.9272 (m110) REVERT: d 140 LYS cc_start: 0.9052 (mppt) cc_final: 0.8709 (mptt) REVERT: d 141 ILE cc_start: 0.9640 (mt) cc_final: 0.9409 (mt) REVERT: d 215 MET cc_start: 0.3819 (mtp) cc_final: 0.3465 (tpt) REVERT: e 50 GLN cc_start: 0.9089 (mt0) cc_final: 0.8855 (mt0) REVERT: e 66 MET cc_start: 0.9358 (ptp) cc_final: 0.8887 (ptp) REVERT: e 74 ASN cc_start: 0.9740 (m-40) cc_final: 0.9414 (m110) REVERT: e 76 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8698 (mm-30) REVERT: e 111 LEU cc_start: 0.8703 (tp) cc_final: 0.8203 (tp) REVERT: e 167 ARG cc_start: 0.9092 (ptm160) cc_final: 0.8647 (ptt180) REVERT: j 162 ARG cc_start: 0.8397 (mmm160) cc_final: 0.8137 (mmp80) REVERT: j 166 ASP cc_start: 0.9031 (m-30) cc_final: 0.8828 (m-30) REVERT: j 189 LEU cc_start: 0.9056 (tp) cc_final: 0.8809 (tp) REVERT: j 199 LYS cc_start: 0.9353 (tttt) cc_final: 0.8954 (ttmm) REVERT: j 212 GLU cc_start: 0.9515 (pt0) cc_final: 0.9170 (pm20) REVERT: k 18 ARG cc_start: 0.9287 (ptm160) cc_final: 0.8864 (ptm160) REVERT: k 25 LYS cc_start: 0.9594 (mttt) cc_final: 0.8995 (ttpp) REVERT: k 26 VAL cc_start: 0.9377 (p) cc_final: 0.9108 (m) REVERT: k 29 GLU cc_start: 0.8173 (pm20) cc_final: 0.7885 (mp0) REVERT: k 32 PHE cc_start: 0.8649 (m-80) cc_final: 0.8404 (m-80) REVERT: k 40 PHE cc_start: 0.9466 (t80) cc_final: 0.9172 (t80) REVERT: k 50 GLN cc_start: 0.9701 (tt0) cc_final: 0.9474 (tt0) REVERT: k 55 MET cc_start: 0.9632 (mtp) cc_final: 0.9107 (ttm) REVERT: k 66 MET cc_start: 0.9391 (mmp) cc_final: 0.9161 (mmt) REVERT: k 71 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8711 (mt-10) REVERT: k 72 THR cc_start: 0.9075 (m) cc_final: 0.8524 (m) REVERT: k 76 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8904 (mm-30) REVERT: k 79 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8884 (tm-30) REVERT: k 111 LEU cc_start: 0.8323 (tt) cc_final: 0.7938 (tt) REVERT: k 129 ILE cc_start: 0.9266 (mt) cc_final: 0.8697 (mm) REVERT: k 131 LYS cc_start: 0.9471 (ttmt) cc_final: 0.9190 (ttmt) REVERT: k 132 ARG cc_start: 0.9164 (ptp90) cc_final: 0.8147 (ptp-170) REVERT: k 136 LEU cc_start: 0.9714 (tt) cc_final: 0.9448 (mt) REVERT: k 139 ASN cc_start: 0.9434 (m-40) cc_final: 0.8954 (m110) REVERT: k 154 ARG cc_start: 0.9149 (mmm-85) cc_final: 0.8725 (mmm160) REVERT: k 175 GLU cc_start: 0.8934 (tp30) cc_final: 0.8667 (tm-30) REVERT: k 176 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8551 (tm-30) REVERT: k 187 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9100 (tm-30) REVERT: k 212 GLU cc_start: 0.8354 (pm20) cc_final: 0.8084 (pm20) REVERT: k 213 GLU cc_start: 0.9147 (mp0) cc_final: 0.8684 (mp0) REVERT: k 214 MET cc_start: 0.9562 (mtt) cc_final: 0.9256 (mtt) outliers start: 1 outliers final: 0 residues processed: 913 average time/residue: 0.3829 time to fit residues: 494.1505 Evaluate side-chains 747 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 747 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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: 6.9990 chunk 128 optimal weight: 0.0070 chunk 3 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 20.0000 chunk 156 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 115 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN A 112 GLN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN D 74 ASN ** G 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS J 35 ASN ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 112 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.6429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 18824 Z= 0.226 Angle : 0.646 8.483 25567 Z= 0.333 Chirality : 0.044 0.196 2848 Planarity : 0.005 0.060 3345 Dihedral : 4.401 23.592 2500 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.15 % Allowed : 3.20 % Favored : 96.65 % 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: 0.30 (0.17), residues: 2338 helix: 0.62 (0.14), residues: 1430 sheet: -1.12 (0.56), residues: 70 loop : -0.22 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP G 117 HIS 0.003 0.001 HIS d 62 PHE 0.022 0.002 PHE C 161 TYR 0.027 0.002 TYR D 169 ARG 0.009 0.001 ARG H 143 *********************** 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 889 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 886 time to evaluate : 2.101 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: A 21 ASN cc_start: 0.9525 (t0) cc_final: 0.9311 (t0) REVERT: A 25 LYS cc_start: 0.9685 (tttt) cc_final: 0.9399 (ttmm) REVERT: A 29 GLU cc_start: 0.9256 (pm20) cc_final: 0.8998 (pm20) REVERT: A 45 GLU cc_start: 0.9516 (tm-30) cc_final: 0.9229 (tm-30) REVERT: A 52 LEU cc_start: 0.9757 (mt) cc_final: 0.9527 (mt) REVERT: A 55 MET cc_start: 0.9418 (ttp) cc_final: 0.9186 (tmm) REVERT: A 74 ASN cc_start: 0.9363 (m-40) cc_final: 0.9143 (m110) REVERT: A 76 GLU cc_start: 0.9545 (mm-30) cc_final: 0.9202 (mm-30) REVERT: A 96 MET cc_start: 0.6952 (mpp) cc_final: 0.6484 (mtp) REVERT: B 18 ARG cc_start: 0.9435 (mtm-85) cc_final: 0.9126 (mtm-85) REVERT: B 21 ASN cc_start: 0.9555 (m-40) cc_final: 0.9318 (m-40) REVERT: B 28 GLU cc_start: 0.9406 (tt0) cc_final: 0.9184 (tt0) REVERT: B 32 PHE cc_start: 0.8909 (m-80) cc_final: 0.8692 (m-80) REVERT: B 33 SER cc_start: 0.8554 (m) cc_final: 0.8342 (t) REVERT: B 39 MET cc_start: 0.9620 (tpp) cc_final: 0.9157 (tpt) REVERT: B 43 LEU cc_start: 0.8832 (mt) cc_final: 0.8231 (mt) REVERT: B 51 ASP cc_start: 0.8956 (m-30) cc_final: 0.8690 (m-30) REVERT: B 52 LEU cc_start: 0.9651 (mp) cc_final: 0.9388 (mp) REVERT: B 68 MET cc_start: 0.8220 (mtm) cc_final: 0.7910 (mtt) REVERT: B 74 ASN cc_start: 0.9530 (m-40) cc_final: 0.9166 (m110) REVERT: B 96 MET cc_start: 0.7806 (mpp) cc_final: 0.7314 (mpp) REVERT: B 154 ARG cc_start: 0.9092 (ttm-80) cc_final: 0.8457 (tpt170) REVERT: B 173 ARG cc_start: 0.9127 (ttt180) cc_final: 0.8886 (ptm160) REVERT: B 175 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8325 (tm-30) REVERT: B 182 LYS cc_start: 0.9569 (mttt) cc_final: 0.9102 (mttt) REVERT: B 205 LEU cc_start: 0.6972 (mp) cc_final: 0.5695 (mp) REVERT: B 213 GLU cc_start: 0.9631 (tp30) cc_final: 0.9337 (tp30) REVERT: B 215 MET cc_start: 0.8334 (ttt) cc_final: 0.7936 (ttm) REVERT: C 25 LYS cc_start: 0.9427 (ptmm) cc_final: 0.9160 (pttm) REVERT: C 103 ASP cc_start: 0.8971 (m-30) cc_final: 0.8723 (m-30) REVERT: C 108 THR cc_start: 0.9554 (p) cc_final: 0.9353 (p) REVERT: C 140 LYS cc_start: 0.9765 (mttt) cc_final: 0.9376 (tptp) REVERT: C 154 ARG cc_start: 0.9284 (mtp85) cc_final: 0.8648 (mmm160) REVERT: C 167 ARG cc_start: 0.9345 (ttm110) cc_final: 0.9111 (ttp-110) REVERT: C 178 SER cc_start: 0.8797 (m) cc_final: 0.8528 (t) REVERT: D 114 GLN cc_start: 0.9423 (mm-40) cc_final: 0.8791 (mp10) REVERT: G 45 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8256 (mt-10) REVERT: G 57 ASN cc_start: 0.9272 (m-40) cc_final: 0.9027 (m110) REVERT: G 62 HIS cc_start: 0.7994 (m-70) cc_final: 0.7530 (m170) REVERT: G 79 GLU cc_start: 0.9299 (tm-30) cc_final: 0.8885 (tm-30) REVERT: G 82 ARG cc_start: 0.9442 (tmm-80) cc_final: 0.9201 (tmm-80) REVERT: G 128 GLU cc_start: 0.8931 (pp20) cc_final: 0.8695 (pm20) REVERT: G 159 GLU cc_start: 0.8525 (tt0) cc_final: 0.8315 (tt0) REVERT: G 187 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9127 (mp0) REVERT: G 197 ASP cc_start: 0.9322 (m-30) cc_final: 0.9021 (p0) REVERT: G 203 LYS cc_start: 0.9313 (mttp) cc_final: 0.9103 (mttp) REVERT: H 23 TRP cc_start: 0.8893 (t-100) cc_final: 0.8083 (t60) REVERT: H 50 GLN cc_start: 0.9572 (tt0) cc_final: 0.9157 (pt0) REVERT: H 51 ASP cc_start: 0.9014 (m-30) cc_final: 0.8314 (m-30) REVERT: H 55 MET cc_start: 0.9123 (tpp) cc_final: 0.8689 (tpt) REVERT: H 79 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9146 (mm-30) REVERT: H 80 TRP cc_start: 0.8949 (t60) cc_final: 0.8086 (t60) REVERT: H 86 VAL cc_start: 0.7549 (p) cc_final: 0.7294 (t) REVERT: H 96 MET cc_start: 0.3908 (ptp) cc_final: 0.3461 (ptp) REVERT: H 103 ASP cc_start: 0.9121 (m-30) cc_final: 0.8902 (m-30) REVERT: H 132 ARG cc_start: 0.9327 (ptp-110) cc_final: 0.9074 (mtm110) REVERT: H 143 ARG cc_start: 0.8968 (mtm-85) cc_final: 0.8295 (mtm110) REVERT: H 149 SER cc_start: 0.8614 (t) cc_final: 0.8215 (t) REVERT: J 8 PHE cc_start: 0.8315 (m-80) cc_final: 0.7967 (m-10) REVERT: J 22 PHE cc_start: 0.8921 (m-80) cc_final: 0.8528 (m-80) REVERT: J 48 TYR cc_start: 0.8491 (m-80) cc_final: 0.7971 (m-80) REVERT: J 53 PHE cc_start: 0.9151 (m-80) cc_final: 0.8209 (m-80) REVERT: J 57 ILE cc_start: 0.8653 (mp) cc_final: 0.8285 (mp) REVERT: J 100 MET cc_start: 0.8923 (mmt) cc_final: 0.8722 (tpt) REVERT: J 108 ASN cc_start: 0.8450 (m-40) cc_final: 0.7926 (m110) REVERT: J 138 ILE cc_start: 0.8398 (mm) cc_final: 0.7818 (mm) REVERT: J 142 MET cc_start: 0.8895 (mtm) cc_final: 0.8475 (mtm) REVERT: N 163 ASP cc_start: 0.9087 (m-30) cc_final: 0.8201 (t0) REVERT: N 167 ARG cc_start: 0.7049 (ptt-90) cc_final: 0.6691 (ptt-90) REVERT: N 181 VAL cc_start: 0.9378 (p) cc_final: 0.9060 (p) REVERT: N 183 ASN cc_start: 0.9362 (m-40) cc_final: 0.9147 (m-40) REVERT: N 203 LYS cc_start: 0.9091 (mtpt) cc_final: 0.8750 (ptmt) REVERT: Y 39 MET cc_start: 0.9650 (ttt) cc_final: 0.9435 (ttt) REVERT: Y 49 PRO cc_start: 0.9271 (Cg_exo) cc_final: 0.9031 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9309 (m-30) cc_final: 0.8876 (m-30) REVERT: Y 53 ASN cc_start: 0.9507 (m-40) cc_final: 0.9214 (m-40) REVERT: Y 75 GLU cc_start: 0.8847 (pt0) cc_final: 0.8367 (pp20) REVERT: Y 96 MET cc_start: 0.3095 (mpp) cc_final: 0.2211 (mtp) REVERT: Y 114 GLN cc_start: 0.9271 (mt0) cc_final: 0.8951 (mt0) REVERT: Y 117 TRP cc_start: 0.8883 (m-10) cc_final: 0.8498 (m-90) REVERT: Y 144 MET cc_start: 0.8963 (ttt) cc_final: 0.8548 (ttt) REVERT: d 74 ASN cc_start: 0.9073 (m110) cc_final: 0.8854 (m110) REVERT: d 103 ASP cc_start: 0.8826 (t0) cc_final: 0.8478 (t0) REVERT: d 126 VAL cc_start: 0.8765 (m) cc_final: 0.8362 (m) REVERT: d 128 GLU cc_start: 0.9649 (mm-30) cc_final: 0.9260 (mp0) REVERT: d 139 ASN cc_start: 0.9508 (m110) cc_final: 0.9298 (m110) REVERT: d 189 LEU cc_start: 0.9367 (mp) cc_final: 0.9009 (mt) REVERT: e 50 GLN cc_start: 0.9147 (mt0) cc_final: 0.8911 (mt0) REVERT: e 66 MET cc_start: 0.9420 (ptp) cc_final: 0.8900 (ptp) REVERT: e 68 MET cc_start: 0.8767 (mtt) cc_final: 0.8483 (mtt) REVERT: e 74 ASN cc_start: 0.9747 (m-40) cc_final: 0.9430 (m110) REVERT: e 76 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8634 (mm-30) REVERT: e 111 LEU cc_start: 0.8761 (tp) cc_final: 0.8275 (tp) REVERT: e 167 ARG cc_start: 0.9107 (ptm160) cc_final: 0.8675 (ptt180) REVERT: e 173 ARG cc_start: 0.8933 (ttt180) cc_final: 0.8720 (ttt180) REVERT: j 189 LEU cc_start: 0.9087 (tp) cc_final: 0.8837 (tp) REVERT: j 199 LYS cc_start: 0.9339 (tttt) cc_final: 0.8901 (ttmm) REVERT: j 212 GLU cc_start: 0.9472 (pt0) cc_final: 0.9266 (pm20) REVERT: k 18 ARG cc_start: 0.9255 (ptm160) cc_final: 0.8926 (ptm160) REVERT: k 25 LYS cc_start: 0.9564 (mttt) cc_final: 0.9110 (ttpp) REVERT: k 26 VAL cc_start: 0.9472 (p) cc_final: 0.9171 (m) REVERT: k 29 GLU cc_start: 0.8203 (pm20) cc_final: 0.7748 (mp0) REVERT: k 32 PHE cc_start: 0.8714 (m-80) cc_final: 0.8426 (m-80) REVERT: k 40 PHE cc_start: 0.9445 (t80) cc_final: 0.9137 (t80) REVERT: k 50 GLN cc_start: 0.9702 (tt0) cc_final: 0.9470 (tt0) REVERT: k 55 MET cc_start: 0.9643 (mtp) cc_final: 0.9096 (ttm) REVERT: k 66 MET cc_start: 0.9403 (mmp) cc_final: 0.9148 (mmt) REVERT: k 71 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8701 (mt-10) REVERT: k 72 THR cc_start: 0.9064 (m) cc_final: 0.8419 (m) REVERT: k 76 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8928 (mm-30) REVERT: k 79 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8856 (tm-30) REVERT: k 111 LEU cc_start: 0.8278 (tt) cc_final: 0.7850 (tt) REVERT: k 128 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9085 (mm-30) REVERT: k 129 ILE cc_start: 0.9261 (mt) cc_final: 0.8740 (mm) REVERT: k 131 LYS cc_start: 0.9475 (ttmt) cc_final: 0.9180 (ttmt) REVERT: k 132 ARG cc_start: 0.9190 (ptp90) cc_final: 0.8199 (ptp-170) REVERT: k 139 ASN cc_start: 0.9433 (m-40) cc_final: 0.8972 (m110) REVERT: k 154 ARG cc_start: 0.9254 (mmm-85) cc_final: 0.8850 (mmm-85) REVERT: k 164 TYR cc_start: 0.8377 (t80) cc_final: 0.7313 (t80) REVERT: k 175 GLU cc_start: 0.8963 (tp30) cc_final: 0.8714 (tm-30) REVERT: k 176 GLN cc_start: 0.8895 (tm-30) cc_final: 0.8568 (tm-30) REVERT: k 187 GLU cc_start: 0.9439 (mt-10) cc_final: 0.9106 (tm-30) REVERT: k 193 ASN cc_start: 0.9010 (m110) cc_final: 0.8142 (m110) REVERT: k 213 GLU cc_start: 0.9088 (mp0) cc_final: 0.8642 (mp0) REVERT: k 214 MET cc_start: 0.9550 (mtt) cc_final: 0.9250 (mtt) REVERT: k 215 MET cc_start: 0.8614 (mtp) cc_final: 0.8357 (mtp) outliers start: 3 outliers final: 1 residues processed: 887 average time/residue: 0.3844 time to fit residues: 480.9458 Evaluate side-chains 729 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 728 time to evaluate : 2.150 ------------------------------------------------------------------------------- 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: 10.0000 chunk 203 optimal weight: 8.9990 chunk 44 optimal weight: 50.0000 chunk 132 optimal weight: 30.0000 chunk 55 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 104 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN ** D 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 HIS ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 195 ASN j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 18824 Z= 0.253 Angle : 0.662 8.676 25567 Z= 0.340 Chirality : 0.044 0.191 2848 Planarity : 0.006 0.167 3345 Dihedral : 4.440 23.584 2500 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % 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: 0.24 (0.17), residues: 2338 helix: 0.58 (0.14), residues: 1450 sheet: -1.49 (0.47), residues: 88 loop : -0.20 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 117 HIS 0.006 0.001 HIS J 54 PHE 0.021 0.002 PHE J 83 TYR 0.018 0.002 TYR Y 130 ARG 0.011 0.001 ARG d 143 *********************** 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 866 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 865 time to evaluate : 2.072 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: A 21 ASN cc_start: 0.9539 (t0) cc_final: 0.9260 (t0) REVERT: A 45 GLU cc_start: 0.9531 (tm-30) cc_final: 0.9218 (tm-30) REVERT: A 52 LEU cc_start: 0.9725 (mt) cc_final: 0.9395 (mt) REVERT: A 74 ASN cc_start: 0.9351 (m-40) cc_final: 0.9107 (m110) REVERT: A 76 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9190 (mm-30) REVERT: B 21 ASN cc_start: 0.9566 (m-40) cc_final: 0.9292 (m-40) REVERT: B 28 GLU cc_start: 0.9410 (tt0) cc_final: 0.9202 (tt0) REVERT: B 39 MET cc_start: 0.9635 (tpp) cc_final: 0.9059 (tpt) REVERT: B 43 LEU cc_start: 0.8867 (mt) cc_final: 0.8163 (mt) REVERT: B 51 ASP cc_start: 0.8993 (m-30) cc_final: 0.8780 (m-30) REVERT: B 52 LEU cc_start: 0.9616 (mp) cc_final: 0.9382 (mp) REVERT: B 66 MET cc_start: 0.9205 (mmm) cc_final: 0.8662 (mmm) REVERT: B 74 ASN cc_start: 0.9540 (m-40) cc_final: 0.9163 (m110) REVERT: B 75 GLU cc_start: 0.8713 (pt0) cc_final: 0.8487 (pt0) REVERT: B 96 MET cc_start: 0.7875 (mpp) cc_final: 0.7494 (mpp) REVERT: B 173 ARG cc_start: 0.9176 (ttt180) cc_final: 0.8919 (ptm160) REVERT: B 175 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8410 (tm-30) REVERT: B 205 LEU cc_start: 0.7206 (mp) cc_final: 0.5926 (mp) REVERT: B 213 GLU cc_start: 0.9655 (tp30) cc_final: 0.9389 (tp30) REVERT: C 25 LYS cc_start: 0.9397 (ptmm) cc_final: 0.9174 (pttm) REVERT: C 56 LEU cc_start: 0.9499 (mt) cc_final: 0.9284 (mt) REVERT: C 103 ASP cc_start: 0.9028 (m-30) cc_final: 0.8762 (m-30) REVERT: C 108 THR cc_start: 0.9565 (p) cc_final: 0.9346 (p) REVERT: C 140 LYS cc_start: 0.9770 (mttt) cc_final: 0.9452 (tmtt) REVERT: C 154 ARG cc_start: 0.9327 (mtp85) cc_final: 0.8634 (mmm-85) REVERT: C 219 GLN cc_start: 0.9247 (tp-100) cc_final: 0.8747 (tm-30) REVERT: D 103 ASP cc_start: 0.8888 (t0) cc_final: 0.8107 (t0) REVERT: D 114 GLN cc_start: 0.9463 (mm-40) cc_final: 0.8728 (mp10) REVERT: D 118 MET cc_start: 0.9154 (mmp) cc_final: 0.8930 (mmp) REVERT: G 45 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8293 (mt-10) REVERT: G 57 ASN cc_start: 0.9285 (m-40) cc_final: 0.9042 (m110) REVERT: G 62 HIS cc_start: 0.7969 (m-70) cc_final: 0.7565 (m170) REVERT: G 79 GLU cc_start: 0.9299 (tm-30) cc_final: 0.8849 (tm-30) REVERT: G 82 ARG cc_start: 0.9440 (tmm-80) cc_final: 0.9176 (tmm-80) REVERT: G 182 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8764 (mtpp) REVERT: G 187 GLU cc_start: 0.9421 (mt-10) cc_final: 0.9123 (mp0) REVERT: G 197 ASP cc_start: 0.9303 (m-30) cc_final: 0.9013 (p0) REVERT: G 203 LYS cc_start: 0.9324 (mttp) cc_final: 0.9111 (mttp) REVERT: H 23 TRP cc_start: 0.8867 (t-100) cc_final: 0.8101 (t60) REVERT: H 50 GLN cc_start: 0.9566 (tt0) cc_final: 0.9101 (pt0) REVERT: H 51 ASP cc_start: 0.9041 (m-30) cc_final: 0.8323 (m-30) REVERT: H 55 MET cc_start: 0.9095 (tpp) cc_final: 0.8682 (tpt) REVERT: H 66 MET cc_start: 0.9259 (mmp) cc_final: 0.8756 (mmm) REVERT: H 80 TRP cc_start: 0.8674 (t60) cc_final: 0.8062 (t60) REVERT: H 86 VAL cc_start: 0.7691 (p) cc_final: 0.7414 (t) REVERT: H 143 ARG cc_start: 0.8865 (mtm-85) cc_final: 0.8383 (mtm-85) REVERT: H 149 SER cc_start: 0.8655 (t) cc_final: 0.8258 (t) REVERT: J 8 PHE cc_start: 0.8353 (m-80) cc_final: 0.7990 (m-10) REVERT: J 22 PHE cc_start: 0.8955 (m-80) cc_final: 0.8540 (m-80) REVERT: J 48 TYR cc_start: 0.8498 (m-80) cc_final: 0.7974 (m-80) REVERT: J 53 PHE cc_start: 0.9149 (m-80) cc_final: 0.8267 (m-80) REVERT: J 57 ILE cc_start: 0.8615 (mp) cc_final: 0.8165 (mp) REVERT: J 138 ILE cc_start: 0.8335 (mm) cc_final: 0.7768 (mm) REVERT: J 142 MET cc_start: 0.8798 (mtm) cc_final: 0.8377 (mtp) REVERT: N 163 ASP cc_start: 0.9157 (m-30) cc_final: 0.8261 (t0) REVERT: N 167 ARG cc_start: 0.7040 (ptt-90) cc_final: 0.6735 (ptt-90) REVERT: N 203 LYS cc_start: 0.9038 (mtpt) cc_final: 0.8699 (ptmt) REVERT: Y 25 LYS cc_start: 0.9505 (ptmm) cc_final: 0.9257 (ptmm) REVERT: Y 49 PRO cc_start: 0.9430 (Cg_exo) cc_final: 0.9093 (Cg_endo) REVERT: Y 51 ASP cc_start: 0.9339 (m-30) cc_final: 0.8942 (m-30) REVERT: Y 53 ASN cc_start: 0.9525 (m-40) cc_final: 0.9234 (m-40) REVERT: Y 75 GLU cc_start: 0.8938 (pt0) cc_final: 0.8470 (pp20) REVERT: Y 96 MET cc_start: 0.2981 (mpp) cc_final: 0.2127 (mtp) REVERT: Y 114 GLN cc_start: 0.9277 (mt0) cc_final: 0.8957 (mt0) REVERT: Y 117 TRP cc_start: 0.8982 (m-10) cc_final: 0.8560 (m-90) REVERT: Y 144 MET cc_start: 0.8867 (ttt) cc_final: 0.8619 (ttt) REVERT: d 74 ASN cc_start: 0.9067 (m110) cc_final: 0.8855 (m110) REVERT: d 126 VAL cc_start: 0.8720 (m) cc_final: 0.8312 (m) REVERT: d 128 GLU cc_start: 0.9652 (mm-30) cc_final: 0.9242 (mp0) REVERT: d 132 ARG cc_start: 0.9345 (ttp-110) cc_final: 0.9011 (mtm110) REVERT: d 143 ARG cc_start: 0.9106 (ttm-80) cc_final: 0.8892 (ttm-80) REVERT: d 215 MET cc_start: 0.2963 (mmm) cc_final: 0.2718 (mmt) REVERT: e 2 ILE cc_start: 0.9151 (tt) cc_final: 0.8950 (tt) REVERT: e 10 MET cc_start: 0.8924 (mmp) cc_final: 0.8485 (tpp) REVERT: e 25 LYS cc_start: 0.9569 (pptt) cc_final: 0.9310 (pptt) REVERT: e 50 GLN cc_start: 0.9130 (mt0) cc_final: 0.8867 (mt0) REVERT: e 66 MET cc_start: 0.9403 (ptp) cc_final: 0.8894 (ptp) REVERT: e 76 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8721 (mm-30) REVERT: e 111 LEU cc_start: 0.8809 (tp) cc_final: 0.8291 (tp) REVERT: e 167 ARG cc_start: 0.9179 (ptm160) cc_final: 0.8641 (ptt180) REVERT: j 162 ARG cc_start: 0.8313 (mmm-85) cc_final: 0.7822 (mmm160) REVERT: j 166 ASP cc_start: 0.9107 (m-30) cc_final: 0.8804 (m-30) REVERT: j 183 ASN cc_start: 0.9853 (m110) cc_final: 0.9479 (m110) REVERT: j 189 LEU cc_start: 0.9089 (tp) cc_final: 0.8840 (tp) REVERT: j 199 LYS cc_start: 0.9360 (tttt) cc_final: 0.9132 (ttmm) REVERT: j 212 GLU cc_start: 0.9492 (pt0) cc_final: 0.9246 (pm20) REVERT: k 25 LYS cc_start: 0.9562 (mttt) cc_final: 0.9087 (ttpp) REVERT: k 26 VAL cc_start: 0.9462 (p) cc_final: 0.9086 (m) REVERT: k 29 GLU cc_start: 0.8328 (pm20) cc_final: 0.7876 (mp0) REVERT: k 32 PHE cc_start: 0.8773 (m-80) cc_final: 0.8494 (m-80) REVERT: k 40 PHE cc_start: 0.9478 (t80) cc_final: 0.9163 (t80) REVERT: k 50 GLN cc_start: 0.9691 (tt0) cc_final: 0.9452 (tt0) REVERT: k 55 MET cc_start: 0.9640 (mtp) cc_final: 0.9088 (ttm) REVERT: k 66 MET cc_start: 0.9464 (mmp) cc_final: 0.9165 (mmt) REVERT: k 71 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8617 (mt-10) REVERT: k 76 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8912 (mm-30) REVERT: k 79 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8847 (tm-30) REVERT: k 111 LEU cc_start: 0.8405 (tt) cc_final: 0.8026 (tp) REVERT: k 128 GLU cc_start: 0.9322 (mm-30) cc_final: 0.9109 (mm-30) REVERT: k 131 LYS cc_start: 0.9478 (ttmt) cc_final: 0.9171 (ttmt) REVERT: k 139 ASN cc_start: 0.9448 (m-40) cc_final: 0.8968 (m110) REVERT: k 153 ILE cc_start: 0.8504 (mm) cc_final: 0.7935 (mm) REVERT: k 154 ARG cc_start: 0.9286 (mmm-85) cc_final: 0.8849 (mmm-85) REVERT: k 164 TYR cc_start: 0.8426 (t80) cc_final: 0.7376 (t80) REVERT: k 175 GLU cc_start: 0.9019 (tp30) cc_final: 0.8790 (tm-30) REVERT: k 176 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8656 (tm-30) REVERT: k 187 GLU cc_start: 0.9465 (mt-10) cc_final: 0.9107 (tm-30) REVERT: k 190 LEU cc_start: 0.9470 (tp) cc_final: 0.9186 (tp) REVERT: k 192 GLN cc_start: 0.9133 (mt0) cc_final: 0.8845 (mp10) REVERT: k 193 ASN cc_start: 0.8997 (m110) cc_final: 0.8171 (m110) REVERT: k 213 GLU cc_start: 0.8923 (mp0) cc_final: 0.8410 (mp0) REVERT: k 214 MET cc_start: 0.9505 (mtt) cc_final: 0.9214 (mtt) outliers start: 1 outliers final: 1 residues processed: 866 average time/residue: 0.3759 time to fit residues: 457.9334 Evaluate side-chains 729 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 728 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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: 10.0000 chunk 25 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 190 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 225 optimal weight: 0.8980 chunk 141 optimal weight: 10.0000 chunk 137 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 74 ASN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 ASN D 53 ASN D 74 ASN ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 35 ASN J 111 GLN ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.7034 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= 0.247 Angle : 0.678 9.652 25567 Z= 0.348 Chirality : 0.046 0.292 2848 Planarity : 0.005 0.057 3345 Dihedral : 4.485 24.441 2500 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.23 (0.17), residues: 2338 helix: 0.57 (0.14), residues: 1442 sheet: -1.53 (0.46), residues: 88 loop : -0.19 (0.23), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP J 121 HIS 0.005 0.001 HIS C 84 PHE 0.027 0.002 PHE N 168 TYR 0.028 0.002 TYR D 169 ARG 0.013 0.001 ARG G 132 *********************** 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 864 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 864 time to evaluate : 2.113 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: A 45 GLU cc_start: 0.9510 (tm-30) cc_final: 0.9207 (tm-30) REVERT: A 48 THR cc_start: 0.9359 (p) cc_final: 0.9053 (p) REVERT: A 50 GLN cc_start: 0.9315 (tm-30) cc_final: 0.9073 (pp30) REVERT: A 52 LEU cc_start: 0.9748 (mt) cc_final: 0.9510 (mt) REVERT: A 76 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9228 (mm-30) REVERT: A 79 GLU cc_start: 0.9531 (tm-30) cc_final: 0.9257 (tp30) REVERT: A 96 MET cc_start: 0.7116 (mpp) cc_final: 0.6898 (mpp) REVERT: A 103 ASP cc_start: 0.8694 (m-30) cc_final: 0.8030 (m-30) REVERT: B 18 ARG cc_start: 0.9432 (mtm-85) cc_final: 0.9105 (mtm-85) REVERT: B 21 ASN cc_start: 0.9570 (m-40) cc_final: 0.9296 (m-40) REVERT: B 30 LYS cc_start: 0.9219 (mmtm) cc_final: 0.8940 (mmtm) REVERT: B 39 MET cc_start: 0.9650 (tpp) cc_final: 0.9165 (tpt) REVERT: B 43 LEU cc_start: 0.8903 (mt) cc_final: 0.8325 (mt) REVERT: B 52 LEU cc_start: 0.9612 (mp) cc_final: 0.9354 (mp) REVERT: B 66 MET cc_start: 0.9154 (mmm) cc_final: 0.8733 (mmm) REVERT: B 70 LYS cc_start: 0.9570 (mtpt) cc_final: 0.9261 (mttp) REVERT: B 74 ASN cc_start: 0.9525 (m-40) cc_final: 0.9106 (m110) REVERT: B 75 GLU cc_start: 0.8876 (pt0) cc_final: 0.8480 (pt0) REVERT: B 79 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9188 (mm-30) REVERT: B 96 MET cc_start: 0.7939 (mpp) cc_final: 0.7496 (mpp) REVERT: B 175 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8466 (tm-30) REVERT: B 205 LEU cc_start: 0.7288 (mp) cc_final: 0.5941 (mp) REVERT: B 213 GLU cc_start: 0.9651 (tp30) cc_final: 0.9355 (tp30) REVERT: C 25 LYS cc_start: 0.9367 (ptmm) cc_final: 0.9154 (pttm) REVERT: C 55 MET cc_start: 0.9590 (ttm) cc_final: 0.9380 (ttp) REVERT: C 56 LEU cc_start: 0.9514 (mt) cc_final: 0.9279 (mt) REVERT: C 103 ASP cc_start: 0.9049 (m-30) cc_final: 0.8767 (m-30) REVERT: C 108 THR cc_start: 0.9574 (p) cc_final: 0.9361 (p) REVERT: C 140 LYS cc_start: 0.9769 (mttt) cc_final: 0.9355 (tptp) REVERT: C 154 ARG cc_start: 0.9407 (mtp85) cc_final: 0.8712 (mmm160) REVERT: C 219 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8771 (tm-30) REVERT: D 103 ASP cc_start: 0.8609 (t0) cc_final: 0.7904 (t0) REVERT: D 114 GLN cc_start: 0.9456 (mm-40) cc_final: 0.8878 (mp10) REVERT: D 118 MET cc_start: 0.9177 (mmp) cc_final: 0.8649 (tmm) REVERT: D 128 GLU cc_start: 0.9361 (mp0) cc_final: 0.9035 (mp0) REVERT: D 132 ARG cc_start: 0.9583 (ptp-110) cc_final: 0.9171 (ptp90) REVERT: G 45 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8283 (mt-10) REVERT: G 57 ASN cc_start: 0.9339 (m-40) cc_final: 0.9106 (m110) REVERT: G 79 GLU cc_start: 0.9305 (tm-30) cc_final: 0.8813 (tm-30) REVERT: G 82 ARG cc_start: 0.9450 (tmm-80) cc_final: 0.9184 (tmm-80) REVERT: G 132 ARG cc_start: 0.9357 (mtm110) cc_final: 0.8986 (mtm180) REVERT: G 139 ASN cc_start: 0.9452 (m-40) cc_final: 0.9249 (m110) REVERT: G 182 LYS cc_start: 0.9103 (mtpt) cc_final: 0.8696 (mtpp) REVERT: G 187 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9130 (mp0) REVERT: G 197 ASP cc_start: 0.9274 (m-30) cc_final: 0.8994 (p0) REVERT: G 203 LYS cc_start: 0.9335 (mttp) cc_final: 0.9037 (mttp) REVERT: H 23 TRP cc_start: 0.8882 (t-100) cc_final: 0.8172 (t60) REVERT: H 50 GLN cc_start: 0.9562 (tt0) cc_final: 0.9146 (pt0) REVERT: H 51 ASP cc_start: 0.9080 (m-30) cc_final: 0.8463 (m-30) REVERT: H 52 LEU cc_start: 0.9552 (mt) cc_final: 0.9349 (mt) REVERT: H 55 MET cc_start: 0.9088 (tpp) cc_final: 0.8691 (tpt) REVERT: H 80 TRP cc_start: 0.8647 (t60) cc_final: 0.8014 (t60) REVERT: H 81 ASP cc_start: 0.8533 (m-30) cc_final: 0.7884 (m-30) REVERT: H 86 VAL cc_start: 0.8050 (p) cc_final: 0.7803 (t) REVERT: H 96 MET cc_start: 0.4508 (ptp) cc_final: 0.4076 (ptp) REVERT: H 149 SER cc_start: 0.8719 (t) cc_final: 0.8331 (t) REVERT: J 8 PHE cc_start: 0.8386 (m-80) cc_final: 0.7939 (m-10) REVERT: J 10 ILE cc_start: 0.8528 (mp) cc_final: 0.8257 (mp) REVERT: J 22 PHE cc_start: 0.8915 (m-80) cc_final: 0.8452 (m-80) REVERT: J 36 PHE cc_start: 0.8860 (t80) cc_final: 0.8585 (t80) REVERT: J 39 LEU cc_start: 0.9363 (mt) cc_final: 0.9087 (mt) REVERT: J 48 TYR cc_start: 0.8525 (m-80) cc_final: 0.7981 (m-80) REVERT: J 53 PHE cc_start: 0.9116 (m-80) cc_final: 0.8317 (m-80) REVERT: J 57 ILE cc_start: 0.8660 (mp) cc_final: 0.8228 (mp) REVERT: J 84 GLU cc_start: 0.8981 (pm20) cc_final: 0.8492 (pm20) REVERT: J 138 ILE cc_start: 0.8278 (mm) cc_final: 0.7699 (mm) REVERT: J 142 MET cc_start: 0.8807 (mtm) cc_final: 0.8420 (mtp) REVERT: N 163 ASP cc_start: 0.9143 (m-30) cc_final: 0.8210 (t0) REVERT: N 167 ARG cc_start: 0.7259 (ptt-90) cc_final: 0.6938 (ptt-90) REVERT: N 172 LEU cc_start: 0.9434 (tp) cc_final: 0.8947 (tp) REVERT: N 183 ASN cc_start: 0.9384 (m-40) cc_final: 0.9134 (m-40) REVERT: N 185 MET cc_start: 0.9549 (ptp) cc_final: 0.9096 (ptp) REVERT: N 203 LYS cc_start: 0.8973 (mtpt) cc_final: 0.8645 (ptmt) REVERT: N 205 LEU cc_start: 0.7485 (tt) cc_final: 0.7277 (tt) REVERT: N 211 LEU cc_start: 0.8717 (tt) cc_final: 0.8283 (tt) REVERT: N 214 MET cc_start: 0.8545 (mtm) cc_final: 0.8265 (mmp) REVERT: Y 25 LYS cc_start: 0.9592 (ptmm) cc_final: 0.9360 (ptmm) REVERT: Y 45 GLU cc_start: 0.8934 (mm-30) cc_final: 0.8502 (mp0) REVERT: Y 51 ASP cc_start: 0.9318 (m-30) cc_final: 0.8999 (m-30) REVERT: Y 53 ASN cc_start: 0.9497 (m-40) cc_final: 0.9297 (m-40) REVERT: Y 67 GLN cc_start: 0.9137 (mt0) cc_final: 0.8266 (mt0) REVERT: Y 74 ASN cc_start: 0.8993 (m-40) cc_final: 0.8688 (m-40) REVERT: Y 75 GLU cc_start: 0.8878 (pt0) cc_final: 0.8487 (pp20) REVERT: Y 96 MET cc_start: 0.3058 (mpp) cc_final: 0.2642 (mtp) REVERT: Y 114 GLN cc_start: 0.9265 (mt0) cc_final: 0.8975 (mt0) REVERT: Y 117 TRP cc_start: 0.9054 (m-10) cc_final: 0.8607 (m-90) REVERT: Y 118 MET cc_start: 0.9092 (mmp) cc_final: 0.8892 (mmp) REVERT: Y 128 GLU cc_start: 0.8964 (pp20) cc_final: 0.8636 (pp20) REVERT: Y 144 MET cc_start: 0.8949 (ttt) cc_final: 0.8737 (ttt) REVERT: d 74 ASN cc_start: 0.9070 (m110) cc_final: 0.8845 (m110) REVERT: d 126 VAL cc_start: 0.8826 (m) cc_final: 0.8459 (m) REVERT: d 128 GLU cc_start: 0.9675 (mm-30) cc_final: 0.9249 (mp0) REVERT: d 132 ARG cc_start: 0.9355 (ttp-110) cc_final: 0.8895 (mtp-110) REVERT: d 143 ARG cc_start: 0.9057 (ttm-80) cc_final: 0.8464 (ttm-80) REVERT: d 167 ARG cc_start: 0.9220 (ptm160) cc_final: 0.8971 (ptt180) REVERT: d 215 MET cc_start: 0.2811 (mmm) cc_final: 0.2572 (mmt) REVERT: e 25 LYS cc_start: 0.9624 (pptt) cc_final: 0.9294 (pptt) REVERT: e 50 GLN cc_start: 0.9123 (mt0) cc_final: 0.8861 (mt0) REVERT: e 66 MET cc_start: 0.9410 (ptp) cc_final: 0.8925 (ptp) REVERT: e 76 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8906 (mm-30) REVERT: e 111 LEU cc_start: 0.8857 (tp) cc_final: 0.8345 (tp) REVERT: e 118 MET cc_start: 0.9229 (mmt) cc_final: 0.8981 (mmm) REVERT: e 124 ILE cc_start: 0.8689 (mm) cc_final: 0.8475 (mm) REVERT: e 128 GLU cc_start: 0.8890 (pm20) cc_final: 0.8094 (pm20) REVERT: e 129 ILE cc_start: 0.9684 (mt) cc_final: 0.9198 (mm) REVERT: e 132 ARG cc_start: 0.9456 (ttm110) cc_final: 0.8997 (ptp-110) REVERT: e 167 ARG cc_start: 0.9062 (ptm160) cc_final: 0.8645 (ptt180) REVERT: e 169 TYR cc_start: 0.8801 (m-10) cc_final: 0.8317 (m-80) REVERT: j 162 ARG cc_start: 0.8173 (mmm-85) cc_final: 0.7812 (mmm-85) REVERT: j 166 ASP cc_start: 0.9053 (m-30) cc_final: 0.8810 (m-30) REVERT: j 183 ASN cc_start: 0.9763 (m110) cc_final: 0.9493 (m110) REVERT: j 189 LEU cc_start: 0.9080 (tp) cc_final: 0.8833 (tp) REVERT: j 212 GLU cc_start: 0.9478 (pt0) cc_final: 0.9212 (pm20) REVERT: k 25 LYS cc_start: 0.9612 (mttt) cc_final: 0.9205 (ttpp) REVERT: k 26 VAL cc_start: 0.9553 (p) cc_final: 0.9328 (m) REVERT: k 29 GLU cc_start: 0.8485 (pm20) cc_final: 0.8081 (mp0) REVERT: k 32 PHE cc_start: 0.8832 (m-80) cc_final: 0.8574 (m-80) REVERT: k 40 PHE cc_start: 0.9488 (t80) cc_final: 0.9163 (t80) REVERT: k 50 GLN cc_start: 0.9696 (tt0) cc_final: 0.9467 (tt0) REVERT: k 55 MET cc_start: 0.9657 (mtp) cc_final: 0.9101 (ttm) REVERT: k 66 MET cc_start: 0.9456 (mmp) cc_final: 0.9149 (mmt) REVERT: k 70 LYS cc_start: 0.9446 (mtmm) cc_final: 0.9205 (mtmm) REVERT: k 71 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8539 (mt-10) REVERT: k 76 GLU cc_start: 0.9337 (mm-30) cc_final: 0.8925 (mm-30) REVERT: k 79 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8898 (tm-30) REVERT: k 111 LEU cc_start: 0.8349 (tt) cc_final: 0.7930 (tt) REVERT: k 121 ASN cc_start: 0.9274 (m-40) cc_final: 0.8862 (t0) REVERT: k 131 LYS cc_start: 0.9464 (ttmt) cc_final: 0.9189 (ttmt) REVERT: k 139 ASN cc_start: 0.9474 (m-40) cc_final: 0.9006 (m110) REVERT: k 153 ILE cc_start: 0.8482 (mm) cc_final: 0.8026 (mm) REVERT: k 154 ARG cc_start: 0.9302 (mmm-85) cc_final: 0.8827 (mmm-85) REVERT: k 164 TYR cc_start: 0.8542 (t80) cc_final: 0.7177 (t80) REVERT: k 167 ARG cc_start: 0.9328 (ptm160) cc_final: 0.9116 (ptm160) REVERT: k 175 GLU cc_start: 0.8989 (tp30) cc_final: 0.8763 (tm-30) REVERT: k 176 GLN cc_start: 0.8959 (tm-30) cc_final: 0.8688 (tm-30) REVERT: k 187 GLU cc_start: 0.9477 (mt-10) cc_final: 0.9121 (tm-30) REVERT: k 192 GLN cc_start: 0.9181 (mt0) cc_final: 0.8586 (mt0) REVERT: k 193 ASN cc_start: 0.9053 (m110) cc_final: 0.8159 (m110) REVERT: k 203 LYS cc_start: 0.9095 (mmtm) cc_final: 0.8892 (mtpt) REVERT: k 213 GLU