Starting phenix.real_space_refine on Wed Feb 14 14:43:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/02_2024/7rkm_24500_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/02_2024/7rkm_24500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/02_2024/7rkm_24500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/02_2024/7rkm_24500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/02_2024/7rkm_24500_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rkm_24500/02_2024/7rkm_24500_updated.pdb" } resolution = 3.5 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 6056 2.51 5 N 1604 2.21 5 O 1759 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "D ASP 109": "OD1" <-> "OD2" Residue "D ASP 211": "OD1" <-> "OD2" Residue "R TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 27": "OD1" <-> "OD2" Residue "R TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 128": "OD1" <-> "OD2" Residue "R PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 308": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9491 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1747 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2592 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Conformer: "B" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} bond proxies already assigned to first conformer: 2622 Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "D" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "L" Number of atoms: 531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 531 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'PCA:plan-2': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "R" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2423 Unusual residues: {'CLR': 1} Classifications: {'peptide': 294, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 283, None: 1} Not linked: pdbres="GLU R 308 " pdbres="CLR R 401 " Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 6.48, per 1000 atoms: 0.68 Number of scatterers: 9491 At special positions: 0 Unit cell: (98.4, 134.48, 132.84, 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 72 16.00 O 1759 8.00 N 1604 7.00 C 6056 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.04 Simple disulfide: pdb=" SG CYS L 8 " - pdb=" SG CYS L 34 " distance=2.04 Simple disulfide: pdb=" SG CYS L 12 " - pdb=" SG CYS L 50 " distance=2.03 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 104 " - pdb=" SG CYS R 173 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 2.3 seconds 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 15 sheets defined 32.3% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.312A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.917A pdb=" N ASP A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 35 Processing helix chain 'C' and resid 10 through 23 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'L' and resid 3 through 5 No H-bonds generated for 'chain 'L' and resid 3 through 5' Processing helix chain 'L' and resid 56 through 66 removed outlier: 4.034A pdb=" N LEU L 65 " --> pdb=" O MET L 62 " (cutoff:3.500A) Processing helix chain 'R' and resid 26 through 58 Proline residue: R 34 - end of helix removed outlier: 3.610A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 94 Proline residue: R 87 - end of helix Processing helix chain 'R' and resid 104 through 133 Processing helix chain 'R' and resid 141 through 157 removed outlier: 3.799A pdb=" N LEU R 146 " --> pdb=" O LYS R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 163 No H-bonds generated for 'chain 'R' and resid 160 through 163' Processing helix chain 'R' and resid 184 through 194 removed outlier: 4.150A pdb=" N GLU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 198 through 217 removed outlier: 3.541A pdb=" N VAL R 217 " --> pdb=" O ARG R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 255 removed outlier: 3.787A pdb=" N VAL R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Proline residue: R 243 - end of helix Processing helix chain 'R' and resid 264 through 291 Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 296 through 303 Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.764A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.755A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.782A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.560A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 6.772A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.643A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 251 through 254 removed outlier: 6.521A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.087A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA D 40 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU D 45 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'D' and resid 134 through 136 removed outlier: 6.539A pdb=" N LYS D 232 " --> pdb=" O VAL D 135 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 214 through 219 removed outlier: 5.911A pdb=" N LEU D 166 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N LEU D 175 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'L' and resid 48 through 51 412 hydrogen bonds defined for protein. 