Starting phenix.real_space_refine on Sun Aug 11 04:16:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/08_2024/8vxq_43629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/08_2024/8vxq_43629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/08_2024/8vxq_43629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/08_2024/8vxq_43629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/08_2024/8vxq_43629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/08_2024/8vxq_43629.cif" } resolution = 3.1 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= 0.158 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 162 5.16 5 C 18963 2.51 5 N 5967 2.21 5 O 6480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J GLU 56": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J GLU 154": "OE1" <-> "OE2" Residue "K ARG 216": "NH1" <-> "NH2" Residue "L GLU 56": "OE1" <-> "OE2" Residue "M GLU 154": "OE1" <-> "OE2" Residue "Q ARG 216": "NH1" <-> "NH2" Residue "C ASP 103": "OD1" <-> "OD2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "H ASP 103": "OD1" <-> "OD2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31572 Number of models: 1 Model: "" Number of chains: 18 Chain: "R" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "J" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "K" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "L" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "M" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "N" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "O" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "P" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "Q" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2342 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 3, 'TRANS': 303} Chain: "A" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "B" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "C" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "D" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "E" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "F" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "G" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "H" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Chain: "I" Number of atoms: 1166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1166 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 147} Time building chain proxies: 18.26, per 1000 atoms: 0.58 Number of scatterers: 31572 At special positions: 0 Unit cell: (130.68, 135.52, 309.76, 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 162 16.00 O 6480 8.00 N 5967 7.00 C 18963 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 13.03 Conformation dependent library (CDL) restraints added in 5.6 seconds 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7596 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 9 sheets defined 71.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'R' and resid 28 through 68 removed outlier: 3.613A pdb=" N ILE R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN R 65 " --> pdb=" O SER R 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL R 66 " --> pdb=" O TYR R 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 70 through 76 Processing helix chain 'R' and resid 78 through 88 removed outlier: 3.522A pdb=" N GLY R 82 " --> pdb=" O ASP R 78 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN R 86 " --> pdb=" O GLY R 82 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG R 87 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 141 removed outlier: 5.279A pdb=" N GLY R 131 " --> pdb=" O VAL R 127 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE R 132 " --> pdb=" O GLY R 128 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL R 133 " --> pdb=" O GLN R 129 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA R 141 " --> pdb=" O ARG R 137 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 155 removed outlier: 3.712A pdb=" N GLU R 154 " --> pdb=" O GLN R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 259 removed outlier: 3.671A pdb=" N GLU R 166 " --> pdb=" O GLU R 162 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA R 189 " --> pdb=" O GLN R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 280 through 291 removed outlier: 4.271A pdb=" N ASN R 286 " --> pdb=" O SER R 282 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY R 289 " --> pdb=" O LEU R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 295 through 305 removed outlier: 3.509A pdb=" N ARG R 299 " --> pdb=" O SER R 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 331 removed outlier: 3.835A pdb=" N ILE R 317 " --> pdb=" O SER R 313 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA R 318 " --> pdb=" O SER R 314 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLN R 319 " --> pdb=" O LYS R 315 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN R 322 " --> pdb=" O ALA R 318 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU R 323 " --> pdb=" O GLN R 319 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU R 331 " --> pdb=" O ARG R 327 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 68 removed outlier: 4.187A pdb=" N ILE J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL J 66 " --> pdb=" O TYR J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 76 Processing helix chain 'J' and resid 78 through 90 removed outlier: 3.532A pdb=" N GLY J 82 " --> pdb=" O ASP J 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN J 86 " --> pdb=" O GLY J 82 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG J 87 " --> pdb=" O LEU J 83 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 141 removed outlier: 3.570A pdb=" N LYS J 105 " --> pdb=" O ASP J 101 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY J 131 " --> pdb=" O VAL J 127 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE J 132 " --> pdb=" O GLY J 128 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN J 135 " --> pdb=" O GLY J 131 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 155 removed outlier: 5.438A pdb=" N ALA J 153 " --> pdb=" O ASN J 149 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU J 154 " --> pdb=" O GLN J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 259 removed outlier: 3.814A pdb=" N THR J 168 " --> pdb=" O ARG J 164 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE J 174 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN J 175 " --> pdb=" O GLN J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 287 removed outlier: 4.290A pdb=" N ASN J 286 " --> pdb=" O SER J 282 " (cutoff:3.500A) Processing helix chain 'J' and resid 295 through 305 Processing helix chain 'J' and resid 316 through 331 removed outlier: 4.579A pdb=" N GLN J 322 " --> pdb=" O ALA J 318 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLU J 323 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU J 331 " --> pdb=" O ARG J 327 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 68 removed outlier: 4.307A pdb=" N ILE K 39 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN K 65 " --> pdb=" O SER K 61 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL K 66 " --> pdb=" O TYR K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 76 Processing helix chain 'K' and resid 78 through 90 removed outlier: 3.513A pdb=" N GLY K 82 " --> pdb=" O ASP K 78 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG K 87 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N MET K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 141 removed outlier: 5.242A pdb=" N GLY K 131 " --> pdb=" O VAL K 127 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ILE K 132 " --> pdb=" O GLY K 128 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA K 141 " --> pdb=" O ARG K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 155 removed outlier: 3.717A pdb=" N ILE K 151 " --> pdb=" O GLU K 147 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA K 153 " --> pdb=" O ASN K 149 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU K 154 " --> pdb=" O GLN K 150 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN K 155 " --> pdb=" O ILE K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 259 removed outlier: 4.265A pdb=" N THR K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 280 through 287 removed outlier: 4.230A pdb=" N ASN K 286 " --> pdb=" O SER K 282 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 305 Processing helix chain 'K' and resid 313 through 331 removed outlier: 4.106A pdb=" N ILE K 317 " --> pdb=" O SER K 313 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA K 318 " --> pdb=" O SER K 314 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLN K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLN K 322 " --> pdb=" O ALA K 318 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLU K 323 " --> pdb=" O GLN K 319 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU K 331 " --> pdb=" O ARG K 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 68 removed outlier: 4.271A pdb=" N ILE L 39 " --> pdb=" O ALA L 35 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN L 65 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL L 66 " --> pdb=" O TYR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 76 Processing helix chain 'L' and resid 78 through 86 removed outlier: 3.616A pdb=" N GLY L 82 " --> pdb=" O ASP L 78 " (cutoff:3.500A) Processing helix chain 'L' and resid 101 through 141 removed outlier: 3.838A pdb=" N LYS L 105 " --> pdb=" O ASP L 101 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLY L 131 " --> pdb=" O VAL L 127 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N ILE L 132 " --> pdb=" O GLY L 128 