Starting phenix.real_space_refine on Sun Apr 14 12:19:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/04_2024/8vxq_43629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/04_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_43629/04_2024/8vxq_43629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/04_2024/8vxq_43629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/04_2024/8vxq_43629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vxq_43629/04_2024/8vxq_43629.pdb" } 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 15.60, per 1000 atoms: 0.49 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: 12.21 Conformation dependent library (CDL) restraints added in 5.7 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: 2.38 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: 9.75 Time building geometry restraints manager: 13.17 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 2.440 nonbonded pdb=" OH TYR R 240 " pdb=" OE2 GLU R 298 " model vdw 2.214 2.440 nonbonded pdb=" O ASP L 95 " pdb=" OG1 THR L 99 " model vdw 2.217 2.440 nonbonded pdb=" OH TYR M 240 " pdb=" OE2 GLU M 298 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR P 240 " pdb=" OE2 GLU P 298 " model vdw 2.222 2.440 ... (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 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 15.450 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 75.950 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.010 ------------------------------------------------------------------------------- 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 : 3.325 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: 0.4431 time to fit residues: 302.0202 Evaluate side-chains 415 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 411 time to evaluate : 3.554 ------------------------------------------------------------------------------- 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: 1.9990 chunk 306 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 317 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 236 optimal weight: 2.9990 chunk 367 optimal weight: 0.1980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 159 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN H 41 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.0792 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= 0.198 Angle : 0.511 6.938 42867 Z= 0.274 Chirality : 0.034 0.154 4635 Planarity : 0.004 0.183 5985 Dihedral : 3.696 47.809 4588 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 1.99 % Allowed : 29.83 % Favored : 68.19 % 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 (0.14), residues: 4122 helix: 3.15 (0.10), residues: 2925 sheet: None (None), residues: 0 loop : -3.26 (0.16), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 77 HIS 0.002 0.000 HIS R 198 PHE 0.031 0.001 PHE B 112 TYR 0.021 0.001 TYR B 116 ARG 0.010 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 487 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 423 time to evaluate : 3.294 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: K 42 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7151 (mpt-90) REVERT: L 90 MET cc_start: 0.9183 (mtp) cc_final: 0.8900 (mtp) REVERT: M 202 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8391 (mmm) REVERT: N 56 GLU cc_start: 0.8961 (tp30) cc_final: 0.8698 (tp30) REVERT: N 159 ASN cc_start: 0.9158 (t0) cc_final: 0.8927 (t0) REVERT: O 221 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7865 (ttm110) REVERT: P 215 GLN cc_start: 0.8673 (tt0) cc_final: 0.8382 (tt0) REVERT: P 251 MET cc_start: -0.0980 (mmp) cc_final: -0.1557 (mmp) REVERT: P 260 MET cc_start: 0.1430 (OUTLIER) cc_final: 0.0293 (ptp) REVERT: Q 36 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7767 (tt) REVERT: Q 42 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7751 (mtt-85) REVERT: Q 90 MET cc_start: 0.8904 (mmt) cc_final: 0.8379 (mmt) REVERT: Q 101 ASP cc_start: 0.8589 (p0) cc_final: 0.8147 (p0) REVERT: Q 126 GLU cc_start: 0.8348 (tm-30) cc_final: 0.7993 (tm-30) REVERT: Q 185 GLN cc_start: 0.8596 (tm-30) cc_final: 0.8213 (tm-30) REVERT: Q 260 MET cc_start: -0.2259 (mmp) cc_final: -0.2859 (tmm) REVERT: A 63 MET cc_start: 0.7538 (mpt) cc_final: 0.7040 (mpt) REVERT: B 99 ARG cc_start: 0.7708 (mmm-85) cc_final: 0.7099 (tpp-160) REVERT: B 148 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7304 (m-80) REVERT: B 151 ARG cc_start: 0.8267 (ttt180) cc_final: 0.7959 (ptm160) REVERT: C 33 MET cc_start: 0.1194 (ttp) cc_final: 0.0586 (ttp) REVERT: C 111 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8345 (mp10) REVERT: C 132 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7312 (mmm160) REVERT: D 102 ARG cc_start: 0.7816 (mtp-110) cc_final: 0.7534 (ttm-80) REVERT: E 98 GLN cc_start: 0.8682 (tt0) cc_final: 0.8426 (tp40) REVERT: E 104 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8241 (tm-30) REVERT: F 98 GLN cc_start: 0.8485 (tt0) cc_final: 0.8179 (tp40) REVERT: F 99 ARG cc_start: 0.8243 (mmm-85) cc_final: 0.7262 (ttt-90) REVERT: F 102 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8321 (ttp-110) REVERT: F 132 ARG cc_start: 0.7998 (tpt90) cc_final: 0.7686 (mmp80) REVERT: F 149 MET cc_start: 0.8961 (tpt) cc_final: 0.8099 (ptt) REVERT: H 95 ASN cc_start: 0.8973 (t0) cc_final: 0.8749 (t0) outliers start: 64 outliers final: 32 residues processed: 460 average time/residue: 0.4478 time to fit residues: 320.4745 Evaluate side-chains 453 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 415 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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 J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 126 GLU Chi-restraints excluded: chain K residue 138 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 138 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 202 MET Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain P residue 159 ASN Chi-restraints excluded: chain P residue 228 LEU Chi-restraints excluded: chain P residue 260 MET Chi-restraints excluded: chain Q residue 36 LEU 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 A residue 74 THR 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 111 GLN Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain C residue 132 ARG Chi-restraints excluded: chain D residue 67 VAL 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 74 THR 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: 0.1980 chunk 114 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 368 optimal weight: 0.8980 chunk 398 optimal weight: 2.9990 chunk 328 optimal weight: 9.9990 chunk 365 optimal weight: 10.0000 chunk 125 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 159 ASN Q 159 ASN A 121 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1146 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= 0.204 Angle : 0.503 7.167 42867 Z= 0.269 Chirality : 0.034 0.156 4635 Planarity : 0.003 0.126 5985 Dihedral : 3.625 50.280 4587 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.72 % Favored : 93.11 % Rotamer: Outliers : 3.26 % Allowed : 29.05 % Favored : 67.69 % 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: 2.18 (0.15), residues: 4122 helix: 3.06 (0.10), residues: 2979 sheet: -2.53 (0.59), residues: 90 loop : -3.37 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 77 HIS 0.001 0.000 HIS R 198 PHE 0.031 0.001 PHE A 112 TYR 0.016 0.001 TYR G 116 ARG 0.007 0.000 ARG B 132 *********************** 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 528 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 423 time to evaluate : 3.385 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 95 ASP cc_start: 0.8321 (t70) cc_final: 0.8086 (t70) REVERT: R 260 MET cc_start: -0.0477 (mmp) cc_final: -0.0833 (tpt) REVERT: J 42 ARG cc_start: 0.7702 (ptp90) cc_final: 0.7494 (ptp90) REVERT: J 162 GLU cc_start: 0.8208 (mt-10) cc_final: 0.8008 (mt-10) REVERT: K 36 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7799 (tt) REVERT: K 42 ARG cc_start: 0.7788 (mtt-85) cc_final: 0.7329 (mpt-90) REVERT: L 90 MET cc_start: 0.9275 (mtp) cc_final: 0.8969 (mtp) REVERT: M 202 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8472 (mmm) REVERT: N 56 GLU cc_start: 0.8944 (tp30) cc_final: 0.8707 (tp30) REVERT: N 159 ASN cc_start: 0.9204 (t0) cc_final: 0.8912 (t0) REVERT: N 221 ARG cc_start: 0.8225 (ttm110) cc_final: 0.8004 (ttm110) REVERT: N 305 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6594 (ptpp) REVERT: O 95 ASP cc_start: 0.9020 (t0) cc_final: 0.8742 (t0) REVERT: O 221 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8020 (ttm110) REVERT: P 101 ASP cc_start: 0.8773 (p0) cc_final: 0.8448 (p0) REVERT: P 215 GLN cc_start: 0.8799 (tt0) cc_final: 0.8408 (tt0) REVERT: P 260 MET cc_start: 0.1828 (OUTLIER) cc_final: 0.0818 (ptp) REVERT: Q 36 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7748 (tt) REVERT: Q 42 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7657 (mtt-85) REVERT: Q 90 MET cc_start: 0.9036 (mmt) cc_final: 0.8582 (mmt) REVERT: Q 101 ASP cc_start: 0.8680 (p0) cc_final: 0.8377 (p0) REVERT: Q 185 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8235 (tm-30) REVERT: Q 260 MET cc_start: -0.2243 (mmp) cc_final: -0.2828 (tmm) REVERT: A 3 TYR cc_start: 0.1107 (OUTLIER) cc_final: 0.0082 (p90) REVERT: B 99 ARG cc_start: 0.7786 (mmm-85) cc_final: 0.7202 (tpp-160) REVERT: B 148 TYR cc_start: 0.8299 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: B 151 ARG cc_start: 0.8174 (ttt180) cc_final: 0.7874 (ptm160) REVERT: C 1 MET cc_start: 0.4236 (pmm) cc_final: 0.1598 (tpt) REVERT: C 8 MET cc_start: 0.1234 (mmm) cc_final: 0.0809 (mtm) REVERT: C 33 MET cc_start: 0.1249 (ttp) cc_final: 0.0687 (ttp) REVERT: D 51 MET cc_start: 0.2474 (tpp) cc_final: 0.1947 (tpp) REVERT: D 102 ARG cc_start: 0.7856 (mtp-110) cc_final: 0.7580 (ttm-80) REVERT: E 14 LEU cc_start: 0.3606 (OUTLIER) cc_final: 0.3372 (pt) REVERT: E 98 GLN cc_start: 0.8767 (tt0) cc_final: 0.8524 (tp40) REVERT: E 104 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8229 (tm-30) REVERT: F 98 GLN cc_start: 0.8427 (tt0) cc_final: 0.8204 (tp40) REVERT: F 149 MET cc_start: 0.8886 (tpt) cc_final: 0.8098 (ptt) REVERT: H 95 ASN cc_start: 0.8988 (t0) cc_final: 0.8754 (t0) REVERT: H 149 MET cc_start: 0.8035 (ttp) cc_final: 0.7551 (ptt) outliers start: 105 outliers final: 64 residues processed: 492 average time/residue: 0.4589 time to fit residues: 353.0611 Evaluate side-chains 483 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 411 time to evaluate : 3.524 ------------------------------------------------------------------------------- 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 201 SER Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 279 ASP 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 138 THR Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 202 MET 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 305 LYS Chi-restraints excluded: chain O residue 66 VAL 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 P residue 260 MET Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain Q residue 36 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 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 B residue 1 MET 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 103 ASP 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 E residue 78 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain G residue 3 TYR 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 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 125 THR 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: 1.9990 chunk 191 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 175 optimal weight: 7.9990 chunk 247 optimal weight: 1.9990 chunk 369 optimal weight: 4.9990 chunk 391 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 350 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 L 275 GLN M 176 ASN P 93 ASN A 121 GLN B 98 GLN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN F 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31860 Z= 0.294 Angle : 0.546 7.650 42867 Z= 0.294 Chirality : 0.036 0.158 4635 Planarity : 0.004 0.104 5985 Dihedral : 3.766 48.747 4585 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.06 % Favored : 92.75 % Rotamer: Outliers : 4.16 % Allowed : 28.68 % Favored : 67.16 % 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: 2.14 (0.14), residues: 4122 helix: 2.96 (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 0.019 0.003 TRP E 77 HIS 0.002 0.001 HIS R 198 PHE 0.040 0.002 PHE O 211 TYR 0.015 0.001 TYR G 116 ARG 0.007 0.000 ARG L 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 560 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 426 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: symmetry clash revert: symmetry clash REVERT: R 95 ASP cc_start: 0.8453 (t70) cc_final: 0.8157 (t70) REVERT: R 260 MET cc_start: -0.0675 (mmp) cc_final: -0.1249 (tpt) REVERT: J 217 ASP cc_start: 0.8912 (t0) cc_final: 0.8482 (t0) REVERT: L 90 MET cc_start: 0.9369 (mtp) cc_final: 0.9045 (mtp) REVERT: L 260 MET cc_start: 0.0599 (mmp) cc_final: -0.0290 (mmt) REVERT: N 101 ASP cc_start: 0.8972 (p0) cc_final: 0.8713 (p0) REVERT: N 305 LYS cc_start: 0.7040 (OUTLIER) cc_final: 0.6621 (ptpp) REVERT: O 36 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7210 (tt) REVERT: O 95 ASP cc_start: 0.9088 (t0) cc_final: 0.8785 (t0) REVERT: O 176 ASN cc_start: 0.8674 (t0) cc_final: 0.8449 (m110) REVERT: O 221 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8148 (ttm110) REVERT: P 101 ASP cc_start: 0.8901 (p0) cc_final: 0.8652 (p0) REVERT: P 215 GLN cc_start: 0.8882 (tt0) cc_final: 0.8477 (tt0) REVERT: P 260 MET cc_start: 0.2321 (OUTLIER) cc_final: 0.2046 (pmm) REVERT: Q 36 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7817 (tt) REVERT: Q 42 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7722 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8891 (tp30) cc_final: 0.8597 (tp30) REVERT: Q 101 ASP cc_start: 0.8951 (p0) cc_final: 0.8569 (p0) REVERT: Q 185 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8250 (tm-30) REVERT: Q 214 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8251 (tt0) REVERT: Q 221 ARG cc_start: 0.8351 (ttm110) cc_final: 0.7763 (ttm110) REVERT: Q 260 MET cc_start: -0.2265 (mmp) cc_final: -0.2827 (tmm) REVERT: A 3 TYR cc_start: 0.1153 (OUTLIER) cc_final: 0.0079 (p90) REVERT: B 99 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7210 (tpp-160) REVERT: B 148 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.7514 (m-80) REVERT: B 151 ARG cc_start: 0.8155 (ttt180) cc_final: 0.7834 (ptm160) REVERT: C 1 MET cc_start: 0.4313 (pmm) cc_final: 0.3122 (ppp) REVERT: C 8 MET cc_start: 0.1185 (mmm) cc_final: 0.0756 (mtm) REVERT: C 51 MET cc_start: 0.3918 (mmp) cc_final: 0.1827 (mtt) REVERT: C 111 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: D 102 ARG cc_start: 0.7952 (mtp-110) cc_final: 0.7709 (ttm-80) REVERT: E 98 GLN cc_start: 0.8737 (tt0) cc_final: 0.8496 (tp40) REVERT: E 104 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8289 (tm-30) REVERT: F 114 MET cc_start: 0.9084 (tmm) cc_final: 0.8728 (tmm) REVERT: H 95 ASN cc_start: 0.9005 (t0) cc_final: 0.8772 (t0) REVERT: I 114 MET cc_start: 0.9133 (tpp) cc_final: 0.8880 (ttm) outliers start: 134 outliers final: 85 residues processed: 527 average time/residue: 0.4434 time to fit residues: 366.3322 Evaluate side-chains 512 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 420 time to evaluate : 3.