cc_start: 0.8861 (mp0) cc_final: 0.8541 (mp0) REVERT: k 214 MET cc_start: 0.9487 (mtt) cc_final: 0.9165 (mtt) outliers start: 0 outliers final: 0 residues processed: 864 average time/residue: 0.3753 time to fit residues: 458.4435 Evaluate side-chains 719 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 719 time to evaluate : 1.926 ------------------------------------------------------------------------------- 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: 0.0970 chunk 134 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 40.0000 chunk 43 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 153 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 21 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 205 optimal weight: 20.0000 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN H 179 GLN H 183 ASN ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN d 183 ASN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 84 HIS ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.7219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 18824 Z= 0.231 Angle : 0.684 10.847 25567 Z= 0.348 Chirality : 0.046 0.274 2848 Planarity : 0.005 0.049 3345 Dihedral : 4.492 23.707 2500 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: 0.51 (0.14), residues: 1456 sheet: -1.65 (0.43), residues: 97 loop : -0.16 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 121 HIS 0.004 0.001 HIS k 62 PHE 0.034 0.002 PHE C 168 TYR 0.020 0.002 TYR Y 130 ARG 0.012 0.001 ARG A 82 *********************** 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 861 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 861 time to evaluate : 2.084 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: A 23 TRP cc_start: 0.9277 (t-100) cc_final: 0.9006 (t-100) REVERT: A 45 GLU cc_start: 0.9503 (tm-30) cc_final: 0.9191 (tm-30) REVERT: A 48 THR cc_start: 0.9420 (p) cc_final: 0.9101 (p) REVERT: A 50 GLN cc_start: 0.9345 (tm-30) cc_final: 0.9141 (pp30) REVERT: A 52 LEU cc_start: 0.9738 (mt) cc_final: 0.9429 (mt) REVERT: A 74 ASN cc_start: 0.9304 (m110) cc_final: 0.9089 (m110) REVERT: A 76 GLU cc_start: 0.9488 (mm-30) cc_final: 0.9288 (mm-30) REVERT: A 96 MET cc_start: 0.7098 (mpp) cc_final: 0.6839 (mpp) REVERT: A 97 ARG cc_start: 0.8160 (ptt90) cc_final: 0.7622 (ptt90) REVERT: B 21 ASN cc_start: 0.9570 (m-40) cc_final: 0.9325 (m-40) REVERT: B 33 SER cc_start: 0.8676 (m) cc_final: 0.8370 (t) REVERT: B 39 MET cc_start: 0.9657 (tpp) cc_final: 0.9144 (tpt) REVERT: B 43 LEU cc_start: 0.8923 (mt) cc_final: 0.8332 (mt) REVERT: B 51 ASP cc_start: 0.9096 (m-30) cc_final: 0.8887 (m-30) REVERT: B 52 LEU cc_start: 0.9618 (mp) cc_final: 0.9376 (mp) REVERT: B 66 MET cc_start: 0.9106 (mmm) cc_final: 0.8643 (mmm) REVERT: B 70 LYS cc_start: 0.9559 (mtpt) cc_final: 0.9205 (ttmm) REVERT: B 74 ASN cc_start: 0.9532 (m-40) cc_final: 0.9077 (m110) REVERT: B 75 GLU cc_start: 0.8899 (pt0) cc_final: 0.8489 (pt0) REVERT: B 96 MET cc_start: 0.7965 (mpp) cc_final: 0.7586 (mpp) REVERT: B 128 GLU cc_start: 0.9597 (mp0) cc_final: 0.9382 (mp0) REVERT: B 131 LYS cc_start: 0.9744 (mttt) cc_final: 0.9514 (mmtt) REVERT: B 175 GLU cc_start: 0.8729 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 205 LEU cc_start: 0.7345 (mp) cc_final: 0.6236 (mt) REVERT: B 215 MET cc_start: 0.7859 (ttp) cc_final: 0.7595 (tmm) REVERT: C 25 LYS cc_start: 0.9336 (ptmm) cc_final: 0.9131 (ptpp) REVERT: C 56 LEU cc_start: 0.9496 (mt) cc_final: 0.9286 (mt) REVERT: C 103 ASP cc_start: 0.9059 (m-30) cc_final: 0.8757 (m-30) REVERT: C 108 THR cc_start: 0.9573 (p) cc_final: 0.9341 (p) REVERT: C 140 LYS cc_start: 0.9751 (mttt) cc_final: 0.9331 (tptp) REVERT: C 154 ARG cc_start: 0.9241 (mmt90) cc_final: 0.8931 (mmm160) REVERT: C 219 GLN cc_start: 0.9257 (tp-100) cc_final: 0.8788 (tm-30) REVERT: D 41 SER cc_start: 0.9288 (p) cc_final: 0.9009 (p) REVERT: D 57 ASN cc_start: 0.9379 (m-40) cc_final: 0.9095 (m110) REVERT: D 103 ASP cc_start: 0.8780 (t0) cc_final: 0.8100 (t0) REVERT: D 128 GLU cc_start: 0.9364 (mp0) cc_final: 0.9031 (mp0) REVERT: D 132 ARG cc_start: 0.9576 (ptp-110) cc_final: 0.9131 (ptp90) REVERT: G 45 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8193 (mt-10) REVERT: G 57 ASN cc_start: 0.9343 (m-40) cc_final: 0.9139 (m110) REVERT: G 79 GLU cc_start: 0.9298 (tm-30) cc_final: 0.8871 (tm-30) REVERT: G 82 ARG cc_start: 0.9436 (tmm-80) cc_final: 0.9157 (tmm-80) REVERT: G 96 MET cc_start: 0.4523 (mpp) cc_final: 0.3945 (mpp) REVERT: G 182 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8766 (mtpp) REVERT: G 187 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9107 (mp0) REVERT: G 197 ASP cc_start: 0.9237 (m-30) cc_final: 0.8964 (p0) REVERT: G 203 LYS cc_start: 0.9353 (mttp) cc_final: 0.9057 (mttp) REVERT: G 215 MET cc_start: 0.8321 (ptp) cc_final: 0.8111 (ptt) REVERT: H 23 TRP cc_start: 0.8884 (t-100) cc_final: 0.8207 (t60) REVERT: H 50 GLN cc_start: 0.9560 (tt0) cc_final: 0.9082 (tt0) REVERT: H 51 ASP cc_start: 0.9068 (m-30) cc_final: 0.8584 (m-30) REVERT: H 52 LEU cc_start: 0.9546 (mt) cc_final: 0.9341 (mt) REVERT: H 55 MET cc_start: 0.9081 (tpp) cc_final: 0.8693 (tpt) REVERT: H 66 MET cc_start: 0.9253 (mmp) cc_final: 0.8809 (mmm) REVERT: H 80 TRP cc_start: 0.8782 (t60) cc_final: 0.8218 (t60) REVERT: H 86 VAL cc_start: 0.7490 (p) cc_final: 0.7243 (t) REVERT: H 96 MET cc_start: 0.4367 (ptp) cc_final: 0.3859 (ptp) REVERT: H 114 GLN cc_start: 0.9610 (mm-40) cc_final: 0.9299 (pt0) REVERT: H 149 SER cc_start: 0.8749 (t) cc_final: 0.8363 (t) REVERT: J 8 PHE cc_start: 0.8389 (m-80) cc_final: 0.7947 (m-10) REVERT: J 10 ILE cc_start: 0.8531 (mp) cc_final: 0.8294 (mp) REVERT: J 22 PHE cc_start: 0.8909 (m-80) cc_final: 0.8391 (m-80) REVERT: J 48 TYR cc_start: 0.8593 (m-80) cc_final: 0.8153 (m-80) REVERT: J 53 PHE cc_start: 0.9097 (m-80) cc_final: 0.8325 (m-80) REVERT: J 57 ILE cc_start: 0.8654 (mp) cc_final: 0.8199 (mp) REVERT: J 84 GLU cc_start: 0.9040 (pm20) cc_final: 0.8667 (pm20) REVERT: J 138 ILE cc_start: 0.8219 (mm) cc_final: 0.7676 (mm) REVERT: J 142 MET cc_start: 0.8791 (mtm) cc_final: 0.8423 (mtp) REVERT: N 163 ASP cc_start: 0.9175 (m-30) cc_final: 0.8168 (t0) REVERT: N 167 ARG cc_start: 0.7149 (ptt-90) cc_final: 0.6938 (ptt-90) REVERT: N 172 LEU cc_start: 0.9358 (tp) cc_final: 0.9027 (tp) REVERT: N 183 ASN cc_start: 0.9393 (m-40) cc_final: 0.9164 (m-40) REVERT: N 185 MET cc_start: 0.9591 (ptp) cc_final: 0.9036 (ptp) REVERT: Y 25 LYS cc_start: 0.9490 (ptmm) cc_final: 0.9254 (ptmm) REVERT: Y 45 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8594 (mm-30) REVERT: Y 50 GLN cc_start: 0.9617 (tm-30) cc_final: 0.9378 (tm-30) REVERT: Y 51 ASP cc_start: 0.9415 (m-30) cc_final: 0.9081 (m-30) REVERT: Y 53 ASN cc_start: 0.9497 (m-40) cc_final: 0.9281 (m-40) REVERT: Y 67 GLN cc_start: 0.9180 (mt0) cc_final: 0.8746 (mt0) REVERT: Y 75 GLU cc_start: 0.8816 (pt0) cc_final: 0.8463 (pp20) REVERT: Y 96 MET cc_start: 0.3111 (mpp) cc_final: 0.2734 (mtp) REVERT: Y 114 GLN cc_start: 0.9327 (mt0) cc_final: 0.9016 (mt0) REVERT: Y 117 TRP cc_start: 0.9065 (m-10) cc_final: 0.8702 (m-90) REVERT: Y 144 MET cc_start: 0.8941 (ttt) cc_final: 0.8682 (ttt) REVERT: d 32 PHE cc_start: 0.8764 (m-80) cc_final: 0.8188 (m-80) REVERT: d 67 GLN cc_start: 0.9539 (tp40) cc_final: 0.9289 (tt0) REVERT: d 74 ASN cc_start: 0.9065 (m110) cc_final: 0.8819 (m110) REVERT: d 112 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9018 (mm-40) REVERT: d 126 VAL cc_start: 0.8806 (m) cc_final: 0.8470 (m) REVERT: d 128 GLU cc_start: 0.9686 (mm-30) cc_final: 0.9316 (mp0) REVERT: d 132 ARG cc_start: 0.9357 (ttp-110) cc_final: 0.9115 (mtp-110) REVERT: d 133 TRP cc_start: 0.9423 (m-10) cc_final: 0.8991 (m-10) REVERT: d 167 ARG cc_start: 0.9177 (ptm160) cc_final: 0.8858 (ptm160) REVERT: d 215 MET cc_start: 0.2861 (mmm) cc_final: 0.2601 (mmt) REVERT: e 10 MET cc_start: 0.8903 (mmp) cc_final: 0.8543 (tpp) REVERT: e 30 LYS cc_start: 0.8850 (mttm) cc_final: 0.8636 (mtpp) REVERT: e 50 GLN cc_start: 0.9143 (mt0) cc_final: 0.8904 (mt0) REVERT: e 66 MET cc_start: 0.9401 (ptp) cc_final: 0.8918 (ptp) REVERT: e 76 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8868 (mm-30) REVERT: e 111 LEU cc_start: 0.8901 (tp) cc_final: 0.8367 (tp) REVERT: e 124 ILE cc_start: 0.8638 (mm) cc_final: 0.8167 (mp) REVERT: e 128 GLU cc_start: 0.8830 (pm20) cc_final: 0.8558 (pm20) REVERT: e 167 ARG cc_start: 0.9068 (ptm160) cc_final: 0.8669 (ptt180) REVERT: e 173 ARG cc_start: 0.8923 (ttt180) cc_final: 0.8575 (ttt180) REVERT: j 162 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7761 (mmm-85) REVERT: j 166 ASP cc_start: 0.9028 (m-30) cc_final: 0.8725 (m-30) REVERT: j 183 ASN cc_start: 0.9770 (m110) cc_final: 0.9499 (m110) REVERT: j 189 LEU cc_start: 0.9060 (tp) cc_final: 0.8815 (tp) REVERT: j 212 GLU cc_start: 0.9611 (pt0) cc_final: 0.9301 (pm20) REVERT: k 25 LYS cc_start: 0.9579 (mttt) cc_final: 0.9167 (ttpp) REVERT: k 26 VAL cc_start: 0.9568 (p) cc_final: 0.9314 (m) REVERT: k 29 GLU cc_start: 0.8461 (pm20) cc_final: 0.7896 (mp0) REVERT: k 32 PHE cc_start: 0.8851 (m-80) cc_final: 0.8580 (m-80) REVERT: k 40 PHE cc_start: 0.9470 (t80) cc_final: 0.9143 (t80) REVERT: k 50 GLN cc_start: 0.9692 (tt0) cc_final: 0.9460 (tt0) REVERT: k 55 MET cc_start: 0.9671 (mtp) cc_final: 0.9108 (ttm) REVERT: k 66 MET cc_start: 0.9458 (mmp) cc_final: 0.9159 (mmt) REVERT: k 70 LYS cc_start: 0.9427 (mtmm) cc_final: 0.9161 (mtmm) REVERT: k 71 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8514 (mt-10) REVERT: k 76 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8839 (mm-30) REVERT: k 111 LEU cc_start: 0.8346 (tt) cc_final: 0.7930 (tp) REVERT: k 121 ASN cc_start: 0.9269 (m-40) cc_final: 0.8893 (t0) REVERT: k 131 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9138 (ttmt) REVERT: k 139 ASN cc_start: 0.9466 (m-40) cc_final: 0.8968 (m110) REVERT: k 154 ARG cc_start: 0.9308 (mmm-85) cc_final: 0.8732 (mmm-85) REVERT: k 175 GLU cc_start: 0.8996 (tp30) cc_final: 0.8771 (tm-30) REVERT: k 176 GLN cc_start: 0.8967 (tm-30) cc_final: 0.8708 (tm-30) REVERT: k 179 GLN cc_start: 0.9422 (tp-100) cc_final: 0.9214 (tp-100) REVERT: k 187 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9121 (tm-30) REVERT: k 192 GLN cc_start: 0.9197 (mt0) cc_final: 0.8667 (mt0) REVERT: k 193 ASN cc_start: 0.9026 (m110) cc_final: 0.8489 (m110) REVERT: k 213 GLU cc_start: 0.8840 (mp0) cc_final: 0.8564 (mp0) REVERT: k 214 MET cc_start: 0.9471 (mtt) cc_final: 0.9171 (mtt) REVERT: k 215 MET cc_start: 0.8856 (mtp) cc_final: 0.8455 (mtp) outliers start: 0 outliers final: 0 residues processed: 861 average time/residue: 0.3669 time to fit residues: 444.0292 Evaluate side-chains 705 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 705 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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: 20.0000 chunk 197 optimal weight: 8.9990 chunk 210 optimal weight: 50.0000 chunk 126 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 64 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 198 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 138 optimal weight: 30.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 50 GLN ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 57 ASN ** k 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 18824 Z= 0.275 Angle : 0.710 10.531 25567 Z= 0.367 Chirality : 0.046 0.250 2848 Planarity : 0.006 0.145 3345 Dihedral : 4.658 26.256 2500 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.17), residues: 2338 helix: 0.38 (0.13), residues: 1453 sheet: -1.59 (0.43), residues: 97 loop : -0.18 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 121 HIS 0.005 0.001 HIS k 62 PHE 0.019 0.002 PHE N 168 TYR 0.028 0.002 TYR A 130 ARG 0.027 0.001 ARG d 143 *********************** 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 845 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 845 time to evaluate : 2.188 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: A 45 GLU cc_start: 0.9491 (tm-30) cc_final: 0.9177 (tm-30) REVERT: A 48 THR cc_start: 0.9352 (p) cc_final: 0.9049 (p) REVERT: A 52 LEU cc_start: 0.9731 (mt) cc_final: 0.9496 (mt) REVERT: A 97 ARG cc_start: 0.8148 (ptt90) cc_final: 0.7862 (ptt90) REVERT: A 128 GLU cc_start: 0.9464 (pm20) cc_final: 0.9105 (tm-30) REVERT: B 21 ASN cc_start: 0.9577 (m-40) cc_final: 0.9318 (m-40) REVERT: B 33 SER cc_start: 0.8555 (m) cc_final: 0.8311 (t) REVERT: B 39 MET cc_start: 0.9649 (tpp) cc_final: 0.9139 (tpt) REVERT: B 43 LEU cc_start: 0.8921 (mt) cc_final: 0.8316 (mt) REVERT: B 51 ASP cc_start: 0.9057 (m-30) cc_final: 0.8853 (m-30) REVERT: B 52 LEU cc_start: 0.9635 (mp) cc_final: 0.9390 (mp) REVERT: B 66 MET cc_start: 0.9106 (mmm) cc_final: 0.8652 (mmm) REVERT: B 70 LYS cc_start: 0.9560 (mtpt) cc_final: 0.9211 (ttmm) REVERT: B 74 ASN cc_start: 0.9502 (m-40) cc_final: 0.8973 (m110) REVERT: B 75 GLU cc_start: 0.8916 (pt0) cc_final: 0.8572 (pt0) REVERT: B 96 MET cc_start: 0.7966 (mpp) cc_final: 0.7724 (mpp) REVERT: B 128 GLU cc_start: 0.9601 (mp0) cc_final: 0.9382 (mp0) REVERT: B 131 LYS cc_start: 0.9703 (mttt) cc_final: 0.9491 (mmtt) REVERT: C 51 ASP cc_start: 0.9217 (m-30) cc_final: 0.8995 (m-30) REVERT: C 56 LEU cc_start: 0.9507 (mt) cc_final: 0.9301 (mt) REVERT: C 103 ASP cc_start: 0.9067 (m-30) cc_final: 0.8752 (m-30) REVERT: C 108 THR cc_start: 0.9592 (p) cc_final: 0.9372 (p) REVERT: C 140 LYS cc_start: 0.9763 (mttt) cc_final: 0.9331 (tptp) REVERT: C 154 ARG cc_start: 0.9315 (mmt90) cc_final: 0.8948 (mmm160) REVERT: D 68 MET cc_start: 0.8587 (mtt) cc_final: 0.8048 (mtt) REVERT: D 103 ASP cc_start: 0.8677 (t0) cc_final: 0.7890 (t0) REVERT: D 118 MET cc_start: 0.9103 (mmp) cc_final: 0.8556 (tmm) REVERT: G 57 ASN cc_start: 0.9312 (m-40) cc_final: 0.9065 (m110) REVERT: G 79 GLU cc_start: 0.9297 (tm-30) cc_final: 0.8845 (tm-30) REVERT: G 82 ARG cc_start: 0.9450 (tmm-80) cc_final: 0.9155 (tmm-80) REVERT: G 182 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8782 (mtpp) REVERT: G 187 GLU cc_start: 0.9409 (mt-10) cc_final: 0.9125 (mp0) REVERT: G 215 MET cc_start: 0.8299 (ptp) cc_final: 0.8034 (ptt) REVERT: H 23 TRP cc_start: 0.8887 (t-100) cc_final: 0.8233 (t60) REVERT: H 51 ASP cc_start: 0.9063 (m-30) cc_final: 0.8640 (m-30) REVERT: H 52 LEU cc_start: 0.9551 (mt) cc_final: 0.9339 (mt) REVERT: H 55 MET cc_start: 0.9057 (tpp) cc_final: 0.8672 (tpt) REVERT: H 66 MET cc_start: 0.9315 (mmp) cc_final: 0.8903 (mmm) REVERT: H 80 TRP cc_start: 0.8819 (t60) cc_final: 0.8153 (t60) REVERT: H 86 VAL cc_start: 0.7566 (p) cc_final: 0.7329 (t) REVERT: H 96 MET cc_start: 0.3739 (ptp) cc_final: 0.3180 (ptp) REVERT: H 149 SER cc_start: 0.8788 (t) cc_final: 0.8412 (t) REVERT: J 8 PHE cc_start: 0.8448 (m-80) cc_final: 0.8037 (m-10) REVERT: J 10 ILE cc_start: 0.8459 (mp) cc_final: 0.8232 (mp) REVERT: J 22 PHE cc_start: 0.8952 (m-80) cc_final: 0.8399 (m-80) REVERT: J 24 LEU cc_start: 0.8922 (mm) cc_final: 0.8665 (mm) REVERT: J 36 PHE cc_start: 0.8833 (t80) cc_final: 0.8617 (t80) REVERT: J 39 LEU cc_start: 0.9389 (mt) cc_final: 0.9099 (mt) REVERT: J 48 TYR cc_start: 0.8694 (m-80) cc_final: 0.8102 (m-80) REVERT: J 53 PHE cc_start: 0.9048 (m-80) cc_final: 0.8282 (m-80) REVERT: J 57 ILE cc_start: 0.8685 (mp) cc_final: 0.8232 (mp) REVERT: J 84 GLU cc_start: 0.9101 (pm20) cc_final: 0.8715 (pm20) REVERT: J 138 ILE cc_start: 0.8192 (mm) cc_final: 0.7539 (mm) REVERT: J 142 MET cc_start: 0.8710 (mtm) cc_final: 0.8319 (mtp) REVERT: N 163 ASP cc_start: 0.9259 (m-30) cc_final: 0.8268 (t0) REVERT: N 179 GLN cc_start: 0.9213 (pm20) cc_final: 0.8979 (pm20) REVERT: N 183 ASN cc_start: 0.9406 (m-40) cc_final: 0.9115 (m-40) REVERT: N 185 MET cc_start: 0.9598 (ptp) cc_final: 0.9076 (ptp) REVERT: Y 25 LYS cc_start: 0.9501 (ptmm) cc_final: 0.9276 (ptmm) REVERT: Y 45 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8485 (mm-30) REVERT: Y 50 GLN cc_start: 0.9618 (tm-30) cc_final: 0.9390 (tm-30) REVERT: Y 51 ASP cc_start: 0.9391 (m-30) cc_final: 0.9050 (m-30) REVERT: Y 53 ASN cc_start: 0.9541 (m-40) cc_final: 0.9266 (m-40) REVERT: Y 55 MET cc_start: 0.9455 (ttp) cc_final: 0.8971 (tmm) REVERT: Y 67 GLN cc_start: 0.9184 (mt0) cc_final: 