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL L 133 " --> pdb=" O GLN L 129 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 141 " --> pdb=" O ARG L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 155 removed outlier: 3.598A pdb=" N ILE L 151 " --> pdb=" O GLU L 147 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA L 153 " --> pdb=" O ASN L 149 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU L 154 " --> pdb=" O GLN L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 259 removed outlier: 3.656A pdb=" N GLU L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N THR L 168 " --> pdb=" O ARG L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 280 through 287 removed outlier: 4.365A pdb=" N ASN L 286 " --> pdb=" O SER L 282 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 305 Processing helix chain 'L' and resid 316 through 331 removed outlier: 4.128A pdb=" N GLN L 322 " --> pdb=" O ALA L 318 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU L 323 " --> pdb=" O GLN L 319 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU L 331 " --> pdb=" O ARG L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 68 removed outlier: 3.668A pdb=" N ILE M 39 " --> pdb=" O ALA M 35 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL M 66 " --> pdb=" O TYR M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 76 Processing helix chain 'M' and resid 78 through 90 removed outlier: 3.503A pdb=" N GLY M 82 " --> pdb=" O ASP M 78 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN M 86 " --> pdb=" O GLY M 82 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG M 87 " --> pdb=" O LEU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 129 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 145 through 155 removed outlier: 4.157A pdb=" N ASN M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 259 removed outlier: 3.725A pdb=" N GLU M 166 " --> pdb=" O GLU M 162 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU M 196 " --> pdb=" O ASN M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 280 through 287 removed outlier: 4.288A pdb=" N ASN M 286 " --> pdb=" O SER M 282 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 305 Processing helix chain 'M' and resid 316 through 331 removed outlier: 4.213A pdb=" N GLN M 322 " --> pdb=" O ALA M 318 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLU M 323 " --> pdb=" O GLN M 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 68 removed outlier: 4.394A pdb=" N GLN N 31 " --> pdb=" O THR N 27 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE N 39 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN N 65 " --> pdb=" O SER N 61 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL N 66 " --> pdb=" O TYR N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 76 Processing helix chain 'N' and resid 78 through 86 removed outlier: 3.638A pdb=" N GLN N 86 " --> pdb=" O GLY N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 102 through 141 removed outlier: 5.232A pdb=" N GLY N 131 " --> pdb=" O VAL N 127 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ILE N 132 " --> pdb=" O GLY N 128 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 259 removed outlier: 4.007A pdb=" N GLU N 166 " --> pdb=" O GLU N 162 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU N 167 " --> pdb=" O ILE N 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 280 through 291 removed outlier: 4.320A pdb=" N ASN N 286 " --> pdb=" O SER N 282 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA N 288 " --> pdb=" O ALA N 284 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLY N 289 " --> pdb=" O LEU N 285 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 305 Processing helix chain 'N' and resid 316 through 331 removed outlier: 4.306A pdb=" N GLN N 322 " --> pdb=" O ALA N 318 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N GLU N 323 " --> pdb=" O GLN N 319 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU N 331 " --> pdb=" O ARG N 327 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 68 removed outlier: 4.265A pdb=" N ILE O 39 " --> pdb=" O ALA O 35 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN O 65 " --> pdb=" O SER O 61 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 76 Processing helix chain 'O' and resid 78 through 90 removed outlier: 3.563A pdb=" N GLY O 82 " --> pdb=" O ASP O 78 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG O 87 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET O 90 " --> pdb=" O GLN O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 141 removed outlier: 3.692A pdb=" N LYS O 105 " --> pdb=" O ASP O 101 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLY O 131 " --> pdb=" O VAL O 127 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ILE O 132 " --> pdb=" O GLY O 128 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP O 134 " --> pdb=" O ARG O 130 " (cutoff:3.500A) Processing helix chain 'O' and resid 162 through 259 removed outlier: 3.637A pdb=" N LEU O 167 " --> pdb=" O ILE O 163 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR O 168 " --> pdb=" O ARG O 164 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA O 189 " --> pdb=" O GLN O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 280 through 291 removed outlier: 4.088A pdb=" N ASN O 286 " --> pdb=" O SER O 282 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA O 288 " --> pdb=" O ALA O 284 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N GLY O 289 " --> pdb=" O LEU O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 305 removed outlier: 3.501A pdb=" N ARG O 299 " --> pdb=" O SER O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 316 through 331 removed outlier: 4.370A pdb=" N GLN O 322 " --> pdb=" O ALA O 318 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU O 323 " --> pdb=" O GLN O 319 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLU O 331 " --> pdb=" O ARG O 327 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 68 removed outlier: 3.606A pdb=" N ILE P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL P 66 " --> pdb=" O TYR P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 76 Processing helix chain 'P' and resid 78 through 86 removed outlier: 3.534A pdb=" N GLY P 82 " --> pdb=" O ASP P 78 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 141 removed outlier: 5.239A pdb=" N GLY P 131 " --> pdb=" O VAL P 127 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE P 132 " --> pdb=" O GLY P 128 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL P 133 " --> pdb=" O GLN P 129 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP P 134 " --> pdb=" O ARG P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 145 through 150 removed outlier: 3.844A pdb=" N ASN P 149 " --> pdb=" O ALA P 145 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN P 150 " --> pdb=" O GLY P 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 145 through 150' Processing helix chain 'P' and resid 150 through 155 removed outlier: 3.545A pdb=" N GLU P 154 " --> pdb=" O GLN P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 162 through 259 removed outlier: 4.084A pdb=" N GLU P 166 " --> pdb=" O GLU P 162 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR P 168 " --> pdb=" O ARG P 164 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN P 171 " --> pdb=" O LEU P 167 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA P 189 " --> pdb=" O GLN P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 280 through 291 removed outlier: 4.280A pdb=" N ASN P 286 " --> pdb=" O SER P 282 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ALA P 288 " --> pdb=" O ALA P 284 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N GLY P 289 " --> pdb=" O LEU P 285 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 305 Processing helix chain 'P' and resid 316 through 331 removed outlier: 4.510A pdb=" N GLN P 322 " --> pdb=" O ALA P 318 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU P 323 " --> pdb=" O GLN P 319 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU P 331 " --> pdb=" O ARG P 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 68 removed outlier: 3.915A pdb=" N ILE Q 39 " --> pdb=" O ALA Q 35 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER Q 41 " --> pdb=" O GLY Q 37 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN Q 65 " --> pdb=" O SER Q 61 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL Q 66 " --> pdb=" O TYR Q 62 " (cutoff:3.500A) Processing helix chain 'Q' and resid 70 through 76 Processing helix chain 'Q' and resid 78 through 87 removed outlier: 3.624A pdb=" N GLY Q 82 " --> pdb=" O ASP Q 78 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG Q 87 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 141 removed outlier: 3.687A pdb=" N LYS Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLY Q 131 " --> pdb=" O VAL Q 127 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE Q 132 " --> pdb=" O GLY Q 128 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 155 removed outlier: 3.833A pdb=" N GLU Q 154 " --> pdb=" O GLN Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 259 removed outlier: 4.001A pdb=" N GLU Q 166 " --> pdb=" O GLU Q 162 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR Q 168 " --> pdb=" O ARG Q 164 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 291 removed outlier: 4.279A pdb=" N ASN Q 286 " --> pdb=" O SER Q 282 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ALA Q 288 " --> pdb=" O ALA Q 284 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLY Q 289 " --> pdb=" O LEU Q 285 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 305 removed