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 81 SER 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 212 THR Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 170 VAL 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 279 ASP 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 138 THR Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU 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 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 48 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 94 LEU Chi-restraints excluded: chain N residue 127 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 140 SER Chi-restraints excluded: chain N residue 157 LEU Chi-restraints excluded: chain N residue 201 SER Chi-restraints excluded: chain N residue 305 LYS Chi-restraints excluded: chain O residue 36 LEU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 201 SER Chi-restraints excluded: chain O residue 215 GLN 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 P residue 260 MET Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain Q residue 36 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 138 THR 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 B residue 1 MET 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 55 SER 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 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 114 MET Chi-restraints excluded: chain D residue 127 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 74 THR 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 G residue 74 THR Chi-restraints excluded: chain H residue 67 VAL 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 125 THR 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: 0.9980 chunk 5 optimal weight: 0.5980 chunk 291 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 334 optimal weight: 40.0000 chunk 270 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 199 optimal weight: 0.8980 chunk 351 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 K 176 ASN M 156 GLN M 176 ASN P 176 ASN Q 30 GLN B 98 GLN D 121 GLN F 111 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31860 Z= 0.197 Angle : 0.516 9.449 42867 Z= 0.272 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.084 5985 Dihedral : 3.668 46.951 4585 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.67 % Favored : 93.11 % Rotamer: Outliers : 3.88 % Allowed : 29.21 % Favored : 66.91 % 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: 2.18 (0.14), residues: 4122 helix: 3.05 (0.10), residues: 2979 sheet: -2.68 (0.57), residues: 90 loop : -3.32 (0.16), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 77 HIS 0.001 0.000 HIS R 198 PHE 0.030 0.001 PHE G 112 TYR 0.014 0.001 TYR G 116 ARG 0.016 0.000 ARG L 216 *********************** 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 545 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 420 time to evaluate : 3.391 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 95 ASP cc_start: 0.8387 (t70) cc_final: 0.8008 (t70) REVERT: R 260 MET cc_start: -0.0048 (mmp) cc_final: -0.0860 (tpt) REVERT: R 305 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7027 (ptpp) REVERT: J 42 ARG cc_start: 0.7695 (ptp90) cc_final: 0.7475 (ptp90) REVERT: J 217 ASP cc_start: 0.8880 (t0) cc_final: 0.8448 (t0) REVERT: K 36 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7601 (tt) REVERT: K 42 ARG cc_start: 0.7505 (mtm-85) cc_final: 0.6857 (mtm-85) REVERT: L 90 MET cc_start: 0.9336 (mtp) cc_final: 0.9057 (mtp) REVERT: L 101 ASP cc_start: 0.8988 (p0) cc_final: 0.8495 (p0) REVERT: L 126 GLU cc_start: 0.8933 (tt0) cc_final: 0.8732 (tm-30) REVERT: L 260 MET cc_start: 0.0462 (mmp) cc_final: -0.1354 (tmm) REVERT: N 101 ASP cc_start: 0.8931 (p0) cc_final: 0.8514 (p0) REVERT: O 36 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7277 (tt) REVERT: O 159 ASN cc_start: 0.8982 (OUTLIER) cc_final: 0.8638 (t0) REVERT: O 214 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7943 (mt-10) REVERT: O 221 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8100 (ttm110) REVERT: P 101 ASP cc_start: 0.8950 (p0) cc_final: 0.8691 (p0) REVERT: P 188 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: P 215 GLN cc_start: 0.8890 (tt0) cc_final: 0.8495 (tt0) REVERT: P 260 MET cc_start: 0.2250 (OUTLIER) cc_final: 0.1976 (pmm) REVERT: Q 42 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7716 (mtt-85) REVERT: Q 90 MET cc_start: 0.9105 (mmt) cc_final: 0.8711 (mmt) REVERT: Q 101 ASP cc_start: 0.8967 (p0) cc_final: 0.8558 (p0) REVERT: Q 185 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8258 (tm-30) REVERT: Q 214 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8263 (tt0) REVERT: Q 221 ARG cc_start: 0.8326 (ttm110) cc_final: 0.7745 (ttm110) REVERT: Q 260 MET cc_start: -0.2258 (mmp) cc_final: -0.2810 (tmm) REVERT: A 3 TYR cc_start: 0.1375 (OUTLIER) cc_final: 0.0129 (p90) REVERT: B 99 ARG cc_start: 0.7813 (mmm-85) cc_final: 0.7223 (tpp-160) REVERT: B 148 TYR cc_start: 0.8415 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 149 MET cc_start: 0.7749 (mmm) cc_final: 0.7094 (ptt) REVERT: B 151 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7909 (ptm160) REVERT: C 1 MET cc_start: 0.4565 (pmm) cc_final: 0.3314 (ppp) REVERT: C 8 MET cc_start: 0.1181 (mmm) cc_final: 0.0755 (mtm) REVERT: C 51 MET cc_start: 0.3368 (mmp) cc_final: 0.1327 (mtt) REVERT: C 111 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: D 102 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7692 (ttm-80) REVERT: D 121 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: E 35 MET cc_start: -0.1492 (pmm) cc_final: -0.1774 (ptt) REVERT: E 98 GLN cc_start: 0.8729 (tt0) cc_final: 0.8466 (tp40) REVERT: E 99 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.6832 (ttt-90) REVERT: E 104 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8244 (tm-30) REVERT: E 109 ARG cc_start: 0.8735 (ttm-80) cc_final: 0.8180 (tpp80) REVERT: E 132 ARG cc_start: 0.7872 (tpt90) cc_final: 0.7466 (mmp80) REVERT: E 149 MET cc_start: 0.8395 (mmp) cc_final: 0.7673 (tpt) REVERT: E 155 ARG cc_start: 0.6513 (ttp80) cc_final: 0.5981 (tmm-80) REVERT: F 114 MET cc_start: 0.9060 (tmm) cc_final: 0.8771 (tmm) REVERT: H 95 ASN cc_start: 0.9001 (t0) cc_final: 0.8769 (t0) REVERT: H 149 MET cc_start: 0.8041 (ttp) cc_final: 0.7487 (ptt) outliers start: 125 outliers final: 85 residues processed: 510 average time/residue: 0.4451 time to fit residues: 352.9383 Evaluate side-chains 507 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 412 time to evaluate : 3.246 ------------------------------------------------------------------------------- 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 59 THR Chi-restraints excluded: chain R residue 81 SER 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 40 ILE Chi-restraints excluded: chain J residue 199 