0.8379 (mt0) REVERT: Y 75 GLU cc_start: 0.8643 (pt0) cc_final: 0.8421 (pp20) REVERT: Y 114 GLN cc_start: 0.9287 (mt0) cc_final: 0.9032 (mt0) REVERT: Y 117 TRP cc_start: 0.9089 (m-10) cc_final: 0.8732 (m-90) REVERT: Y 128 GLU cc_start: 0.9092 (pp20) cc_final: 0.8883 (pp20) REVERT: Y 144 MET cc_start: 0.8960 (ttt) cc_final: 0.8734 (ttt) REVERT: d 97 ARG cc_start: 0.7621 (ptt90) cc_final: 0.7395 (ttp-170) REVERT: d 126 VAL cc_start: 0.8863 (m) cc_final: 0.8547 (m) REVERT: d 128 GLU cc_start: 0.9698 (mm-30) cc_final: 0.9362 (mp0) REVERT: d 133 TRP cc_start: 0.9389 (m-10) cc_final: 0.9020 (m-10) REVERT: d 139 ASN cc_start: 0.9611 (m110) cc_final: 0.9400 (m110) REVERT: d 143 ARG cc_start: 0.9231 (ttm-80) cc_final: 0.9025 (ttm-80) REVERT: d 167 ARG cc_start: 0.9150 (ptm160) cc_final: 0.8814 (ptm160) REVERT: d 215 MET cc_start: 0.2896 (mmm) cc_final: 0.2632 (mmt) REVERT: e 2 ILE cc_start: 0.9213 (tt) cc_final: 0.9005 (tt) REVERT: e 7 GLN cc_start: 0.9219 (tp40) cc_final: 0.8843 (mm-40) REVERT: e 10 MET cc_start: 0.8939 (mmp) cc_final: 0.8578 (tpp) REVERT: e 25 LYS cc_start: 0.9562 (pptt) cc_final: 0.9276 (pptt) REVERT: e 50 GLN cc_start: 0.9205 (mt0) cc_final: 0.8974 (mt0) REVERT: e 57 ASN cc_start: 0.9383 (m-40) cc_final: 0.9111 (m110) REVERT: e 66 MET cc_start: 0.9421 (ptp) cc_final: 0.8952 (ptp) REVERT: e 76 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8834 (mm-30) REVERT: e 111 LEU cc_start: 0.8925 (tp) cc_final: 0.8389 (tp) REVERT: e 118 MET cc_start: 0.9257 (mmt) cc_final: 0.9030 (mmm) REVERT: e 124 ILE cc_start: 0.8591 (mm) cc_final: 0.8031 (mp) REVERT: e 129 ILE cc_start: 0.9524 (mm) cc_final: 0.9157 (mt) REVERT: e 132 ARG cc_start: 0.9444 (ttm110) cc_final: 0.9130 (ptp-110) REVERT: e 167 ARG cc_start: 0.9078 (ptm160) cc_final: 0.8673 (ptt180) REVERT: e 169 TYR cc_start: 0.8890 (m-10) cc_final: 0.8336 (m-80) REVERT: e 185 MET cc_start: 0.9692 (ptp) cc_final: 0.9358 (ptp) REVERT: j 162 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7672 (mmm160) REVERT: j 166 ASP cc_start: 0.8994 (m-30) cc_final: 0.8603 (m-30) REVERT: j 183 ASN cc_start: 0.9771 (m110) cc_final: 0.9506 (m110) REVERT: j 189 LEU cc_start: 0.9086 (tp) cc_final: 0.8839 (tp) REVERT: j 212 GLU cc_start: 0.9550 (pt0) cc_final: 0.9269 (pm20) REVERT: k 25 LYS cc_start: 0.9577 (mttt) cc_final: 0.9155 (ttpp) REVERT: k 26 VAL cc_start: 0.9581 (p) cc_final: 0.9312 (m) REVERT: k 29 GLU cc_start: 0.8453 (pm20) cc_final: 0.7876 (mp0) REVERT: k 32 PHE cc_start: 0.8898 (m-80) cc_final: 0.8663 (m-80) REVERT: k 40 PHE cc_start: 0.9475 (t80) cc_final: 0.9187 (t80) REVERT: k 53 ASN cc_start: 0.9122 (m110) cc_final: 0.8845 (m110) REVERT: k 55 MET cc_start: 0.9663 (mtp) cc_final: 0.9106 (ttm) REVERT: k 57 ASN cc_start: 0.9382 (m110) cc_final: 0.9156 (m110) REVERT: k 66 MET cc_start: 0.9453 (mmp) cc_final: 0.9123 (mmt) REVERT: k 70 LYS cc_start: 0.9468 (mtmm) cc_final: 0.9201 (mtmm) REVERT: k 71 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8509 (mt-10) REVERT: k 111 LEU cc_start: 0.8379 (tt) cc_final: 0.8052 (tp) REVERT: k 121 ASN cc_start: 0.9249 (m-40) cc_final: 0.8894 (t0) REVERT: k 131 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9165 (ttmt) REVERT: k 139 ASN cc_start: 0.9491 (m-40) cc_final: 0.9028 (m110) REVERT: k 153 ILE cc_start: 0.8686 (mm) cc_final: 0.8014 (mm) REVERT: k 154 ARG cc_start: 0.9291 (mmm-85) cc_final: 0.8849 (mmm-85) REVERT: k 164 TYR cc_start: 0.8913 (t80) cc_final: 0.7808 (t80) REVERT: k 175 GLU cc_start: 0.9003 (tp30) cc_final: 0.8773 (tm-30) REVERT: k 176 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8719 (tm-30) REVERT: k 182 LYS cc_start: 0.9280 (mtpt) cc_final: 0.8714 (mttm) REVERT: k 187 GLU cc_start: 0.9480 (mt-10) cc_final: 0.9123 (tm-30) REVERT: k 192 GLN cc_start: 0.9208 (mt0) cc_final: 0.8657 (mt0) REVERT: k 193 ASN cc_start: 0.9126 (m110) cc_final: 0.8072 (m110) REVERT: k 200 THR cc_start: 0.9507 (p) cc_final: 0.9190 (p) REVERT: k 203 LYS cc_start: 0.9075 (mmtm) cc_final: 0.8773 (mtpt) REVERT: k 213 GLU cc_start: 0.8814 (mp0) cc_final: 0.8506 (mp0) REVERT: k 214 MET cc_start: 0.9499 (mtt) cc_final: 0.9220 (mtt) outliers start: 0 outliers final: 0 residues processed: 845 average time/residue: 0.3757 time to fit residues: 447.2224 Evaluate side-chains 681 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 681 time to evaluate : 2.210 ------------------------------------------------------------------------------- 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: 4.9990 chunk 135 optimal weight: 30.0000 chunk 105 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 233 optimal weight: 9.9990 chunk 214 optimal weight: 0.7980 chunk 185 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 143 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 147 optimal weight: 40.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** G 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.7602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 18824 Z= 0.233 Angle : 0.731 12.994 25567 Z= 0.373 Chirality : 0.047 0.270 2848 Planarity : 0.005 0.102 3345 Dihedral : 4.688 27.245 2500 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.10 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.17), residues: 2338 helix: 0.41 (0.13), residues: 1451 sheet: -1.99 (0.37), residues: 128 loop : -0.14 (0.24), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 80 HIS 0.003 0.001 HIS Y 12 PHE 0.021 0.002 PHE N 168 TYR 0.021 0.002 TYR Y 130 ARG 0.024 0.001 ARG d 143 ********************** 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 846 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 846 time to evaluate : 2.030 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: A 28 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9240 (tm-30) REVERT: A 45 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9165 (tm-30) REVERT: A 52 LEU cc_start: 0.9710 (mt) cc_final: 0.9417 (mt) REVERT: A 68 MET cc_start: 0.9111 (mtt) cc_final: 0.8729 (mtp) REVERT: A 79 GLU cc_start: 0.9570 (tm-30) cc_final: 0.9277 (tp30) REVERT: B 21 ASN cc_start: 0.9562 (m-40) cc_final: 0.9301 (m-40) REVERT: B 33 SER cc_start: 0.8595 (m) cc_final: 0.8343 (t) REVERT: B 39 MET cc_start: 0.9640 (tpp) cc_final: 0.9124 (tpt) REVERT: B 43 LEU cc_start: 0.8920 (mt) cc_final: 0.8304 (mt) REVERT: B 51 ASP cc_start: 0.9046 (m-30) cc_final: 0.8838 (m-30) REVERT: B 52 LEU cc_start: 0.9621 (mp) cc_final: 0.9386 (mp) REVERT: B 66 MET cc_start: 0.9593 (mmt) cc_final: 0.9371 (mmm) REVERT: B 68 MET cc_start: 0.8560 (mtt) cc_final: 0.8101 (mtt) REVERT: B 70 LYS cc_start: 0.9547 (mtpt) cc_final: 0.9113 (ttmm) REVERT: B 71 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8595 (tm-30) REVERT: B 74 ASN cc_start: 0.9492 (m-40) cc_final: 0.8928 (m110) REVERT: B 75 GLU cc_start: 0.8910 (pt0) cc_final: 0.8493 (pt0) REVERT: B 128 GLU cc_start: 0.9565 (mp0) cc_final: 0.9307 (mp0) REVERT: B 131 LYS cc_start: 0.9747 (mttt) cc_final: 0.9512 (mmtt) REVERT: B 205 LEU cc_start: 0.7451 (mt) cc_final: 0.6636 (mt) REVERT: C 51 ASP cc_start: 0.9201 (m-30) cc_final: 0.8986 (m-30) REVERT: C 56 LEU cc_start: 0.9487 (mt) cc_final: 0.9279 (mt) REVERT: C 75 GLU cc_start: 0.9423 (mm-30) cc_final: 0.8823 (tm-30) REVERT: C 76 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8520 (mm-30) REVERT: C 79 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8912 (mm-30) REVERT: C 103 ASP cc_start: 0.9059 (m-30) cc_final: 0.8718 (m-30) REVERT: C 108 THR cc_start: 0.9586 (p) cc_final: 0.9364 (p) REVERT: C 140 LYS cc_start: 0.9773 (mttt) cc_final: 0.9341 (tptp) REVERT: C 154 ARG cc_start: 0.9344 (mmt90) cc_final: 0.8966 (mmm160) REVERT: D 10 MET cc_start: 0.6972 (mmp) cc_final: 0.6191 (mmm) REVERT: D 103 ASP cc_start: 0.8664 (t0) cc_final: 0.7804 (t0) REVERT: D 132 ARG cc_start: 0.9682 (ptp-110) cc_final: 0.9410 (ptp90) REVERT: D 141 ILE cc_start: 0.9706 (mt) cc_final: 0.9477 (pt) REVERT: G 57 ASN cc_start: 0.9324 (m-40) cc_final: 0.9088 (m110) REVERT: G 79 GLU cc_start: 0.9292 (tm-30) cc_final: 0.8796 (tm-30) REVERT: G 82 ARG cc_start: 0.9445 (tmm-80) cc_final: 0.9108 (tmm-80) REVERT: G 96 MET cc_start: 0.4947 (mpp) cc_final: 0.4305 (mpp) REVERT: G 182 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8800 (mtpp) REVERT: G 187 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9133 (mp0) REVERT: G 193 ASN cc_start: 0.9025 (m110) cc_final: 0.8708 (m110) REVERT: G 203 LYS cc_start: 0.9409 (mttp) cc_final: 0.9095 (mttp) REVERT: H 23 TRP cc_start: 0.8906 (t-100) cc_final: 0.7915 (t-100) REVERT: H 37 ILE cc_start: 0.8487 (mt) cc_final: 0.8278 (mt) REVERT: H 50 GLN cc_start: 0.9402 (tt0) cc_final: 0.9038 (pt0) REVERT: H 51 ASP cc_start: 0.8992 (m-30) cc_final: 0.8544 (m-30) REVERT: H 52 LEU cc_start: 0.9545 (mt) cc_final: 0.9316 (mt) REVERT: H 55 MET cc_start: 0.9067 (tpp) cc_final: 0.8561 (tpp) REVERT: H 66 MET cc_start: 0.9297 (mmp) cc_final: 0.8876 (mmm) REVERT: H 80 TRP cc_start: 0.8895 (t60) cc_final: 0.8244 (t60) REVERT: H 86 VAL cc_start: 0.7544 (p) cc_final: 0.7339 (t) REVERT: H 96 MET cc_start: 0.3879 (ptp) cc_final: 0.3339 (ptp) REVERT: H 139 ASN cc_start: 0.9134 (m-40) cc_final: 0.8921 (m-40) REVERT: H 149 SER cc_start: 0.8837 (t) cc_final: 0.8444 (t) REVERT: J 8 PHE cc_start: 0.8407 (m-80) cc_final: 0.7839 (m-10) REVERT: J 10 ILE cc_start: 0.8379 (mp) cc_final: 0.8146 (mp) REVERT: J 22 PHE cc_start: 0.8939 (m-80) cc_final: 0.8363 (m-80) REVERT: J 48 TYR cc_start: 0.8674 (m-80) cc_final: 0.8184 (m-80) REVERT: J 53 PHE cc_start: 0.9028 (m-80) cc_final: 0.8298 (m-80) REVERT: J 57 ILE cc_start: 0.8652 (mp) cc_final: 0.8195 (mp) REVERT: J 69 ARG cc_start: 0.8853 (mpp80) cc_final: 0.8560 (mtt-85) REVERT: J 84 GLU cc_start: 0.9126 (pm20) cc_final: 0.8795 (pm20) REVERT: J 138 ILE cc_start: 0.8126 (mm) cc_final: 0.7644 (mm) REVERT: J 142 MET cc_start: 0.8730 (mtm) cc_final: 0.8425 (mtm) REVERT: N 163 ASP cc_start: 0.9295 (m-30) cc_final: 0.8024 (t0) REVERT: N 167 ARG cc_start: 0.7205 (ptt-90) cc_final: 0.6875 (ptt-90) REVERT: N 179 GLN cc_start: 0.9241 (pm20) cc_final: 0.8937 (pm20) REVERT: N 183 ASN cc_start: 0.9396 (m-40) cc_final: 0.9134 (m-40) REVERT: N 185 MET cc_start: 0.9595 (ptp) cc_final: 0.9114 (ptp) REVERT: N 188 THR cc_start: 0.8789 (m) cc_final: 0.8572 (m) REVERT: Y 25 LYS cc_start: 0.9509 (ptmm) cc_final: 0.9285 (ptmm) REVERT: Y 50 GLN cc_start: 0.9616 (tm-30) cc_final: 0.9378 (tm-30) REVERT: Y 51 ASP cc_start: 0.9386 (m-30) cc_final: 0.8990 (m-30) REVERT: Y 53 ASN cc_start: 0.9532 (m-40) cc_final: 0.9276 (m-40) REVERT: Y 67 GLN cc_start: 0.9172 (mt0) cc_final: 0.8383 (mt0) REVERT: Y 75 GLU cc_start: 0.8657 (pt0) cc_final: 0.8396 (pp20) REVERT: Y 114 GLN cc_start: 0.9279 (mt0) cc_final: 0.9025 (mt0) REVERT: Y 144 MET cc_start: 0.8977 (ttt) cc_final: 0.8739 (ttt) REVERT: d 32 PHE cc_start: 0.8814 (m-80) cc_final: 0.8253 (m-80) REVERT: d 97 ARG cc_start: 0.7629 (ptt90) cc_final: 0.7284 (tmm160) REVERT: d 126 VAL cc_start: 0.8864 (m) cc_final: 0.8576 (m) REVERT: d 133 TRP cc_start: 0.9411 (m-10) cc_final: 0.9050 (m-10) REVERT: d 139 ASN cc_start: 0.9596 (m110) cc_final: 0.9388 (m110) REVERT: d 215 MET cc_start: 0.2931 (mmm) cc_final: 0.2687 (mmt) REVERT: e 2 ILE cc_start: 0.9220 (tt) cc_final: 0.9012 (tt) REVERT: e 7 GLN cc_start: 0.9172 (tp40) cc_final: 0.8869 (mm-40) REVERT: e 10 MET cc_start: 0.8897 (mmp) cc_final: 0.8535 (tpp) REVERT: e 25 LYS cc_start: 0.9599 (pptt) cc_final: 0.9227 (pptt) REVERT: e 50 GLN cc_start: 0.9188 (mt0) cc_final: 0.8939 (mt0) REVERT: e 66 MET cc_start: 0.9387 (ptp) cc_final: 0.8914 (ptp) REVERT: e 76 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8868 (mm-30) REVERT: e 111 LEU cc_start: 0.8952 (tp) cc_final: 0.8428 (tp) REVERT: e 118 MET cc_start: 0.9276 (mmt) cc_final: 0.9069 (mmm) REVERT: e 124 ILE cc_start: 0.8553 (mm) cc_final: 0.7990 (mp) REVERT: e 167 ARG cc_start: 0.9073 (ptm160) cc_final: 0.8670 (ptt180) REVERT: e 169 TYR cc_start: 0.8883 (m-10) cc_final: 0.8454 (m-80) REVERT: j 162 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7674 (mmm-85) REVERT: j 166 ASP cc_start: 0.8982 (m-30) cc_final: 0.8696 (m-30) REVERT: j 183 ASN cc_start: 0.9773 (m110) cc_final: 0.9504 (m110) REVERT: j 189 LEU cc_start: 0.9070 (tp) cc_final: 0.8813 (tp) REVERT: j 212 GLU cc_start: 0.9514 (pt0) cc_final: 0.9259 (pm20) REVERT: k 25 LYS cc_start: 0.9575 (mttt) cc_final: 0.9142 (ttpp) REVERT: k 26 VAL cc_start: 0.9573 (p) cc_final: 0.9313 (m) REVERT: k 29 GLU cc_start: 0.8437 (pm20) cc_final: 0.7813 (mp0) REVERT: k 32 PHE cc_start: 0.8851 (m-80) cc_final: 0.8552 (m-80) REVERT: k 40 PHE cc_start: 0.9494 (t80) cc_final: 0.9136 (t80) REVERT: k 44 SER cc_start: 0.9367 (p) cc_final: 0.8982 (p) REVERT: k 53 ASN cc_start: 0.9085 (m110) cc_final: 0.8811 (m110) REVERT: k 55 MET cc_start: 0.9666 (mtp) cc_final: 0.9094 (ttm) REVERT: k 57 ASN cc_start: 0.9365 (m110) cc_final: 0.9094 (m110) REVERT: k 66 MET cc_start: 0.9453 (mmp) cc_final: 0.9143 (mmt) REVERT: k 70 LYS cc_start: 0.9432 (mtmm) cc_final: 0.9179 (mtmm) REVERT: k 71 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8273 (mt-10) REVERT: k 111 LEU cc_start: 0.8384 (tt) cc_final: 0.8127 (tp) REVERT: k 121 ASN cc_start: 0.9258 (m-40) cc_final: 0.8936 (t0) REVERT: k 129 ILE cc_start: 0.9154 (mm) cc_final: 0.8902 (mm) REVERT: k 131 LYS cc_start: 0.9435 (ttmt) cc_final: 0.9137 (ttmt) REVERT: k 132 ARG cc_start: 0.9266 (ptp-170) cc_final: 0.8244 (ptp-170) REVERT: k 139 ASN cc_start: 0.9493 (m-40) cc_final: 0.9044 (m110) REVERT: k 153 ILE cc_start: 0.8568 (mm) cc_final: 0.8121 (mm) REVERT: k 154 ARG cc_start: 0.9383 (mmm-85) cc_final: 0.8857 (mmm-85) REVERT: k 164 TYR cc_start: 0.8247 (t80) cc_final: 0.7048 (t80) REVERT: k 175 GLU cc_start: 0.8992 (tp30) cc_final: 0.8733 (tm-30) REVERT: k 176 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8639 (tm-30) REVERT: k 179 GLN cc_start: 0.9382 (tp-100) cc_final: 0.9070 (tp-100) REVERT: k 182 LYS cc_start: 0.9258 (mtpt) cc_final: 0.9024 (mtpp) REVERT: k 187 GLU cc_start: 0.9478 (mt-10) cc_final: 0.9116 (tm-30) REVERT: k 192 GLN cc_start: 0.9205 (mt0) cc_final: 0.8713 (mt0) REVERT: k 193 ASN cc_start: 0.9016 (m110) cc_final: 0.8219 (m110) REVERT: k 213 GLU cc_start: 0.8874 (mp0) cc_final: 0.8628 (mp0) REVERT: k 214 MET cc_start: 0.9410 (mtt) cc_final: 0.9152 (mtt) outliers start: 0 outliers final: 0 residues processed: 846 average time/residue: 0.3711 time to fit residues: 442.2217 Evaluate side-chains 687 residues out of total 2002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 687 time to evaluate : 2.316 ------------------------------------------------------------------------------- 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: 7.9990 chunk 56 optimal weight: 6.9990 chunk 171 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 0.0000 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 190 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 chunk 34 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 overall best weight: 1.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN D 74 ASN ** J 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 192 GLN ** j 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.086886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.065617 restraints weight = 70428.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.067549 restraints weight = 45749.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068921 restraints weight = 33733.396| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.7685 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= 0.201 Angle : 0.715 11.730 25567 Z= 0.364 Chirality : 0.046 0.267 2848 Planarity : 0.005 0.067 3345 Dihedral : 4.513 24.563 2500 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: 0.10 (0.17), residues: 2338 helix: 0.50 (0.14), residues: 1447 sheet: -1.96 (0.37), residues: 124 loop : -0.16 (0.24), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 133 HIS 0.002 0.000 HIS e 84 PHE 0.024 0.002 PHE J 83 TYR 0.024 0.002 TYR Y 130 ARG 0.022 0.001 ARG d 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6663.94 seconds wall clock time: 120 minutes 40.46 seconds (7240.46 seconds total)