outlier: 3.500A pdb=" N ARG Q 299 " --> pdb=" O SER Q 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 316 through 331 removed outlier: 4.198A pdb=" N GLN Q 322 " --> pdb=" O ALA Q 318 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU Q 323 " --> pdb=" O GLN Q 319 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU Q 331 " --> pdb=" O ARG Q 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 59 through 65 removed outlier: 3.933A pdb=" N MET A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 138 removed outlier: 3.725A pdb=" N ALA A 133 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 152 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 59 through 65 removed outlier: 3.760A pdb=" N MET B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 138 removed outlier: 3.919A pdb=" N ALA B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN B 138 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 152 Processing helix chain 'C' and resid 6 through 15 removed outlier: 4.075A pdb=" N PHE C 10 " --> pdb=" O SER C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 64 removed outlier: 3.594A pdb=" N MET C 63 " --> pdb=" O SER C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 138 removed outlier: 3.975A pdb=" N ALA C 133 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ARG C 134 " --> pdb=" O ARG C 130 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASN C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 152 removed outlier: 3.616A pdb=" N TYR C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 15 removed outlier: 4.212A pdb=" N PHE D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 56 removed outlier: 3.589A pdb=" N SER D 55 " --> pdb=" O MET D 51 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN D 56 " --> pdb=" O ALA D 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 51 through 56' Processing helix chain 'D' and resid 59 through 65 removed outlier: 3.701A pdb=" N MET D 63 " --> pdb=" O SER D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 138 removed outlier: 3.841A pdb=" N ALA D 133 " --> pdb=" O ASP D 129 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 134 " --> pdb=" O ARG D 130 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 152 Processing helix chain 'E' and resid 6 through 15 removed outlier: 4.343A pdb=" N PHE E 10 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 15 " --> pdb=" O GLY E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 65 removed outlier: 3.834A pdb=" N MET E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 138 removed outlier: 3.901A pdb=" N ALA E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ASN E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 152 removed outlier: 3.751A pdb=" N TYR E 148 " --> pdb=" O SER E 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 15 Processing helix chain 'F' and resid 59 through 65 removed outlier: 3.932A pdb=" N MET F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 138 removed outlier: 3.973A pdb=" N ALA F 133 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG F 134 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 152 removed outlier: 3.558A pdb=" N TYR F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 15 removed outlier: 3.800A pdb=" N GLY G 11 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL G 12 " --> pdb=" O MET G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 65 removed outlier: 4.386A pdb=" N MET G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE G 64 " --> pdb=" O ARG G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 138 removed outlier: 3.617A pdb=" N ALA G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG G 134 " --> pdb=" O ARG G 130 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 152 Processing helix chain 'H' and resid 6 through 15 removed outlier: 4.037A pdb=" N PHE H 10 " --> pdb=" O SER H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 49 Processing helix chain 'H' and resid 51 through 56 removed outlier: 4.538A pdb=" N ASN H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 65 removed outlier: 3.658A pdb=" N MET H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 138 removed outlier: 4.098A pdb=" N ALA H 133 " --> pdb=" O ASP H 129 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG H 134 " --> pdb=" O ARG H 130 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN H 138 " --> pdb=" O ARG H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.934A pdb=" N TYR H 148 " --> pdb=" O SER H 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 15 removed outlier: 4.051A pdb=" N PHE I 10 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 64 Processing helix chain 'I' and resid 77 through 138 removed outlier: 4.310A pdb=" N ALA I 133 " --> pdb=" O ASP I 129 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ARG I 134 " --> pdb=" O ARG I 130 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 152 removed outlier: 3.656A pdb=" N TYR I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AA7, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AA9, first strand: chain 'I' and resid 66 through 67 2290 hydrogen bonds defined for protein. 6843 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: 9.60 Time building geometry restraints manager: 14.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5917 1.32 - 1.44: 7681 1.44 - 1.57: 17938 1.57 - 1.69: 0 1.69 - 1.82: 324 Bond restraints: 31860 Sorted by residual: bond pdb=" CA SER I 59 " pdb=" CB SER I 59 " ideal model delta sigma weight residual 1.532 1.457 0.075 1.58e-02 4.01e+03 2.26e+01 bond pdb=" C ALA K 210 " pdb=" N PHE K 211 " ideal model delta sigma weight residual 1.334 1.277 0.058 1.33e-02 5.65e+03 1.89e+01 bond pdb=" C GLN Q 215 " pdb=" N ARG Q 216 " ideal model delta sigma weight residual 1.334 1.278 0.057 1.33e-02 5.65e+03 1.82e+01 bond pdb=" C PHE K 211 " pdb=" O PHE K 211 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.16e-02 7.43e+03 1.53e+01 bond pdb=" C ARG K 216 " pdb=" N ASP K 217 " ideal model delta sigma weight residual 1.332 1.284 0.048 1.40e-02 5.10e+03 1.18e+01 ... (remaining 31855 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.54: 423 105.54 - 112.63: 15374 112.63 - 119.72: 11822 119.72 - 126.82: 15122 126.82 - 133.91: 126 Bond angle restraints: 42867 Sorted by residual: angle pdb=" C GLN Q 215 " pdb=" N ARG Q 216 " pdb=" CA ARG Q 216 " ideal model delta sigma weight residual 120.44 109.67 10.77 1.36e+00 5.41e-01 6.27e+01 angle pdb=" C ARG K 216 " pdb=" CA ARG K 216 " pdb=" CB ARG K 216 " ideal model delta sigma weight residual 110.95 99.74 11.21 1.55e+00 4.16e-01 5.23e+01 angle pdb=" CA PHE P 211 " pdb=" CB PHE P 211 " pdb=" CG PHE P 211 " ideal model delta sigma weight residual 113.80 119.91 -6.11 1.00e+00 1.00e+00 3.73e+01 angle pdb=" C ALA K 210 " pdb=" N PHE K 211 " pdb=" CA PHE K 211 " ideal model delta sigma weight residual 120.44 112.64 7.80 1.36e+00 5.41e-01 3.29e+01 angle pdb=" C PHE P 211 " pdb=" N THR P 212 " pdb=" CA THR P 212 " ideal model delta sigma weight residual 120.38 112.27 8.11 1.46e+00 4.69e-01 3.09e+01 ... (remaining 42862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 16422 17.97 - 35.93: 2412 35.93 - 53.90: 721 53.90 - 71.87: 145 71.87 - 89.83: 46 Dihedral angle restraints: 19746 sinusoidal: 7929 harmonic: 11817 Sorted by residual: dihedral pdb=" CD ARG Q 216 " pdb=" NE ARG Q 216 " pdb=" CZ ARG Q 216 " pdb=" NH1 ARG Q 216 " ideal model delta sinusoidal sigma weight residual 0.00 76.32 -76.32 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CD ARG K 216 " pdb=" NE ARG K 216 " pdb=" CZ ARG K 216 " pdb=" NH1 ARG K 216 " ideal model delta sinusoidal sigma weight residual 0.00 -56.84 56.84 1 1.00e+01 1.00e-02 4.35e+01 dihedral pdb=" C ARG K 216 " pdb=" N ARG K 216 " pdb=" CA ARG K 216 " pdb=" CB ARG K 216 " ideal model delta harmonic sigma weight residual -122.60 -108.72 -13.88 0 2.50e+00 1.60e-01 3.08e+01 ... (remaining 19743 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4065 0.054 - 0.108: 536 0.108 - 0.162: 27 0.162 - 0.216: 6 0.216 - 0.269: 1 Chirality restraints: 4635 Sorted by residual: chirality pdb=" CA ARG K 216 " pdb=" N ARG K 216 " pdb=" C ARG K 216 " pdb=" CB ARG K 216 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA PHE K 211 " pdb=" N PHE K 211 " pdb=" C PHE K 211 " pdb=" CB PHE K 211 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ASP C 103 " pdb=" N ASP C 103 " pdb=" C ASP C 103 " pdb=" CB ASP C 103 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4632 not shown) Planarity restraints: 5985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 216 " -1.038 9.50e-02 1.11e+02 4.65e-01 1.31e+02 pdb=" NE ARG Q 216 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG Q 216 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 216 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 216 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 216 " 0.899 9.50e-02 1.11e+02 4.03e-01 9.85e+01 pdb=" NE ARG K 216 " -0.056 2.00e-02 2.50e+03 pdb=" CZ ARG K 216 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG K 216 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 216 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 252 " -0.548 9.50e-02 1.11e+02 2.46e-01 3.69e+01 pdb=" NE ARG R 252 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG R 252 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG R 252 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG R 252 " -0.019 2.00e-02 2.50e+03 ... (remaining 5982 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3776 2.74 - 3.28: 33202 3.28 - 3.82: 53589 3.82 - 4.36: 53641 4.36 - 4.90: 91940 Nonbonded interactions: 236148 Sorted by model distance: nonbonded pdb=" OH TYR C 116 " pdb=" OXT ARG C 155 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR R 240 " pdb=" OE2 GLU R 298 " model vdw 2.214 3.040 nonbonded pdb=" O ASP L 95 " pdb=" OG1 THR L 99 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR M 240 " pdb=" OE2 GLU M 298 " model vdw 2.219 3.040 nonbonded pdb=" OH TYR P 240 " pdb=" OE2 GLU P 298 " model vdw 2.222 3.040 ... (remaining 236143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.660 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: 0.030 Extract box with map and model: 1.190 Check model and map are aligned: 0.220 Set scattering table: 0.290 Process input model: 82.870 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.004 0.075 31860 Z= 0.267 Angle : 0.708 11.458 42867 Z= 0.391 Chirality : 0.035 0.269 4635 Planarity : 0.010 0.465 5985 Dihedral : 18.785 89.833 12150 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer: Outliers : 0.37 % Allowed : 30.23 % Favored : 69.40 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.14), residues: 4122 helix: 2.54 (0.10), residues: 2997 sheet: None (None), residues: 0 loop : -3.18 (0.16), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 77 HIS 0.004 0.001 HIS R 198 PHE 0.044 0.002 PHE O 211 TYR 0.044 0.001 TYR B 116 ARG 0.016 0.001 ARG J 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 425 time to evaluate : 3.307 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: R 90 MET cc_start: 0.8738 (mmt) cc_final: 0.8468 (mmm) REVERT: J 42 ARG cc_start: 0.7870 (ptp90) cc_final: 0.7661 (ptp90) REVERT: K 42 ARG cc_start: 0.7741 (mtt-85) cc_final: 0.7089 (mpt-90) REVERT: K 72 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8483 (tm-30) REVERT: K 215 GLN cc_start: 0.8294 (mt0) cc_final: 0.8047 (mt0) REVERT: L 42 ARG cc_start: 0.7848 (mtm-85) cc_final: 0.7233 (mtm-85) REVERT: L 90 MET cc_start: 0.9201 (mtp) cc_final: 0.8902 (mtp) REVERT: L 95 ASP cc_start: 0.8692 (t70) cc_final: 0.8214 (t70) REVERT: M 42 ARG cc_start: 0.8567 (ptm160) cc_final: 0.7880 (ptp-170) REVERT: O 221 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7845 (ttm110) REVERT: P 215 GLN cc_start: 0.8690 (tt0) cc_final: 0.8381 (tt0) REVERT: Q 260 MET cc_start: -0.2310 (mmp) cc_final: -0.2935 (tmm) REVERT: B 149 MET cc_start: 0.8008 (mmp) cc_final: 0.7133 (ptt) REVERT: C 33 MET cc_start: 0.0567 (ttp) cc_final: 0.0022 (ttp) REVERT: C 104 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8340 (tm-30) REVERT: D 102 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7505 (ttm-80) REVERT: E 98 GLN cc_start: 0.8697 (tt0) cc_final: 0.8433 (tp40) REVERT: E 104 GLN cc_start: 0.8537 (tm-30) cc_final: 0.8328 (tm-30) REVERT: E 149 MET cc_start: 0.8033 (mmp) cc_final: 0.7674 (tpt) REVERT: F 98 GLN cc_start: 0.8456 (tt0) cc_final: 0.8144 (tp40) REVERT: F 99 ARG cc_start: 0.8209 (mmm-85) cc_final: 0.7242 (ttt-90) REVERT: F 102 ARG cc_start: 0.8688 (ttm170) cc_final: 0.8310 (ttp-110) REVERT: F 132 ARG cc_start: 0.7975 (tpt90) cc_final: 0.7669 (mmp80) REVERT: G 149 MET cc_start: 0.7449 (mmp) cc_final: 0.5955 (pmm) REVERT: H 95 ASN cc_start: 0.8973 (t0) cc_final: 0.8756 (t0) outliers start: 12 outliers final: 4 residues processed: 434 average time/residue: 0.4216 time to fit residues: 286.1835 Evaluate side-chains 415 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 411 time to evaluate : 3.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain H residue 103 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 2.9990 chunk 306 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 207 optimal weight: 10.0000 chunk 163 optimal weight: 0.9990 chunk 317 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 193 optimal weight: 0.2980 chunk 236 optimal weight: 0.0020 chunk 367 optimal weight: 0.0050 overall best weight: 0.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 238 GLN J 159 ASN K 238 GLN L 238 GLN M 238 GLN N 238 GLN O 238 GLN P 238 GLN Q 238 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN H 41 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31860 Z= 0.159 Angle : 0.510 6.615 42867 Z= 0.272 Chirality : 0.034 0.155 4635 Planarity : 0.004 0.170 5985 Dihedral : 3.585 48.859 4588 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 2.02 % Allowed : 27.93 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.14), residues: 4122 helix: 3.04 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.16 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 77 HIS 0.002 0.001 HIS R 198 PHE 0.030 0.001 PHE B 112 TYR 0.022 0.001 TYR B 116 ARG 0.007 0.000 ARG Q 216 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 443 time to evaluate : 3.241 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: R 72 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8385 (tm-30) REVERT: R 260 MET cc_start: 0.3531 (tpt) cc_final: 0.3071 (mmp) REVERT: J 324 MET cc_start: 0.8659 (mmm) cc_final: 0.8395 (mmp) REVERT: K 42 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7445 (mtm-85) REVERT: L 90 MET cc_start: 0.9000 (mtp) cc_final: 0.8758 (mtp) REVERT: L 95 ASP cc_start: 0.8830 (t70) cc_final: 0.8334 (t70) REVERT: M 126 GLU cc_start: 0.8790 (tt0) cc_final: 0.8476 (tm-30) REVERT: O 219 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8705 (tt) REVERT: O 221 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7933 (ttm110) REVERT: P 42 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8104 (mmm-85) REVERT: P 215 GLN cc_start: 0.8688 (tt0) cc_final: 0.8380 (tt0) REVERT: Q 42 ARG cc_start: 0.7938 (mtt90) cc_final: 0.7674 (mtm-85) REVERT: Q 101 ASP cc_start: 0.8561 (p0) cc_final: 0.8151 (p0) REVERT: Q 126 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7993 (tm-30) REVERT: Q 185 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8170 (tm-30) REVERT: Q 260 MET cc_start: -0.2065 (mmp) cc_final: -0.2809 (tmm) REVERT: A 63 MET cc_start: 0.7449 (mpt) cc_final: 0.7062 (mpt) REVERT: B 99 ARG cc_start: 0.7677 (mmm-85) cc_final: 0.7071 (tpp-160) REVERT: B 148 TYR cc_start: 0.8328 (OUTLIER) cc_final: 0.7204 (m-80) REVERT: C 33 MET cc_start: 0.1196 (ttp) cc_final: 0.0590 (ttp) REVERT: C 121 GLN cc_start: 0.8558 (tt0) cc_final: 0.8314 (tt0) REVERT: C 132 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7394 (mmm160) REVERT: D 102 ARG cc_start: 0.7775 (mtp-110) cc_final: 0.7481 (ttm-80) REVERT: E 98 GLN cc_start: 0.8732 (tt0) cc_final: 0.8481 (tp40) REVERT: E 104 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8242 (tm-30) REVERT: F 98 GLN cc_start: 0.8472 (tt0) cc_final: 0.8172 (tp40) REVERT: F 99 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7260 (ttt-90) REVERT: F 102 ARG cc_start: 0.8608 (ttm170) cc_final: 0.8288 (ttp-110) REVERT: F 132 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7700 (mmp80) REVERT: H 95 ASN cc_start: 0.8970 (t0) cc_final: 0.8739 (t0) REVERT: H 149 MET cc_start: 0.8023 (ttp) cc_final: 0.7543 (ptt) outliers start: 65 outliers final: 29 residues processed: 485 average time/residue: 0.4254 time to fit residues: 322.7598 Evaluate side-chains 447 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 415 time to evaluate : 3.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 36 LEU Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 238 GLN Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 238 GLN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 250 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 368 optimal weight: 0.8980 chunk 398 optimal weight: 2.9990 chunk 328 optimal weight: 2.9990 chunk 365 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 295 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 149 ASN J 159 ASN K 156 GLN M 171 GLN Q 58 ASN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN F 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 31860 Z= 0.232 Angle : 0.528 7.440 42867 Z= 0.283 Chirality : 0.035 0.157 4635 Planarity : 0.004 0.128 5985 Dihedral : 3.611 50.434 4587 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.43 % Favored : 93.40 % Rotamer: Outliers : 2.82 % Allowed : 28.06 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.15), residues: 4122 helix: 3.01 (0.10), residues: 2979 sheet: -2.55 (0.60), residues: 90 loop : -3.40 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 77 HIS 0.001 0.000 HIS R 198 PHE 0.034 0.001 PHE A 112 TYR 0.017 0.001 TYR G 116 ARG 0.005 0.000 ARG P 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 418 time to evaluate : 3.424 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: R 95 ASP cc_start: 0.8397 (t70) cc_final: 0.8193 (t70) REVERT: R 101 ASP cc_start: 0.9020 (p0) cc_final: 0.8794 (p0) REVERT: R 260 MET cc_start: 0.3792 (tpt) cc_final: 0.3376 (mmp) REVERT: J 324 MET cc_start: 0.8820 (mmm) cc_final: 0.8545 (mmm) REVERT: K 36 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7621 (tt) REVERT: L 90 MET cc_start: 0.9145 (mtp) cc_final: 0.8864 (mtp) REVERT: L 95 ASP cc_start: 0.8908 (t70) cc_final: 0.8408 (t70) REVERT: N 56 GLU cc_start: 0.8940 (tp30) cc_final: 0.8679 (tp30) REVERT: N 101 ASP cc_start: 0.8950 (p0) cc_final: 0.8494 (p0) REVERT: N 159 ASN cc_start: 0.9197 (t0) cc_final: 0.8929 (t0) REVERT: O 95 ASP cc_start: 0.8968 (t0) cc_final: 0.8705 (t0) REVERT: O 221 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.8088 (ttm110) REVERT: P 101 ASP cc_start: 0.8760 (p0) cc_final: 0.8388 (p0) REVERT: P 215 GLN cc_start: 0.8788 (tt0) cc_final: 0.8393 (tt0) REVERT: Q 101 ASP cc_start: 0.8599 (p0) cc_final: 0.8395 (p0) REVERT: Q 185 GLN cc_start: 0.8624 (tm-30) cc_final: 0.8228 (tm-30) REVERT: Q 221 ARG cc_start: 0.8337 (ttm110) cc_final: 0.7683 (ttm110) REVERT: Q 260 MET cc_start: -0.1983 (mmp) cc_final: -0.2712 (tmm) REVERT: A 3 TYR cc_start: 0.1095 (OUTLIER) cc_final: 0.0077 (p90) REVERT: A 63 MET cc_start: 0.7205 (mpt) cc_final: 0.6807 (mpt) REVERT: B 99 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7220 (tpp-160) REVERT: B 148 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: C 1 MET cc_start: 0.4329 (pmm) cc_final: 0.1777 (tpt) REVERT: C 8 MET cc_start: 0.1240 (mmm) cc_final: 0.0811 (mtm) REVERT: C 33 MET cc_start: 0.1256 (ttp) cc_final: 0.0701 (ttp) REVERT: C 51 MET cc_start: 0.3087 (mmp) cc_final: 0.1009 (mtt) REVERT: C 104 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8127 (tm-30) REVERT: C 111 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8405 (mp10) REVERT: D 51 MET cc_start: 0.2350 (tpp) cc_final: 0.1893 (tpp) REVERT: D 102 ARG cc_start: 0.7852 (mtp-110) cc_final: 0.7567 (ttm-80) REVERT: D 121 GLN cc_start: 0.8084 (tt0) cc_final: 0.7881 (tm-30) REVERT: E 14 LEU cc_start: 0.3577 (OUTLIER) cc_final: 0.3362 (pt) REVERT: E 98 GLN cc_start: 0.8770 (tt0) cc_final: 0.8527 (tp40) REVERT: F 98 GLN cc_start: 0.8433 (tt0) cc_final: 0.8122 (tp40) REVERT: F 99 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7244 (ttt-90) REVERT: F 102 ARG cc_start: 0.8655 (ttm170) cc_final: 0.8326 (ttp-110) REVERT: F 132 ARG cc_start: 0.8184 (tpt90) cc_final: 0.7619 (mmp80) REVERT: F 149 MET cc_start: 0.8943 (tpt) cc_final: 0.8139 (ptt) REVERT: H 95 ASN cc_start: 0.8993 (t0) cc_final: 0.8761 (t0) outliers start: 91 outliers final: 55 residues processed: 476 average time/residue: 0.4274 time to fit residues: 317.6653 Evaluate side-chains 472 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 412 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 THR Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 14 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 50.0000 chunk 277 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 247 optimal weight: 0.2980 chunk 369 optimal weight: 5.9990 chunk 391 optimal weight: 0.6980 chunk 193 optimal weight: 0.9980 chunk 350 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 171 GLN M 176 ASN P 156 GLN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN F 111 GLN H 111 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31860 Z= 0.176 Angle : 0.501 7.728 42867 Z= 0.266 Chirality : 0.034 0.156 4635 Planarity : 0.003 0.084 5985 Dihedral : 3.505 48.805 4585 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.97 % Favored : 93.81 % Rotamer: Outliers : 3.29 % Allowed : 27.13 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.15), residues: 4122 helix: 3.10 (0.10), residues: 2979 sheet: -2.55 (0.60), residues: 90 loop : -3.37 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 77 HIS 0.001 0.000 HIS R 198 PHE 0.037 0.001 PHE O 211 TYR 0.016 0.001 TYR G 116 ARG 0.012 0.000 ARG Q 216 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 428 time to evaluate : 3.685 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: R 94 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8763 (mp) REVERT: R 95 ASP cc_start: 0.8311 (t70) cc_final: 0.7898 (t70) REVERT: R 260 MET cc_start: 0.4083 (tpt) cc_final: 0.3532 (mmp) REVERT: J 126 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8191 (tm-30) REVERT: J 324 MET cc_start: 0.8839 (mmm) cc_final: 0.8568 (mmm) REVERT: K 90 MET cc_start: 0.8565 (mtp) cc_final: 0.8255 (mtt) REVERT: K 228 LEU cc_start: 0.7469 (tt) cc_final: 0.6573 (pp) REVERT: L 38 ASP cc_start: 0.7790 (p0) cc_final: 0.6977 (p0) REVERT: L 42 ARG cc_start: 0.7781 (mtm-85) cc_final: 0.7190 (mtt-85) REVERT: L 90 MET cc_start: 0.9105 (mtp) cc_final: 0.8810 (mtp) REVERT: L 95 ASP cc_start: 0.8848 (t70) cc_final: 0.8361 (t70) REVERT: N 101 ASP cc_start: 0.8831 (p0) cc_final: 0.8427 (p0) REVERT: O 36 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7149 (tt) REVERT: O 95 ASP cc_start: 0.8954 (t0) cc_final: 0.8686 (t0) REVERT: O 159 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8539 (t0) REVERT: O 221 ARG cc_start: 0.8425 (ttm-80) cc_final: 0.8081 (ttm110) REVERT: P 92 MET cc_start: 0.9166 (mmm) cc_final: 0.8882 (mmm) REVERT: P 101 ASP cc_start: 0.8761 (p0) cc_final: 0.8113 (p0) REVERT: P 215 GLN cc_start: 0.8785 (tt0) cc_final: 0.8394 (tt0) REVERT: Q 58 ASN cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (t0) REVERT: Q 101 ASP cc_start: 0.8647 (p0) cc_final: 0.8394 (p0) REVERT: Q 185 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8227 (tm-30) REVERT: Q 221 ARG cc_start: 0.8358 (ttm110) cc_final: 0.7661 (ttm110) REVERT: Q 260 MET cc_start: -0.2018 (mmp) cc_final: -0.2725 (tmm) REVERT: A 3 TYR cc_start: 0.1116 (OUTLIER) cc_final: 0.0079 (p90) REVERT: B 99 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7182 (tpp-160) REVERT: B 148 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: B 152 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.7971 (p0) REVERT: C 1 MET cc_start: 0.4237 (pmm) cc_final: 0.1910 (tpt) REVERT: C 8 MET cc_start: 0.1242 (mmm) cc_final: 0.0811 (mtm) REVERT: C 33 MET cc_start: 0.1256 (ttp) cc_final: 0.0656 (ttp) REVERT: C 51 MET cc_start: 0.2874 (mmp) cc_final: 0.0943 (mtt) REVERT: C 104 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8148 (tm-30) REVERT: D 51 MET cc_start: 0.1987 (tpp) cc_final: 0.1536 (tpp) REVERT: D 102 ARG cc_start: 0.7929 (mtp-110) cc_final: 0.7661 (ttm-80) REVERT: D 121 GLN cc_start: 0.8251 (tt0) cc_final: 0.7996 (tm-30) REVERT: E 35 MET cc_start: -0.1315 (pmm) cc_final: -0.1687 (ptt) REVERT: E 98 GLN cc_start: 0.8763 (tt0) cc_final: 0.8560 (tp40) REVERT: E 149 MET cc_start: 0.8222 (mmp) cc_final: 0.7418 (tpt) REVERT: F 98 GLN cc_start: 0.8415 (tt0) cc_final: 0.8184 (tp40) REVERT: F 99 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.6984 (ttt-90) REVERT: F 114 MET cc_start: 0.9085 (tmm) cc_final: 0.8730 (tmm) REVERT: F 132 ARG cc_start: 0.8180 (tpt90) cc_final: 0.7608 (mmp80) REVERT: F 149 MET cc_start: 0.8875 (tpt) cc_final: 0.8088 (ptt) REVERT: H 95 ASN cc_start: 0.8996 (t0) cc_final: 0.8764 (t0) REVERT: H 149 MET cc_start: 0.8013 (ttp) cc_final: 0.7617 (ptt) REVERT: I 114 MET cc_start: 0.9155 (tpp) cc_final: 0.8793 (ttm) outliers start: 106 outliers final: 60 residues processed: 502 average time/residue: 0.4224 time to fit residues: 332.1937 Evaluate side-chains 488 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 421 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain P residue 93 ASN Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 103 ASP Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 334 optimal weight: 40.0000 chunk 270 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 351 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN L 30 GLN M 171 GLN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN E 111 GLN F 111 GLN I 121 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31860 Z= 0.199 Angle : 0.515 10.273 42867 Z= 0.272 Chirality : 0.035 0.162 4635 Planarity : 0.003 0.062 5985 Dihedral : 3.506 47.904 4585 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.21 % Favored : 93.57 % Rotamer: Outliers : 3.45 % Allowed : 27.37 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.15), residues: 4122 helix: 3.08 (0.10), residues: 2979 sheet: -2.58 (0.59), residues: 90 loop : -3.35 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 77 HIS 0.001 0.000 HIS R 198 PHE 0.039 0.001 PHE O 211 TYR 0.016 0.001 TYR G 116 ARG 0.008 0.000 ARG J 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 428 time to evaluate : 3.648 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: R 95 ASP cc_start: 0.8298 (t70) cc_final: 0.7870 (t70) REVERT: R 260 MET cc_start: 0.4167 (tpt) cc_final: 0.3828 (mmp) REVERT: J 42 ARG cc_start: 0.7760 (ptp90) cc_final: 0.7532 (ptp90) REVERT: J 90 MET cc_start: 0.9181 (ttm) cc_final: 0.8749 (ttt) REVERT: J 126 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8335 (tm-30) REVERT: J 217 ASP cc_start: 0.8870 (t0) cc_final: 0.8399 (t0) REVERT: J 324 MET cc_start: 0.8877 (mmm) cc_final: 0.8650 (mmm) REVERT: K 36 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7599 (tt) REVERT: K 42 ARG cc_start: 0.7637 (mtm-85) cc_final: 0.7326 (mtm-85) REVERT: K 90 MET cc_start: 0.8555 (mtp) cc_final: 0.8246 (mtt) REVERT: L 90 MET cc_start: 0.9216 (mtp) cc_final: 0.8942 (mtp) REVERT: L 95 ASP cc_start: 0.8917 (t70) cc_final: 0.8443 (t70) REVERT: L 260 MET cc_start: 0.0762 (mmp) cc_final: -0.1456 (tmm) REVERT: N 101 ASP cc_start: 0.8835 (p0) cc_final: 0.8469 (p0) REVERT: N 159 ASN cc_start: 0.9179 (t0) cc_final: 0.8897 (t0) REVERT: O 36 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7193 (tt) REVERT: O 42 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7431 (ptp90) REVERT: O 95 ASP cc_start: 0.8981 (t0) cc_final: 0.8703 (t0) REVERT: O 221 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.8050 (ttm110) REVERT: P 92 MET cc_start: 0.9193 (mmm) cc_final: 0.8992 (mmm) REVERT: P 101 ASP cc_start: 0.8804 (p0) cc_final: 0.8225 (p0) REVERT: P 215 GLN cc_start: 0.8818 (tt0) cc_final: 0.8467 (tt0) REVERT: Q 42 ARG cc_start: 0.8042 (mtt90) cc_final: 0.7687 (mtt90) REVERT: Q 58 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8449 (t160) REVERT: Q 101 ASP cc_start: 0.8786 (p0) cc_final: 0.8516 (p0) REVERT: Q 185 GLN cc_start: 0.8567 (tm-30) cc_final: 0.8166 (tm-30) REVERT: Q 214 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8236 (tt0) REVERT: Q 260 MET cc_start: -0.2030 (mmp) cc_final: -0.2566 (tmm) REVERT: A 3 TYR cc_start: 0.1119 (OUTLIER) cc_final: 0.0062 (p90) REVERT: A 114 MET cc_start: 0.8989 (tmm) cc_final: 0.8607 (tmm) REVERT: B 99 ARG cc_start: 0.7784 (mmm-85) cc_final: 0.7165 (tpp-160) REVERT: B 110 ARG cc_start: 0.7231 (ttt-90) cc_final: 0.7014 (ttp80) REVERT: B 148 TYR cc_start: 0.8244 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: B 149 MET cc_start: 0.7801 (mmm) cc_final: 0.7145 (ptt) REVERT: C 1 MET cc_start: 0.4190 (pmm) cc_final: 0.3143 (ppp) REVERT: C 8 MET cc_start: 0.1243 (mmm) cc_final: 0.0814 (mtm) REVERT: C 51 MET cc_start: 0.2844 (mmp) cc_final: 0.0925 (mtt) REVERT: D 102 ARG cc_start: 0.7923 (mtp-110) cc_final: 0.7669 (ttm-80) REVERT: D 121 GLN cc_start: 0.8370 (tt0) cc_final: 0.8074 (tm-30) REVERT: E 35 MET cc_start: -0.1506 (pmm) cc_final: -0.1830 (ptt) REVERT: E 98 GLN cc_start: 0.8779 (tt0) cc_final: 0.8528 (tp40) REVERT: E 111 GLN cc_start: 0.8954 (tp40) cc_final: 0.8751 (tp40) REVERT: E 149 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7563 (tpp) REVERT: F 98 GLN cc_start: 0.8437 (tt0) cc_final: 0.8216 (tp40) REVERT: F 99 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7014 (ttt-90) REVERT: F 114 MET cc_start: 0.9065 (tmm) cc_final: 0.8719 (tmm) REVERT: F 132 ARG cc_start: 0.8230 (tpt90) cc_final: 0.7609 (mmp80) REVERT: H 95 ASN cc_start: 0.9002 (t0) cc_final: 0.8770 (t0) REVERT: I 114 MET cc_start: 0.9132 (tpp) cc_final: 0.8842 (ttm) outliers start: 111 outliers final: 76 residues processed: 502 average time/residue: 0.4330 time to fit residues: 338.2097 Evaluate side-chains 503 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 421 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 131 GLN Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 1.9990 chunk 352 optimal weight: 0.7980 chunk 77 optimal weight: 0.7980 chunk 229 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 391 optimal weight: 0.9980 chunk 325 optimal weight: 2.9990 chunk 181 optimal weight: 0.0670 chunk 32 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 171 GLN P 156 GLN F 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31860 Z= 0.186 Angle : 0.513 9.061 42867 Z= 0.270 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.139 5985 Dihedral : 3.476 46.478 4583 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.11 % Favored : 93.64 % Rotamer: Outliers : 3.20 % Allowed : 27.81 % Favored : 68.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.14), residues: 4122 helix: 3.11 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.10 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 77 HIS 0.001 0.000 HIS R 198 PHE 0.030 0.001 PHE O 211 TYR 0.012 0.001 TYR G 116 ARG 0.012 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 425 time to evaluate : 3.023 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: R 94 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8830 (mp) REVERT: R 95 ASP cc_start: 0.8259 (t70) cc_final: 0.7698 (t70) REVERT: R 260 MET cc_start: 0.4323 (tpt) cc_final: 0.3971 (mmp) REVERT: J 217 ASP cc_start: 0.8855 (t0) cc_final: 0.8367 (t0) REVERT: J 324 MET cc_start: 0.8893 (mmm) cc_final: 0.8675 (mmm) REVERT: K 36 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7564 (tt) REVERT: K 90 MET cc_start: 0.8494 (mtp) cc_final: 0.8199 (mtt) REVERT: L 90 MET cc_start: 0.9227 (mtp) cc_final: 0.8946 (mtp) REVERT: L 95 ASP cc_start: 0.8903 (t70) cc_final: 0.8438 (t70) REVERT: L 260 MET cc_start: 0.0724 (mmp) cc_final: -0.1444 (tmm) REVERT: N 101 ASP cc_start: 0.8825 (p0) cc_final: 0.8472 (p0) REVERT: N 159 ASN cc_start: 0.9159 (t0) cc_final: 0.8879 (t0) REVERT: N 270 MET cc_start: 0.6336 (pmm) cc_final: 0.5980 (pmm) REVERT: O 36 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7197 (tt) REVERT: O 95 ASP cc_start: 0.9014 (t0) cc_final: 0.8747 (t0) REVERT: O 159 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8558 (t0) REVERT: O 214 GLU cc_start: 0.8334 (mm-30) cc_final: 0.7918 (mt-10) REVERT: O 221 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8152 (ttm110) REVERT: P 101 ASP cc_start: 0.8777 (p0) cc_final: 0.8246 (p0) REVERT: P 119 LYS cc_start: 0.9086 (mtpt) cc_final: 0.8868 (ttmm) REVERT: P 188 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8140 (mm-40) REVERT: P 215 GLN cc_start: 0.8717 (tt0) cc_final: 0.8375 (tt0) REVERT: P 216 ARG cc_start: 0.7846 (mtp85) cc_final: 0.7379 (mtp180) REVERT: Q 58 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8195 (t160) REVERT: Q 90 MET cc_start: 0.9259 (mtp) cc_final: 0.8911 (mtp) REVERT: Q 101 ASP cc_start: 0.8808 (p0) cc_final: 0.8528 (p0) REVERT: Q 185 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8183 (tm-30) REVERT: Q 214 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8231 (tt0) REVERT: Q 221 ARG cc_start: 0.8323 (ttm110) cc_final: 0.7750 (ttm110) REVERT: Q 260 MET cc_start: -0.2048 (mmp) cc_final: -0.2557 (tmm) REVERT: A 3 TYR cc_start: 0.1140 (OUTLIER) cc_final: 0.0075 (p90) REVERT: A 114 MET cc_start: 0.9061 (tmm) cc_final: 0.8654 (tmm) REVERT: B 99 ARG cc_start: 0.7792 (mmm-85) cc_final: 0.7161 (tpp-160) REVERT: B 148 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: C 1 MET cc_start: 0.4306 (pmm) cc_final: 0.3305 (ppp) REVERT: C 8 MET cc_start: 0.1244 (mmm) cc_final: 0.0817 (mtm) REVERT: C 51 MET cc_start: 0.2451 (mmp) cc_final: 0.0669 (mtt) REVERT: C 148 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8439 (m-80) REVERT: D 102 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7682 (ttm-80) REVERT: E 35 MET cc_start: -0.1500 (pmm) cc_final: -0.1824 (ptt) REVERT: E 98 GLN cc_start: 0.8775 (tt0) cc_final: 0.8525 (tp40) REVERT: E 149 MET cc_start: 0.8240 (OUTL------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 159 ASN M 171 GLN P 156 GLN D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31860 Z= 0.166 Angle : 0.513 11.506 42867 Z= 0.268 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.112 5985 Dihedral : 3.401 44.990 4581 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.11 % Favored : 93.64 % Rotamer: Outliers : 3.29 % Allowed : 27.93 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.14), residues: 4122 helix: 3.15 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.08 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 77 HIS 0.000 0.000 HIS K 198 PHE 0.027 0.001 PHE O 211 TYR 0.013 0.001 TYR B 148 ARG 0.010 0.000 ARG L 216 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 429 time to evaluate : 2.797 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: R 94 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8828 (mp) REVERT: R 95 ASP cc_start: 0.8191 (t70) cc_final: 0.7645 (t70) REVERT: R 260 MET cc_start: 0.4340 (tpt) cc_final: 0.3969 (mmp) REVERT: J 42 ARG cc_start: 0.7724 (ptp90) cc_final: 0.7513 (ptp90) REVERT: J 217 ASP cc_start: 0.8803 (t0) cc_final: 0.8341 (t0) REVERT: K 36 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7608 (tt) REVERT: K 42 ARG cc_start: 0.7640 (mtm-85) cc_final: 0.7362 (mtm-85) REVERT: K 90 MET cc_start: 0.8455 (mtp) cc_final: 0.8179 (mtt) REVERT: K 159 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8668 (t0) REVERT: L 90 MET cc_start: 0.9203 (mtp) cc_final: 0.8930 (mtp) REVERT: L 95 ASP cc_start: 0.8878 (t70) cc_final: 0.8423 (t70) REVERT: L 101 ASP cc_start: 0.8875 (p0) cc_final: 0.8444 (p0) REVERT: L 260 MET cc_start: 0.0420 (mmp) cc_final: -0.1613 (tmm) REVERT: N 101 ASP cc_start: 0.8810 (p0) cc_final: 0.8468 (p0) REVERT: O 36 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7198 (tt) REVERT: O 95 ASP cc_start: 0.9004 (t0) cc_final: 0.8752 (t0) REVERT: O 159 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8601 (t0) REVERT: O 214 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7954 (mt-10) REVERT: O 221 ARG cc_start: 0.8526 (ttm-80) cc_final: 0.8145 (ttm110) REVERT: P 101 ASP cc_start: 0.8797 (p0) cc_final: 0.8299 (p0) REVERT: P 119 LYS cc_start: 0.9078 (mtpt) cc_final: 0.8861 (ttmm) REVERT: P 188 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8103 (mm-40) REVERT: P 216 ARG cc_start: 0.7579 (mtp85) cc_final: 0.6869 (mtp180) REVERT: P 260 MET cc_start: 0.2453 (pmm) cc_final: 0.0322 (mmt) REVERT: Q 56 GLU cc_start: 0.8859 (tp30) cc_final: 0.8586 (tp30) REVERT: Q 58 ASN cc_start: 0.8778 (OUTLIER) cc_final: 0.8179 (t160) REVERT: Q 90 MET cc_start: 0.9217 (mtp) cc_final: 0.8860 (mtp) REVERT: Q 101 ASP cc_start: 0.8806 (p0) cc_final: 0.8495 (p0) REVERT: Q 185 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8159 (tm-30) REVERT: Q 214 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8218 (tt0) REVERT: Q 221 ARG cc_start: 0.8296 (ttm110) cc_final: 0.7728 (ttm110) REVERT: Q 260 MET cc_start: -0.2050 (mmp) cc_final: -0.2547 (tmm) REVERT: A 3 TYR cc_start: 0.1362 (OUTLIER) cc_final: 0.0123 (p90) REVERT: A 114 MET cc_start: 0.9079 (tmm) cc_final: 0.8674 (tmm) REVERT: A 121 GLN cc_start: 0.8226 (tt0) cc_final: 0.8014 (tt0) REVERT: B 148 TYR cc_start: 0.8604 (OUTLIER) cc_final: 0.8002 (m-80) REVERT: B 149 MET cc_start: 0.7853 (mmm) cc_final: 0.7034 (ptt) REVERT: C 1 MET cc_start: 0.4330 (pmm) cc_final: 0.3272 (ppp) REVERT: C 8 MET cc_start: 0.1246 (mmm) cc_final: 0.0818 (mtm) REVERT: C 51 MET cc_start: 0.2430 (mmp) cc_final: 0.0664 (mtt) REVERT: C 148 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.8506 (m-80) REVERT: D 102 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7679 (ttm-80) REVERT: D 121 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.8153 (tm-30) REVERT: E 35 MET cc_start: -0.1498 (pmm) cc_final: -0.1823 (ptt) REVERT: E 98 GLN cc_start: 0.8710 (tt0) cc_final: 0.8461 (tp40) REVERT: E 99 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.6779 (ttt-90) REVERT: E 109 ARG cc_start: 0.8580 (ttm-80) cc_final: 0.8185 (tpp80) REVERT: E 132 ARG cc_start: 0.8077 (tpt90) cc_final: 0.7471 (mmp80) REVERT: E 149 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7456 (tpp) REVERT: E 155 ARG cc_start: 0.6541 (ttp80) cc_final: 0.5990 (tmm-80) REVERT: F 98 GLN cc_start: 0.8504 (tt0) cc_final: 0.8289 (tp40) REVERT: F 99 ARG cc_start: 0.8206 (mmm-85) cc_final: 0.7047 (ttt-90) REVERT: F 114 MET cc_start: 0.9058 (tmm) cc_final: 0.8815 (tmm) REVERT: F 132 ARG cc_start: 0.8231 (tpt90) cc_final: 0.7596 (mmp80) REVERT: F 149 MET cc_start: 0.8653 (mmm) cc_final: 0.7911 (ppp) REVERT: H 95 ASN cc_start: 0.9057 (t0) cc_final: 0.8789 (t0) outliers start: 106 outliers final: 80 residues processed: 499 average time/residue: 0.3748 time to fit residues: 293.8842 Evaluate side-chains 513 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 421 time to evaluate : 3.