SER Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 279 ASP Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 307 LEU 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 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 199 SER Chi-restraints excluded: chain L residue 201 SER 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 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 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 159 ASN Chi-restraints excluded: chain P residue 93 ASN 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 201 SER Chi-restraints excluded: chain P residue 260 MET Chi-restraints excluded: chain P residue 295 SER Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 319 GLN 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 B residue 1 MET 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 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN 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 78 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 H residue 103 ASP Chi-restraints excluded: chain I residue 16 THR 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 125 THR 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: 0.7980 chunk 352 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 391 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 181 optimal weight: 0.0570 chunk 32 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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 176 ASN N 156 GLN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31860 Z= 0.188 Angle : 0.516 9.481 42867 Z= 0.269 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.065 5985 Dihedral : 3.596 45.960 4585 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.89 % Favored : 92.89 % Rotamer: Outliers : 3.85 % Allowed : 29.48 % Favored : 66.67 % 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: 2.25 (0.15), residues: 4122 helix: 3.10 (0.10), residues: 2979 sheet: -2.69 (0.57), residues: 90 loop : -3.27 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 77 HIS 0.000 0.000 HIS L 198 PHE 0.030 0.001 PHE Q 211 TYR 0.013 0.001 TYR G 116 ARG 0.017 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 549 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 425 time to evaluate : 3.341 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: R 95 ASP cc_start: 0.8372 (t70) cc_final: 0.7951 (t70) REVERT: R 260 MET cc_start: 0.0087 (mmp) cc_final: -0.0761 (tpt) REVERT: R 305 LYS cc_start: 0.7124 (OUTLIER) cc_final: 0.6859 (ptpp) REVERT: J 217 ASP cc_start: 0.8886 (t0) cc_final: 0.8477 (t0) REVERT: K 36 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7640 (tt) REVERT: K 90 MET cc_start: 0.8619 (mtp) cc_final: 0.8297 (mtt) REVERT: L 90 MET cc_start: 0.9328 (mtp) cc_final: 0.9051 (mtp) REVERT: L 101 ASP cc_start: 0.8909 (p0) cc_final: 0.8374 (p0) REVERT: L 260 MET cc_start: 0.0506 (mmp) cc_final: -0.1366 (tmm) REVERT: N 101 ASP cc_start: 0.8927 (p0) cc_final: 0.8518 (p0) REVERT: N 305 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6704 (ptpp) REVERT: O 36 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7323 (tt) REVERT: O 159 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8602 (t0) REVERT: O 214 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7951 (mt-10) REVERT: O 221 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8114 (ttm110) REVERT: P 101 ASP cc_start: 0.8977 (p0) cc_final: 0.8721 (p0) REVERT: P 188 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8142 (mm-40) REVERT: P 215 GLN cc_start: 0.8888 (tt0) cc_final: 0.8496 (tt0) REVERT: P 260 MET cc_start: 0.2225 (OUTLIER) cc_final: 0.1954 (pmm) REVERT: Q 90 MET cc_start: 0.9104 (mmt) cc_final: 0.8714 (mmt) REVERT: Q 101 ASP cc_start: 0.8953 (p0) cc_final: 0.8525 (p0) REVERT: Q 185 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8213 (tm-30) REVERT: Q 214 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8257 (tt0) REVERT: Q 221 ARG cc_start: 0.8341 (ttm110) cc_final: 0.7758 (ttm110) REVERT: Q 260 MET cc_start: -0.2116 (mmp) cc_final: -0.2637 (tmm) REVERT: A 3 TYR cc_start: 0.1324 (OUTLIER) cc_final: 0.0120 (p90) REVERT: B 99 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7248 (tpp-160) REVERT: B 148 TYR cc_start: 0.8419 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: B 151 ARG cc_start: 0.8237 (ttt180) cc_final: 0.7931 (ptm160) REVERT: C 1 MET cc_start: 0.4253 (pmm) cc_final: 0.3005 (ppp) REVERT: C 8 MET cc_start: 0.1185 (mmm) cc_final: 0.0758 (mtm) REVERT: C 33 MET cc_start: 0.1652 (ttp) cc_final: 0.1305 (ttp) REVERT: C 51 MET cc_start: 0.3211 (mmp) cc_final: 0.1273 (mtt) REVERT: C 111 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8318 (mp10) REVERT: D 102 ARG cc_start: 0.7953 (mtp-110) cc_final: 0.7699 (ttm-80) REVERT: D 121 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7850 (pp30) REVERT: E 35 MET cc_start: -0.1496 (pmm) cc_final: -0.1771 (ptt) REVERT: E 98 GLN cc_start: 0.8722 (tt0) cc_final: 0.8461 (tp40) REVERT: E 99 ARG cc_start: 0.8076 (mmm-85) cc_final: 0.6823 (ttt-90) REVERT: E 104 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8231 (tm-30) REVERT: E 109 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8188 (tpp80) REVERT: E 132 ARG cc_start: 0.7876 (tpt90) cc_final: 0.7464 (mmp80) REVERT: E 155 ARG cc_start: 0.6516 (ttp80) cc_final: 0.5988 (tmm-80) REVERT: F 99 ARG cc_start: 0.8160 (mmm-85) cc_final: 0.7057 (ttt-90) REVERT: F 114 MET cc_start: 0.9079 (tmm) cc_final: 0.8803 (tmm) REVERT: F 132 ARG cc_start: 0.8006 (tpt90) cc_final: 0.7680 (mmp80) REVERT: H 95 ASN cc_start: 0.9000 (t0) cc_final: 0.8768 (t0) REVERT: H 149 MET cc_start: 0.8044 (ttp) cc_final: 0.7427 (ptt) outliers start: 124 outliers final: 92 residues processed: 511 average time/residue: 0.4555 time to fit residues: 360.1318 Evaluate side-chains 525 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 422 time to evaluate : 3.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 105 LYS Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 245 GLN Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain J residue 212 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain J residue 245 GLN Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 279 ASP Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 307 LEU 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 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain N residue 40 ILE 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 251 MET Chi-restraints excluded: chain N residue 303 VAL Chi-restraints excluded: chain N residue 305 LYS 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 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 260 MET Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain Q residue 319 GLN 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 82 LEU Chi-restraints excluded: chain B residue 1 MET 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 74 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR 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 16 THR 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 125 THR Chi-restraints excluded: chain I residue 148 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 286 optimal weight: 0.0010 chunk 221 optimal weight: 0.5980 chunk 329 optimal weight: 10.0000 chunk 218 optimal weight: 0.6980 chunk 390 optimal weight: 0.7980 chunk 244 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN K 106 GLN K 159 ASN M 176 ASN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7609 moved from start: 0.1859 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= 0.168 Angle : 0.510 9.657 42867 Z= 0.265 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.033 5985 Dihedral : 3.483 44.208 4583 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.60 % Favored : 93.18 % Rotamer: Outliers : 3.57 % Allowed : 29.95 % Favored : 66.48 % 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: 2.45 (0.14), residues: 4122 helix: 3.20 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -3.03 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 77 HIS 0.001 0.000 HIS J 198 PHE 0.027 0.001 PHE E 112 TYR 0.013 0.001 TYR G 116 ARG 0.008 0.000 ARG J 42 *********************** 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 551 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 436 time to evaluate : 3.395 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: 0.9322 (OUTLIER) cc_final: 0.8899 (mp) REVERT: R 95 ASP cc_start: 0.8389 (t70) cc_final: 0.7895 (t70) REVERT: R 260 MET cc_start: -0.0111 (mmp) cc_final: -0.0917 (tpt) REVERT: R 305 LYS cc_start: 0.7121 (OUTLIER) cc_final: 0.6814 (ptpp) REVERT: J 90 MET cc_start: 0.9107 (ttm) cc_final: 0.8758 (ttt) REVERT: J 217 ASP cc_start: 0.8836 (t0) cc_final: 0.8399 (t0) REVERT: K 36 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7635 (tt) REVERT: K 90 MET cc_start: 0.8509 (mtp) cc_final: 0.8213 (mtt) REVERT: K 202 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8276 (mmm) REVERT: K 221 ARG cc_start: 0.8583 (tpp80) cc_final: 0.8282 (tpp80) REVERT: L 42 ARG cc_start: 0.7803 (mtm-85) cc_final: 0.7162 (mtt-85) REVERT: L 90 MET cc_start: 0.9317 (mtp) cc_final: 0.9037 (mtp) REVERT: L 124 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8837 (mt0) REVERT: L 260 MET cc_start: 0.0079 (mmp) cc_final: -0.1489 (tmm) REVERT: N 101 ASP cc_start: 0.8899 (p0) cc_final: 0.8503 (p0) REVERT: N 119 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8851 (ttmm) REVERT: N 159 ASN cc_start: 0.9207 (t0) cc_final: 0.8875 (t0) REVERT: N 214 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8190 (mt-10) REVERT: O 36 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7317 (tt) REVERT: O 159 ASN cc_start: 0.8912 (OUTLIER) cc_final: 0.8552 (t0) REVERT: O 214 GLU cc_start: 0.8389 (mm-30) cc_final: 0.7984 (mt-10) REVERT: O 221 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8099 (ttm110) REVERT: P 101 ASP cc_start: 0.8993 (p0) cc_final: 0.8742 (p0) REVERT: P 188 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8107 (mm-40) REVERT: P 216 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7591 (ttm170) REVERT: P 221 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8196 (ttm110) REVERT: Q 42 ARG cc_start: 0.8010 (mtt90) cc_final: 0.7573 (mpt-90) REVERT: Q 90 MET cc_start: 0.9130 (mmt) cc_final: 0.8778 (mmt) REVERT: Q 101 ASP cc_start: 0.8977 (p0) cc_final: 0.8512 (p0) REVERT: Q 185 GLN cc_start: 0.8605 (tm-30) cc_final: 0.8186 (tm-30) REVERT: Q 214 GLU cc_start: 0.8475 (mm-30) cc_final: 0.8248 (tt0) REVERT: Q 221 ARG cc_start: 0.8336 (ttm110) cc_final: 0.7713 (ttm110) REVERT: Q 260 MET cc_start: -0.2101 (mmp) cc_final: -0.2612 (tmm) REVERT: A 3 TYR cc_start: 0.1335 (OUTLIER) cc_final: 0.0127 (p90) REVERT: B 99 ARG cc_start: 0.7857 (mmm-85) cc_final: 0.7223 (tpp-160) REVERT: B 110 ARG cc_start: 0.7473 (ttt-90) cc_final: 0.6875 (ttp80) REVERT: B 148 TYR cc_start: 0.8376 (OUTLIER) cc_final: 0.7647 (m-80) REVERT: B 149 MET cc_start: 0.7759 (mmm) cc_final: 0.7173 (ptt) REVERT: B 151 ARG cc_start: 0.8232 (ttt180) cc_final: 0.7925 (ptm160) REVERT: C 1 MET cc_start: 0.4199 (pmm) cc_final: 0.2950 (ppp) REVERT: C 8 MET cc_start: 0.1185 (mmm) cc_final: 0.0760 (mtm) REVERT: C 51 MET cc_start: 0.2902 (mmp) cc_final: 0.0977 (mtt) REVERT: C 111 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.8311 (mp10) REVERT: D 102 ARG cc_start: 0.7954 (mtp-110) cc_final: 0.7708 (ttm-80) REVERT: D 121 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8259 (tm-30) REVERT: E 35 MET cc_start: -0.1495 (pmm) cc_final: -0.1770 (ptt) REVERT: E 98 GLN cc_start: 0.8711 (tt0) cc_final: 0.8456 (tp40) REVERT: E 99 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.6817 (ttt-90) REVERT: E 104 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8206 (tm-30) REVERT: E 109 ARG cc_start: 0.8706 (ttm-80) cc_final: 0.8212 (tpp80) REVERT: E 132 ARG cc_start: 0.7880 (tpt90) cc_final: 0.7457 (mmp80) REVERT: E 155 ARG cc_start: 0.6529 (ttp80) cc_final: 0.5995 (tmm-80) REVERT: F 99 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7053 (ttt-90) REVERT: F 114 MET cc_start: 0.9062 (tmm) cc_final: 0.8807 (tmm) REVERT: F 132 ARG cc_start: 0.8001 (tpt90) cc_final: 0.7621 (mmp80) REVERT: H 95 ASN cc_start: 0.9048 (t0) cc_final: 0.8784 (t0) REVERT: I 148 TYR cc_start: 0.9137 (OUTLIER) cc_final: 0.8133 (m-10) outliers start: 115 outliers final: 82 residues processed: 513 average time/residue: 0.4578 time to fit residues: 363.1596 Evaluate side-chains 520 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 425 time to evaluate : 3.408 ------------------------------------------------------------------------------- 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 59 THR 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 245 GLN Chi-restraints excluded: chain R residue 305 LYS 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 279 ASP Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 307 LEU 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 138 THR Chi-restraints excluded: chain K residue 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 295 SER 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 40 ILE 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 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 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 260 MET Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL 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 82 LEU Chi-restraints excluded: chain B residue 1 MET 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 74 THR Chi-restraints excluded: chain C residue 111 GLN 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 78 VAL Chi-restraints excluded: chain E residue 148 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR 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 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 125 THR 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: 0.9980 chunk 155 optimal weight: 0.7980 chunk 233 optimal weight: 0.4980 chunk 117 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 265 optimal weight: 7.9990 chunk 192 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 306 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 156 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 121 GLN E 111 GLN F 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.1966 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= 0.194 Angle : 0.519 9.853 42867 Z= 0.271 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.034 5985 Dihedral : 3.466 43.109 4581 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.89 % Favored : 92.89 % Rotamer: Outliers : 3.76 % Allowed : 29.36 % Favored : 66.88 % 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: 2.45 (0.14), residues: 4122 helix: 3.19 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -3.01 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 77 HIS 0.000 0.000 HIS Q 198 PHE 0.029 