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 233 optimal weight: 0.0470 chunk 117 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 265 optimal weight: 6.9990 chunk 192 optimal weight: 0.4980 chunk 36 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 159 ASN K 159 ASN M 171 GLN P 156 GLN D 121 GLN F 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31860 Z= 0.171 Angle : 0.521 10.052 42867 Z= 0.272 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.099 5985 Dihedral : 3.375 43.994 4581 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.67 % Rotamer: Outliers : 3.45 % Allowed : 27.90 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.14), residues: 4122 helix: 3.16 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.06 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 77 HIS 0.001 0.000 HIS Q 198 PHE 0.030 0.001 PHE O 211 TYR 0.011 0.001 TYR B 148 ARG 0.008 0.000 ARG Q 220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 424 time to evaluate : 3.244 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: R 94 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8847 (mp) REVERT: R 95 ASP cc_start: 0.8175 (t70) cc_final: 0.7611 (t70) REVERT: J 42 ARG cc_start: 0.7731 (ptp90) cc_final: 0.7445 (ptp90) REVERT: J 90 MET cc_start: 0.9144 (ttt) cc_final: 0.8937 (ttm) REVERT: J 217 ASP cc_start: 0.8821 (t0) cc_final: 0.8351 (t0) REVERT: K 36 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (tt) REVERT: K 42 ARG cc_start: 0.7628 (mtm-85) cc_final: 0.7088 (mtm-85) REVERT: K 90 MET cc_start: 0.8429 (mtp) cc_final: 0.8163 (mtt) REVERT: K 221 ARG cc_start: 0.8453 (tpp80) cc_final: 0.8139 (tpp80) REVERT: L 90 MET cc_start: 0.9212 (mtp) cc_final: 0.8949 (mtp) REVERT: L 95 ASP cc_start: 0.8892 (t70) cc_final: 0.8438 (t70) REVERT: L 260 MET cc_start: 0.0211 (mmp) cc_final: -0.1737 (tmm) REVERT: N 101 ASP cc_start: 0.8819 (p0) cc_final: 0.8476 (p0) REVERT: N 228 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7483 (pp) REVERT: O 36 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7230 (tt) REVERT: O 95 ASP cc_start: 0.8917 (t0) cc_final: 0.8630 (t0) REVERT: O 159 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8600 (t0) REVERT: O 214 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7910 (mt-10) REVERT: O 221 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8208 (ttm110) REVERT: P 101 ASP cc_start: 0.8791 (p0) cc_final: 0.8298 (p0) REVERT: P 119 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8862 (ttmm) REVERT: P 188 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8104 (mm-40) REVERT: P 216 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7065 (ttt180) REVERT: P 260 MET cc_start: 0.2754 (pmm) cc_final: 0.0661 (mmt) REVERT: Q 42 ARG cc_start: 0.8052 (mtt90) cc_final: 0.7737 (mtm-85) REVERT: Q 56 GLU cc_start: 0.8854 (tp30) cc_final: 0.8583 (tp30) REVERT: Q 58 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8424 (t160) REVERT: Q 101 ASP cc_start: 0.8861 (p0) cc_final: 0.8609 (p0) REVERT: Q 185 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8147 (tm-30) REVERT: Q 214 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8218 (tt0) REVERT: Q 260 MET cc_start: -0.2047 (mmp) cc_final: -0.2541 (tmm) REVERT: A 3 TYR cc_start: 0.1307 (OUTLIER) cc_final: 0.0110 (p90) REVERT: A 114 MET cc_start: 0.9099 (tmm) cc_final: 0.8688 (tmm) REVERT: A 121 GLN cc_start: 0.8224 (tt0) cc_final: 0.8017 (tt0) REVERT: B 148 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7980 (m-80) REVERT: C 1 MET cc_start: 0.4295 (pmm) cc_final: 0.3265 (ppp) REVERT: C 8 MET cc_start: 0.1248 (mmm) cc_final: 0.0820 (mtm) REVERT: C 51 MET cc_start: 0.2432 (mmp) cc_final: 0.0673 (mtt) REVERT: C 148 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: D 102 ARG cc_start: 0.7983 (mtp-110) cc_final: 0.7686 (ttm-80) REVERT: D 121 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.8081 (tm-30) REVERT: E 35 MET cc_start: -0.1496 (pmm) cc_final: -0.1820 (ptt) REVERT: E 98 GLN cc_start: 0.8706 (tt0) cc_final: 0.8459 (tp40) REVERT: E 99 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.6769 (ttt-90) REVERT: E 109 ARG cc_start: 0.8568 (ttm-80) cc_final: 0.8198 (tpp80) REVERT: E 132 ARG cc_start: 0.8081 (tpt90) cc_final: 0.7469 (mmp80) REVERT: E 149 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7460 (tpp) REVERT: E 155 ARG cc_start: 0.6549 (ttp80) cc_final: 0.6040 (tmm-80) REVERT: F 98 GLN cc_start: 0.8465 (tt0) cc_final: 0.8260 (tp40) REVERT: F 99 ARG cc_start: 0.8204 (mmm-85) cc_final: 0.7044 (ttt-90) REVERT: F 114 MET cc_start: 0.9023 (tmm) cc_final: 0.8801 (tmm) REVERT: F 132 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7592 (mmp80) REVERT: F 149 MET cc_start: 0.8667 (mmm) cc_final: 0.7909 (ppp) REVERT: H 95 ASN cc_start: 0.9057 (t0) cc_final: 0.8791 (t0) outliers start: 111 outliers final: 86 residues processed: 495 average time/residue: 0.4232 time to fit residues: 328.4882 Evaluate side-chains 516 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 418 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 53 LEU Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 36 LEU Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 81 SER Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 216 ARG Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 chunk 341 optimal weight: 3.9990 chunk 363 optimal weight: 0.5980 chunk 218 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 285 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 328 optimal weight: 0.0170 chunk 344 optimal weight: 10.0000 chunk 362 optimal weight: 20.0000 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 159 ASN K 106 GLN K 159 ASN M 171 GLN P 156 GLN Q 30 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31860 Z= 0.180 Angle : 0.532 12.829 42867 Z= 0.277 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.093 5985 Dihedral : 3.366 42.903 4581 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.72 % Rotamer: Outliers : 3.29 % Allowed : 28.34 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.14), residues: 4122 helix: 3.15 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.05 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 77 HIS 0.000 0.000 HIS J 198 PHE 0.029 0.001 PHE O 211 TYR 0.010 0.001 TYR N 62 ARG 0.009 0.000 ARG Q 220 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 426 time to evaluate : 3.468 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: R 94 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8871 (mp) REVERT: R 95 ASP cc_start: 0.8198 (t70) cc_final: 0.7595 (t70) REVERT: R 260 MET cc_start: 0.1599 (mmp) cc_final: 0.0530 (tpt) REVERT: J 42 ARG cc_start: 0.7660 (ptp90) cc_final: 0.7384 (ptp90) REVERT: J 217 ASP cc_start: 0.8807 (t0) cc_final: 0.8375 (t0) REVERT: K 36 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7547 (tt) REVERT: K 42 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7052 (mtm-85) REVERT: K 90 MET cc_start: 0.8424 (mtp) cc_final: 0.8159 (mtt) REVERT: K 221 ARG cc_start: 0.8554 (tpp80) cc_final: 0.8246 (tpp80) REVERT: L 90 MET cc_start: 0.9248 (mtp) cc_final: 0.8902 (mtp) REVERT: L 95 ASP cc_start: 0.8892 (t70) cc_final: 0.8439 (t70) REVERT: N 101 ASP cc_start: 0.8810 (p0) cc_final: 0.8467 (p0) REVERT: N 214 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8137 (mt-10) REVERT: N 228 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7491 (pp) REVERT: O 36 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7241 (tt) REVERT: O 159 ASN cc_start: 0.8957 (OUTLIER) cc_final: 0.8620 (t0) REVERT: O 214 GLU cc_start: 0.8322 (mm-30) cc_final: 0.8007 (mt-10) REVERT: O 221 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8211 (ttm110) REVERT: P 101 ASP cc_start: 0.8794 (p0) cc_final: 0.8264 (p0) REVERT: P 119 LYS cc_start: 0.9083 (mtpt) cc_final: 0.8864 (ttmm) REVERT: P 188 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.8104 (mm-40) REVERT: P 216 ARG cc_start: 0.7812 (mtp85) cc_final: 0.6920 (mtp180) REVERT: P 221 ARG cc_start: 0.8577 (tpp80) cc_final: 0.8207 (ttm110) REVERT: P 260 MET cc_start: 0.2742 (pmm) cc_final: 0.0665 (mmt) REVERT: Q 58 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8294 (t0) REVERT: Q 90 MET cc_start: 0.9195 (mtp) cc_final: 0.8935 (mtp) REVERT: Q 101 ASP cc_start: 0.8890 (p0) cc_final: 0.8616 (p0) REVERT: Q 185 GLN cc_start: 0.8555 (tm-30) cc_final: 0.8146 (tm-30) REVERT: Q 214 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8255 (tt0) REVERT: Q 221 ARG cc_start: 0.8299 (ttm110) cc_final: 0.7775 (ttm110) REVERT: Q 260 MET cc_start: -0.2043 (mmp) cc_final: -0.2536 (tmm) REVERT: A 3 TYR cc_start: 0.1317 (OUTLIER) cc_final: 0.0121 (p90) REVERT: A 97 GLN cc_start: 0.8033 (mm110) cc_final: 0.7829 (mm110) REVERT: A 114 MET cc_start: 0.9114 (tmm) cc_final: 0.8695 (tmm) REVERT: A 149 MET cc_start: 0.8919 (tpp) cc_final: 0.8119 (ppp) REVERT: B 99 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7168 (tpp-160) REVERT: B 148 TYR cc_start: 0.8407 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: C 1 MET cc_start: 0.4241 (pmm) cc_final: 0.3244 (ppp) REVERT: C 8 MET cc_start: 0.1251 (mmm) cc_final: 0.0825 (mtm) REVERT: C 51 MET cc_start: 0.2460 (mmp) cc_final: 