0.001 PHE E 112 TYR 0.012 0.001 TYR G 116 ARG 0.012 0.000 ARG G 109 *********************** 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 548 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 427 time to evaluate : 3.888 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 94 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8931 (mp) REVERT: R 95 ASP cc_start: 0.8360 (t70) cc_final: 0.7820 (t70) REVERT: R 260 MET cc_start: -0.0063 (mmp) cc_final: -0.0896 (tpt) REVERT: R 305 LYS cc_start: 0.7117 (OUTLIER) cc_final: 0.6835 (ptpp) REVERT: J 90 MET cc_start: 0.9154 (ttm) cc_final: 0.8933 (ttt) REVERT: J 96 ARG cc_start: 0.9371 (OUTLIER) cc_final: 0.6989 (mpt90) REVERT: J 217 ASP cc_start: 0.8856 (t0) cc_final: 0.8455 (t0) REVERT: K 36 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7634 (tt) REVERT: K 90 MET cc_start: 0.8510 (mtp) cc_final: 0.8211 (mtt) REVERT: K 202 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8282 (mmm) REVERT: K 221 ARG cc_start: 0.8654 (tpp80) cc_final: 0.8366 (tpp80) REVERT: K 270 MET cc_start: 0.3457 (tpp) cc_final: 0.3234 (tpp) REVERT: L 90 MET cc_start: 0.9344 (mtp) cc_final: 0.9068 (mtp) REVERT: L 101 ASP cc_start: 0.8908 (p0) cc_final: 0.8480 (p0) REVERT: L 260 MET cc_start: 0.0112 (mmp) cc_final: -0.1550 (tmm) REVERT: M 228 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7458 (pp) REVERT: N 101 ASP cc_start: 0.8900 (p0) cc_final: 0.8504 (p0) REVERT: N 119 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8835 (ttmm) REVERT: N 159 ASN cc_start: 0.9227 (t0) cc_final: 0.8880 (t0) REVERT: N 214 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8194 (mt-10) REVERT: O 36 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7321 (tt) REVERT: O 214 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7981 (mt-10) REVERT: O 221 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8126 (ttm110) REVERT: P 101 ASP cc_start: 0.8999 (p0) cc_final: 0.8741 (p0) REVERT: P 188 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8140 (mm-40) REVERT: P 216 ARG cc_start: 0.8046 (mtp85) cc_final: 0.7575 (ttm170) REVERT: P 221 ARG cc_start: 0.8593 (tpp80) cc_final: 0.8210 (ttm110) REVERT: P 260 MET cc_start: 0.2110 (OUTLIER) cc_final: 0.1819 (pmm) REVERT: Q 42 ARG cc_start: 0.8027 (mtt90) cc_final: 0.7678 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8836 (tp30) cc_final: 0.8548 (tp30) REVERT: Q 90 MET cc_start: 0.9164 (mmt) cc_final: 0.8824 (mmt) REVERT: Q 101 ASP cc_start: 0.8950 (p0) cc_final: 0.8501 (p0) REVERT: Q 185 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8180 (tm-30) REVERT: Q 214 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8241 (tt0) REVERT: Q 221 ARG cc_start: 0.8342 (ttm110) cc_final: 0.7719 (ttm110) REVERT: Q 260 MET cc_start: -0.1528 (mmp) cc_final: -0.2271 (tmm) REVERT: A 3 TYR cc_start: 0.1534 (OUTLIER) cc_final: 0.0331 (p90) REVERT: B 99 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7215 (tpp-160) REVERT: B 110 ARG cc_start: 0.7499 (ttt-90) cc_final: 0.6850 (ttp80) REVERT: B 148 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.7639 (m-80) REVERT: B 149 MET cc_start: 0.7870 (mmm) cc_final: 0.7250 (ptt) REVERT: B 151 ARG cc_start: 0.8223 (ttt180) cc_final: 0.7917 (ptm160) REVERT: C 1 MET cc_start: 0.4188 (pmm) cc_final: 0.2953 (ppp) REVERT: C 8 MET cc_start: 0.1190 (mmm) cc_final: 0.0765 (mtm) REVERT: C 51 MET cc_start: 0.2920 (mmp) cc_final: 0.0995 (mtt) REVERT: C 111 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8377 (mp10) REVERT: D 102 ARG cc_start: 0.8020 (mtp-110) cc_final: 0.7747 (ttm-80) REVERT: E 35 MET cc_start: -0.1497 (pmm) cc_final: -0.1768 (ptt) REVERT: E 98 GLN cc_start: 0.8729 (tt0) cc_final: 0.8486 (tp40) REVERT: E 99 ARG cc_start: 0.8065 (mmm-85) cc_final: 0.6817 (ttt-90) REVERT: E 104 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8199 (tm-30) REVERT: E 109 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8216 (tpp80) REVERT: E 132 ARG cc_start: 0.7908 (tpt90) cc_final: 0.7471 (mmp80) REVERT: E 155 ARG cc_start: 0.6562 (ttp80) cc_final: 0.6026 (tmm-80) REVERT: F 99 ARG cc_start: 0.8195 (mmm-85) cc_final: 0.7089 (ttt-90) REVERT: F 114 MET cc_start: 0.9044 (tmm) cc_final: 0.8815 (tmm) REVERT: F 132 ARG cc_start: 0.8018 (tpt90) cc_final: 0.7615 (mmp80) REVERT: F 149 MET cc_start: 0.8922 (mmm) cc_final: 0.7926 (ptp) REVERT: G 63 MET cc_start: 0.7603 (mtt) cc_final: 0.7396 (mtt) REVERT: H 95 ASN cc_start: 0.9049 (t0) cc_final: 0.8787 (t0) REVERT: I 148 TYR cc_start: 0.9143 (OUTLIER) cc_final: 0.8140 (m-10) outliers start: 121 outliers final: 97 residues processed: 511 average time/residue: 0.4602 time to fit residues: 364.7989 Evaluate side-chains 533 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 423 time to evaluate : 4.148 ------------------------------------------------------------------------------- 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 59 THR 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 212 THR 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 96 ARG Chi-restraints excluded: chain J residue 149 ASN 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 279 ASP Chi-restraints excluded: chain J residue 295 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 48 VAL 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 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 214 GLU Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain N residue 40 ILE 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 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 201 SER 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 260 MET Chi-restraints excluded: chain P residue 317 ILE Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU 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 82 LEU Chi-restraints excluded: chain B residue 1 MET 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 74 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 148 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 79 LEU 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 I residue 16 THR 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 125 THR 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: 0.9990 chunk 373 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 363 optimal weight: 0.6980 chunk 218 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 285 optimal weight: 20.0000 chunk 111 optimal weight: 6.9990 chunk 328 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 362 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 176 ASN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2091 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= 0.198 Angle : 0.532 13.369 42867 Z= 0.277 Chirality : 0.034 0.158 4635 Planarity : 0.003 0.032 5985 Dihedral : 3.473 41.236 4581 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.70 % Favored : 93.06 % Rotamer: Outliers : 3.63 % Allowed : 29.86 % Favored : 66.51 % 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: 2.45 (0.14), residues: 4122 helix: 3.18 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -2.99 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 77 HIS 0.000 0.000 HIS Q 198 PHE 0.029 0.001 PHE A 112 TYR 0.011 0.001 TYR G 116 ARG 0.009 0.000 ARG G 109 *********************** 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 545 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 428 time to evaluate : 3.827 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: 0.8345 (t70) cc_final: 0.7928 (t70) REVERT: R 260 MET cc_start: -0.0016 (mmp) cc_final: -0.0956 (tpt) REVERT: J 42 ARG cc_start: 0.7772 (ptp90) cc_final: 0.7520 (ptp90) REVERT: J 90 MET cc_start: 0.9149 (ttm) cc_final: 0.8878 (ttm) REVERT: J 96 ARG cc_start: 0.9404 (OUTLIER) cc_final: 0.6977 (mpt90) REVERT: J 101 ASP cc_start: 0.8944 (p0) cc_final: 0.8734 (p0) REVERT: J 217 ASP cc_start: 0.8875 (t0) cc_final: 0.8491 (t0) REVERT: K 36 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7636 (tt) REVERT: K 90 MET cc_start: 0.8496 (mtp) cc_final: 0.8206 (mtt) REVERT: K 202 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (mmm) REVERT: K 214 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8298 (mt-10) REVERT: K 270 MET cc_start: 0.3775 (tpp) cc_final: 0.3512 (tpp) REVERT: L 90 MET cc_start: 0.9353 (mtp) cc_final: 0.9067 (mtp) REVERT: L 101 ASP cc_start: 0.8948 (p0) cc_final: 0.8467 (p0) REVERT: L 260 MET cc_start: 0.0057 (mmp) cc_final: -0.0439 (mmp) REVERT: M 101 ASP cc_start: 0.8998 (p0) cc_final: 0.8744 (p0) REVERT: M 228 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7470 (pp) REVERT: N 101 ASP cc_start: 0.8900 (p0) cc_final: 0.8497 (p0) REVERT: N 119 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8838 (ttmm) REVERT: N 159 ASN cc_start: 0.9236 (t0) cc_final: 0.8892 (t0) REVERT: N 214 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8193 (mt-10) REVERT: O 36 LEU cc_start: 0.7624 (OUTLIER) cc_final: 0.7332 (tt) REVERT: O 159 ASN cc_start: 0.9007 (OUTLIER) cc_final: 0.8627 (t0) REVERT: O 214 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7985 (mt-10) REVERT: O 221 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8170 (ttm110) REVERT: P 101 ASP cc_start: 0.8945 (p0) cc_final: 0.8651 (p0) REVERT: P 188 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: P 216 ARG cc_start: 0.8061 (mtp85) cc_final: 0.7607 (ttm170) REVERT: P 221 ARG cc_start: 0.8614 (tpp80) cc_final: 0.8230 (ttm110) REVERT: Q 42 ARG cc_start: 0.8046 (mtt90) cc_final: 0.7673 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8839 (tp30) cc_final: 0.8551 (tp30) REVERT: Q 90 MET cc_start: 0.9177 (mmt) cc_final: 0.8845 (mmt) REVERT: Q 101 ASP cc_start: 0.8979 (p0) cc_final: 0.8575 (p0) REVERT: Q 185 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8184 (tm-30) REVERT: Q 214 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8248 (tt0) REVERT: Q 221 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7741 (ttm110) REVERT: Q 260 MET cc_start: -0.1508 (mmp) cc_final: -0.2254 (tmm) REVERT: A 3 TYR cc_start: 0.1127 (OUTLIER) cc_final: -0.0094 (p90) REVERT: A 149 MET cc_start: 0.8875 (tpp) cc_final: 0.8042 (ppp) REVERT: B 99 ARG cc_start: 0.7788 (mmm-85) cc_final: 0.7152 (tpp-160) REVERT: B 110 ARG cc_start: 0.7531 (ttt-90) cc_final: 0.6872 (ttp80) REVERT: B 148 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 149 MET cc_start: 0.7841 (mmm) cc_final: 0.7267 (ptt) REVERT: B 151 ARG cc_start: 0.8220 (ttt180) cc_final: 0.7912 (ptm160) REVERT: C 1 MET cc_start: 0.4170 (pmm) cc_final: 0.2960 (ppp) REVERT: C 8 MET cc_start: 0.1197 (mmm) cc_final: 0.0773 (mtm) REVERT: C 51 MET cc_start: 0.3385 (mmp) cc_final: 0.1410 (mtt) REVERT: C 111 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8368 (mp10) REVERT: D 102 ARG cc_start: 0.8149 (mtp-110) cc_final: 0.7919 (ttm-80) REVERT: E 35 MET cc_start: -0.1493 (pmm) cc_final: -0.1765 (ptt) REVERT: E 98 GLN cc_start: 0.8726 (tt0) cc_final: 0.8486 (tp40) REVERT: E 99 ARG cc_start: 0.8060 (mmm-85) cc_final: 0.6842 (ttt-90) REVERT: E 104 GLN cc_start: 0.8428 (tm-30) cc_final: 0.8145 (tm-30) REVERT: E 109 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8216 (tpp80) REVERT: E 132 ARG cc_start: 0.8020 (tpt90) cc_final: 0.7360 (mmp80) REVERT: E 155 ARG cc_start: 0.6576 (ttp80) cc_final: 0.6046 (tmm-80) REVERT: F 99 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.6961 (ttt-90) REVERT: F 132 ARG cc_start: 0.8102 (tpt90) cc_final: 0.7646 (mmp80) REVERT: F 149 MET cc_start: 0.8920 (mmm) cc_final: 0.7912 (ptp) REVERT: H 95 ASN cc_start: 0.9051 (t0) cc_final: 0.8787 (t0) REVERT: I 148 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.8151 (m-10) outliers start: 117 outliers final: 94 residues processed: 512 average time/residue: 0.4646 time to fit residues: 368.4743 Evaluate side-chains 528 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 423 time to evaluate : 3.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 59 THR 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 212 THR 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 96 ARG Chi-restraints excluded: chain J residue 149 ASN 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 295 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 48 VAL 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 154 GLU Chi-restraints excluded: chain K residue 157 LEU Chi-restraints excluded: chain K residue 199 SER Chi-restraints excluded: chain K residue 202 MET Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain N residue 40 ILE 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 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 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 317 ILE Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL 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 82 LEU Chi-restraints excluded: chain B residue 1 MET 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 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 148 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 79 LEU 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 I residue 16 THR 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 125 THR 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: 5.9990 chunk 384 optimal weight: 6.9990 chunk 234 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 267 optimal weight: 4.9990 chunk 403 optimal weight: 6.9990 chunk 371 optimal weight: 6.9990 chunk 321 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 197 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN F 111 GLN H 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2201 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= 0.204 Angle : 0.540 13.154 42867 Z= 0.281 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.029 5985 Dihedral : 3.480 39.895 4581 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.67 % Favored : 93.09 % Rotamer: Outliers : 3.51 % Allowed : 30.11 % Favored : 66.39 % 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: 2.43 (0.14), residues: 4122 helix: 3.17 (0.10), residues: 2970 sheet: None (None), residues: 0 loop : -2.98 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 77 HIS 0.000 0.000 HIS Q 198 PHE 0.031 0.001 PHE E 112 TYR 0.013 0.001 TYR E 116 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 538 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 425 time to evaluate : 3.406 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 95 ASP cc_start: 0.8365 (t70) cc_final: 0.7931 (t70) REVERT: R 260 MET cc_start: 0.0041 (mmp) cc_final: -0.0663 (mmp) REVERT: J 90 MET cc_start: 0.9149 (ttm) cc_final: 0.8811 (ttm) REVERT: J 96 ARG cc_start: 0.9367 (OUTLIER) cc_final: 0.6936 (mpt90) REVERT: J 217 ASP cc_start: 0.8885 (t0) cc_final: 0.8496 (t0) REVERT: K 36 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7628 (tt) REVERT: K 42 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.6914 (mtm-85) REVERT: K 72 GLU cc_start: 0.8579 (tt0) cc_final: 0.8377 (tm-30) REVERT: K 90 MET