0.0695 (mtt) REVERT: C 148 TYR cc_start: 0.8775 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: D 102 ARG cc_start: 0.7991 (mtp-110) cc_final: 0.7699 (ttm-80) REVERT: D 121 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8034 (tm-30) REVERT: E 35 MET cc_start: -0.1494 (pmm) cc_final: -0.1816 (ptt) REVERT: E 98 GLN cc_start: 0.8708 (tt0) cc_final: 0.8460 (tp40) REVERT: E 99 ARG cc_start: 0.8019 (mmm-85) cc_final: 0.6766 (ttt-90) REVERT: E 109 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8201 (tpp80) REVERT: E 132 ARG cc_start: 0.8085 (tpt90) cc_final: 0.7466 (mmp80) REVERT: E 149 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7459 (tpp) REVERT: F 98 GLN cc_start: 0.8480 (tt0) cc_final: 0.8264 (tp40) REVERT: F 99 ARG cc_start: 0.8185 (mmm-85) cc_final: 0.6891 (ttt-90) REVERT: F 114 MET cc_start: 0.8994 (tmm) cc_final: 0.8757 (tmm) REVERT: F 132 ARG cc_start: 0.8207 (tpt90) cc_final: 0.7584 (mmp80) REVERT: H 95 ASN cc_start: 0.9057 (t0) cc_final: 0.8790 (t0) outliers start: 106 outliers final: 86 residues processed: 493 average time/residue: 0.4326 time to fit residues: 332.3839 Evaluate side-chains 519 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 421 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 216 ARG Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 0.2980 chunk 384 optimal weight: 7.9990 chunk 234 optimal weight: 9.9990 chunk 182 optimal weight: 0.8980 chunk 267 optimal weight: 0.9980 chunk 403 optimal weight: 7.9990 chunk 371 optimal weight: 4.9990 chunk 321 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 248 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 159 ASN K 159 ASN M 171 GLN A 121 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN F 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31860 Z= 0.188 Angle : 0.542 12.559 42867 Z= 0.283 Chirality : 0.035 0.157 4635 Planarity : 0.003 0.092 5985 Dihedral : 3.384 42.542 4581 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.04 % Favored : 93.72 % Rotamer: Outliers : 3.32 % Allowed : 28.37 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.14), residues: 4122 helix: 3.13 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.03 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 77 HIS 0.000 0.000 HIS K 198 PHE 0.027 0.001 PHE A 112 TYR 0.010 0.001 TYR N 62 ARG 0.010 0.000 ARG Q 220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8244 Ramachandran restraints generated. 4122 Oldfield, 0 Emsley, 4122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 426 time to evaluate : 3.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ASP cc_start: 0.8220 (t70) cc_final: 0.7681 (t70) REVERT: R 260 MET cc_start: 0.1744 (mmp) cc_final: 0.0605 (tpt) REVERT: J 42 ARG cc_start: 0.7698 (ptp90) cc_final: 0.7434 (ptp90) REVERT: J 90 MET cc_start: 0.8908 (ttm) cc_final: 0.8626 (ttm) REVERT: J 217 ASP cc_start: 0.8816 (t0) cc_final: 0.8389 (t0) REVERT: K 36 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7519 (tt) REVERT: K 42 ARG cc_start: 0.7627 (mtm-85) cc_final: 0.7021 (mtm-85) REVERT: K 72 GLU cc_start: 0.8553 (tt0) cc_final: 0.8329 (tm-30) REVERT: K 90 MET cc_start: 0.8420 (mtp) cc_final: 0.8153 (mtt) REVERT: K 159 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8728 (t0) REVERT: K 221 ARG cc_start: 0.8607 (tpp80) cc_final: 0.8318 (tpp80) REVERT: L 90 MET cc_start: 0.9270 (mtp) cc_final: 0.8928 (mtp) REVERT: N 101 ASP cc_start: 0.8797 (p0) cc_final: 0.8414 (p0) REVERT: N 214 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8147 (mt-10) REVERT: N 228 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7498 (pp) REVERT: O 36 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7267 (tt) REVERT: O 159 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8639 (t0) REVERT: O 214 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7997 (mt-10) REVERT: O 221 ARG cc_start: 0.8550 (ttm-80) cc_final: 0.8198 (ttm110) REVERT: P 101 ASP cc_start: 0.8816 (p0) cc_final: 0.8317 (p0) REVERT: P 119 LYS cc_start: 0.9085 (mtpt) cc_final: 0.8865 (ttmm) REVERT: P 188 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8105 (mm-40) REVERT: P 221 ARG cc_start: 0.8652 (tpp80) cc_final: 0.8276 (ttm110) REVERT: P 260 MET cc_start: 0.2918 (pmm) cc_final: 0.1034 (mmt) REVERT: Q 42 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7856 (mtt90) REVERT: Q 58 ASN cc_start: 0.8827 (OUTLIER) cc_final: 0.8334 (t0) REVERT: Q 90 MET cc_start: 0.9231 (mtp) cc_final: 0.9007 (mtp) REVERT: Q 101 ASP cc_start: 0.8913 (p0) cc_final: 0.8650 (p0) REVERT: Q 185 GLN cc_start: 0.8560 (tm-30) cc_final: 0.8152 (tm-30) REVERT: Q 214 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8275 (tt0) REVERT: Q 221 ARG cc_start: 0.8279 (ttm110) cc_final: 0.7748 (ttm110) REVERT: Q 260 MET cc_start: -0.2030 (mmp) cc_final: -0.2526 (tmm) REVERT: A 3 TYR cc_start: 0.1526 (OUTLIER) cc_final: 0.0327 (p90) REVERT: A 97 GLN cc_start: 0.8076 (mm110) cc_final: 0.7860 (mm110) REVERT: A 114 MET cc_start: 0.9131 (tmm) cc_final: 0.8710 (tmm) REVERT: A 149 MET cc_start: 0.8918 (tpp) cc_final: 0.8130 (ppp) REVERT: B 99 ARG cc_start: 0.7795 (mmm-85) cc_final: 0.7151 (tpp-160) REVERT: B 148 TYR cc_start: 0.8401 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: C 1 MET cc_start: 0.4261 (pmm) cc_final: 0.3359 (ppp) REVERT: C 8 MET cc_start: 0.1189 (mmm) cc_final: 0.0760 (mtm) REVERT: C 51 MET cc_start: 0.3011 (mmp) cc_final: 0.0987 (mtt) REVERT: C 148 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8552 (m-80) REVERT: D 102 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7710 (ttm-80) REVERT: D 121 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8221 (tm-30) REVERT: E 35 MET cc_start: -0.1490 (pmm) cc_final: -0.1891 (ptt) REVERT: E 99 ARG cc_start: 0.8022 (mmm-85) cc_final: 0.6802 (ttt-90) REVERT: E 109 ARG cc_start: 0.8574 (ttm-80) cc_final: 0.8337 (ttm-80) REVERT: E 132 ARG cc_start: 0.8121 (tpt90) cc_final: 0.7503 (mmp80) REVERT: E 149 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7465 (tpp) REVERT: F 98 GLN cc_start: 0.8483 (tt0) cc_final: 0.8267 (tp40) REVERT: F 99 ARG cc_start: 0.8194 (mmm-85) cc_final: 0.6903 (ttt-90) REVERT: F 109 ARG cc_start: 0.8415 (tpp80) cc_final: 0.7940 (tpp80) REVERT: F 114 MET cc_start: 0.8964 (tmm) cc_final: 0.8758 (tmm) REVERT: F 132 ARG cc_start: 0.8214 (tpt90) cc_final: 0.7584 (mmp80) REVERT: H 95 ASN cc_start: 0.9058 (t0) cc_final: 0.8790 (t0) REVERT: I 148 TYR cc_start: 0.9102 (OUTLIER) cc_final: 0.8079 (m-10) outliers start: 107 outliers final: 87 residues processed: 494 average time/residue: 0.4348 time to fit residues: 333.0294 Evaluate side-chains 526 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 426 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 140 SER Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 138 THR Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 78 ASP Chi-restraints excluded: chain K residue 105 LYS Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 159 ASN Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 245 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 99 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 46 MET Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 212 THR Chi-restraints excluded: chain N residue 228 LEU Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 53 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 99 THR Chi-restraints excluded: chain O residue 159 ASN Chi-restraints excluded: chain O residue 162 GLU Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 212 THR Chi-restraints excluded: chain P residue 126 GLU Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 188 GLN Chi-restraints excluded: chain P residue 199 SER Chi-restraints excluded: chain P residue 201 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 58 ASN Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 140 SER Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 216 ARG Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 148 TYR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 148 TYR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 67 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain I residue 40 VAL Chi-restraints excluded: chain I residue 59 SER Chi-restraints excluded: chain I residue 67 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 103 ASP Chi-restraints excluded: chain I residue 111 GLN Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 0.9980 chunk 342 optimal weight: 0.8980 chunk 98 optimal weight: 0.5980 chunk 296 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 321 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 330 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN M 171 GLN ** D 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.212943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120451 restraints weight = 48451.693| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.87 r_work: 0.3119 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31860 Z= 0.189 Angle : 0.544 12.352 42867 Z= 0.283 Chirality : 0.035 0.158 4635 Planarity : 0.003 0.090 5985 Dihedral : 3.376 42.215 4581 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.04 % Favored : 93.69 % Rotamer: Outliers : 3.48 % Allowed : 28.12 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.14), residues: 4122 helix: 3.14 (0.10), residues: 2979 sheet: None (None), residues: 0 loop : -3.03 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 77 HIS 0.000 0.000 HIS J 198 PHE 0.029 0.001 PHE E 112 TYR 0.010 0.001 TYR N 62 ARG 0.010 0.000 ARG Q 220 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7277.27 seconds wall clock time: 219 minutes 32.43 seconds (13172.43 seconds total)