cc_start: 0.8498 (mtp) cc_final: 0.8203 (mtt) REVERT: K 202 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8278 (mmm) REVERT: K 214 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8307 (mt-10) REVERT: K 270 MET cc_start: 0.3805 (tpp) cc_final: 0.3517 (tpp) REVERT: L 90 MET cc_start: 0.9356 (mtp) cc_final: 0.9102 (mtp) REVERT: L 260 MET cc_start: -0.0252 (mmp) cc_final: -0.0755 (mmp) REVERT: M 101 ASP cc_start: 0.9056 (p0) cc_final: 0.8784 (p0) REVERT: M 228 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7479 (pp) REVERT: N 101 ASP cc_start: 0.8922 (p0) cc_final: 0.8504 (p0) REVERT: N 119 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8839 (ttmm) REVERT: N 159 ASN cc_start: 0.9237 (t0) cc_final: 0.8880 (t0) REVERT: N 214 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8206 (mt-10) REVERT: O 36 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7243 (tt) REVERT: O 159 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8651 (t0) REVERT: O 214 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7989 (mt-10) REVERT: O 221 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8183 (ttm110) REVERT: P 101 ASP cc_start: 0.8956 (p0) cc_final: 0.8640 (p0) REVERT: P 188 GLN cc_start: 0.8542 (OUTLIER) cc_final: 0.8141 (mm-40) REVERT: P 215 GLN cc_start: 0.8986 (tt0) cc_final: 0.8534 (tt0) REVERT: P 216 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7597 (ttm170) REVERT: P 221 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8234 (ttm110) REVERT: Q 42 ARG cc_start: 0.8051 (mtt90) cc_final: 0.7673 (mpt-90) REVERT: Q 56 GLU cc_start: 0.8838 (tp30) cc_final: 0.8545 (tp30) REVERT: Q 90 MET cc_start: 0.9191 (mmt) cc_final: 0.8863 (mmt) REVERT: Q 101 ASP cc_start: 0.8983 (p0) cc_final: 0.8551 (p0) REVERT: Q 185 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8189 (tm-30) REVERT: Q 214 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8264 (tt0) REVERT: Q 221 ARG cc_start: 0.8354 (ttm110) cc_final: 0.7747 (ttm110) REVERT: Q 260 MET cc_start: -0.1290 (mmp) cc_final: -0.2209 (tmm) REVERT: A 3 TYR cc_start: 0.1121 (OUTLIER) cc_final: -0.0107 (p90) REVERT: B 99 ARG cc_start: 0.7801 (mmm-85) cc_final: 0.7152 (tpp-160) REVERT: B 110 ARG cc_start: 0.7517 (ttt-90) cc_final: 0.6832 (ttp80) REVERT: B 148 TYR cc_start: 0.8509 (OUTLIER) cc_final: 0.7804 (m-10) REVERT: B 149 MET cc_start: 0.7959 (mmm) cc_final: 0.7252 (ptt) REVERT: C 1 MET cc_start: 0.4164 (pmm) cc_final: 0.2939 (ppp) REVERT: C 51 MET cc_start: 0.3419 (mmp) cc_final: 0.1447 (mtt) REVERT: C 111 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: D 102 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7952 (ttm-80) REVERT: E 35 MET cc_start: -0.1597 (pmm) cc_final: -0.1861 (ptt) REVERT: E 99 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7059 (ttt-90) REVERT: E 104 GLN cc_start: 0.8425 (tm-30) cc_final: 0.8141 (tm-30) REVERT: E 109 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8197 (tpp80) REVERT: E 132 ARG cc_start: 0.8022 (tpt90) cc_final: 0.7355 (mmp80) REVERT: E 155 ARG cc_start: 0.6423 (ttp80) cc_final: 0.5916 (tmm-80) REVERT: F 99 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.6949 (ttt-90) REVERT: F 132 ARG cc_start: 0.8105 (tpt90) cc_final: 0.7639 (mmp80) REVERT: F 149 MET cc_start: 0.8915 (mmm) cc_final: 0.7906 (ptp) REVERT: H 95 ASN cc_start: 0.9051 (t0) cc_final: 0.8788 (t0) REVERT: I 148 TYR cc_start: 0.9158 (OUTLIER) cc_final: 0.8349 (m-10) outliers start: 113 outliers final: 98 residues processed: 507 average time/residue: 0.4543 time to fit residues: 356.4614 Evaluate side-chains 534 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 425 time to evaluate : 3.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 59 THR 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 212 THR Chi-restraints excluded: chain R residue 305 LYS Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 96 ARG Chi-restraints excluded: chain J residue 149 ASN 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 295 SER Chi-restraints excluded: chain J residue 307 LEU Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 48 VAL 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 202 MET Chi-restraints excluded: chain K residue 229 VAL Chi-restraints excluded: chain K residue 295 SER Chi-restraints excluded: chain K residue 330 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 124 GLN Chi-restraints excluded: chain L residue 201 SER Chi-restraints excluded: chain L residue 212 THR Chi-restraints excluded: chain L residue 295 SER Chi-restraints excluded: chain M residue 53 LEU Chi-restraints excluded: chain M residue 105 LYS Chi-restraints excluded: chain M residue 124 GLN Chi-restraints excluded: chain M residue 166 GLU Chi-restraints excluded: chain M residue 201 SER Chi-restraints excluded: chain M residue 212 THR Chi-restraints excluded: chain M residue 228 LEU Chi-restraints excluded: chain M residue 270 MET Chi-restraints excluded: chain M residue 295 SER Chi-restraints excluded: chain N residue 40 ILE 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 127 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 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 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 317 ILE Chi-restraints excluded: chain P residue 330 LEU Chi-restraints excluded: chain Q residue 53 LEU Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 212 THR Chi-restraints excluded: chain A residue 3 TYR Chi-restraints excluded: chain A residue 31 LEU 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 82 LEU Chi-restraints excluded: chain B residue 1 MET 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 111 GLN Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 67 VAL Chi-restraints excluded: chain D residue 82 LEU 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 148 TYR Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 79 LEU 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 16 THR 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 125 THR 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: 0.5980 chunk 342 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 296 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 321 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 330 optimal weight: 20.0000 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 176 ASN ** P 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 111 GLN F 111 GLN H 111 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.213916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.119210 restraints weight = 48942.207| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.97 r_work: 0.3074 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2262 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= 0.208 Angle : 0.547 12.646 42867 Z= 0.284 Chirality : 0.034 0.157 4635 Planarity : 0.003 0.032 5985 Dihedral : 3.474 39.169 4581 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.60 % Favored : 93.16 % Rotamer: Outliers : 3.60 % Allowed : 30.20 % Favored : 66.20 % 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: 2.44 (0.14), residues: 4122 helix: 3.22 (0.10), residues: 2934 sheet: None (None), residues: 0 loop : -2.90 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 77 HIS 0.000 0.000 HIS M 198 PHE 0.031 0.001 PHE E 112 TYR 0.010 0.001 TYR G 116 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: 7861.79 seconds wall clock time: 156 minutes 52.82 seconds (9412.82 seconds total)