1164 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: 2.86 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2923 1.34 - 1.46: 2284 1.46 - 1.58: 4390 1.58 - 1.71: 0 1.71 - 1.83: 100 Bond restraints: 9697 Sorted by residual: bond pdb=" N PCA L 1 " pdb=" CD PCA L 1 " ideal model delta sigma weight residual 1.345 1.463 -0.118 2.00e-02 2.50e+03 3.46e+01 bond pdb=" CB MET B 262 " pdb=" CG MET B 262 " ideal model delta sigma weight residual 1.520 1.447 0.073 3.00e-02 1.11e+03 5.88e+00 bond pdb=" C ILE R 160 " pdb=" N PRO R 161 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.96e+00 bond pdb=" SD MET B 262 " pdb=" CE MET B 262 " ideal model delta sigma weight residual 1.791 1.736 0.055 2.50e-02 1.60e+03 4.88e+00 bond pdb=" C ASN R 287 " pdb=" N PRO R 288 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 ... (remaining 9692 not shown) Histogram of bond angle deviations from ideal: 89.71 - 98.60: 4 98.60 - 107.48: 361 107.48 - 116.36: 6112 116.36 - 125.24: 6493 125.24 - 134.12: 174 Bond angle restraints: 13144 Sorted by residual: angle pdb=" CB MET B 262 " pdb=" CG MET B 262 " pdb=" SD MET B 262 " ideal model delta sigma weight residual 112.70 89.71 22.99 3.00e+00 1.11e-01 5.87e+01 angle pdb=" C ARG D 179 " pdb=" N MET D 180 " pdb=" CA MET D 180 " ideal model delta sigma weight residual 121.54 131.97 -10.43 1.91e+00 2.74e-01 2.98e+01 angle pdb=" CB MET R 174 " pdb=" CG MET R 174 " pdb=" SD MET R 174 " ideal model delta sigma weight residual 112.70 125.74 -13.04 3.00e+00 1.11e-01 1.89e+01 angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 110.49 117.48 -6.99 1.69e+00 3.50e-01 1.71e+01 angle pdb=" N ASN R 287 " pdb=" CA ASN R 287 " pdb=" C ASN R 287 " ideal model delta sigma weight residual 113.16 118.58 -5.42 1.42e+00 4.96e-01 1.46e+01 ... (remaining 13139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5410 17.94 - 35.89: 329 35.89 - 53.83: 71 53.83 - 71.77: 7 71.77 - 89.72: 4 Dihedral angle restraints: 5821 sinusoidal: 2317 harmonic: 3504 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 158.42 -65.42 1 1.00e+01 1.00e-02 5.61e+01 dihedral pdb=" CB CYS R 23 " pdb=" SG CYS R 23 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -131.88 45.88 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CA ILE R 259 " pdb=" C ILE R 259 " pdb=" N SER R 260 " pdb=" CA SER R 260 " ideal model delta harmonic sigma weight residual 180.00 154.33 25.67 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 5818 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1248 0.073 - 0.146: 209 0.146 - 0.219: 23 0.219 - 0.292: 9 0.292 - 0.365: 4 Chirality restraints: 1493 Sorted by residual: chirality pdb=" CA ASN R 287 " pdb=" N ASN R 287 " pdb=" C ASN R 287 " pdb=" CB ASN R 287 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CB THR A 324 " pdb=" CA THR A 324 " pdb=" OG1 THR A 324 " pdb=" CG2 THR A 324 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" C14 CLR R 401 " pdb=" C13 CLR R 401 " pdb=" C15 CLR R 401 " pdb=" C8 CLR R 401 " both_signs ideal model delta sigma weight residual False -2.32 -2.62 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 1490 not shown) Planarity restraints: 1654 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 57 " -0.014 2.00e-02 2.50e+03 1.69e-02 7.11e+00 pdb=" CG TRP L 57 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP L 57 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP L 57 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 57 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 57 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 57 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 57 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 44 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.45e+00 pdb=" C PHE R 44 " 0.044 2.00e-02 2.50e+03 pdb=" O PHE R 44 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU R 45 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 94 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00 pdb=" C LEU R 94 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU R 94 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP R 95 " 0.014 2.00e-02 2.50e+03 ... (remaining 1651 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 456 2.73 - 3.27: 9413 3.27 - 3.81: 15625 3.81 - 4.36: 19400 4.36 - 4.90: 33299 Nonbonded interactions: 78193 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.181 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASN R 189 " pdb=" OG1 THR R 252 " model vdw 2.206 2.440 nonbonded pdb=" O LEU R 53 " pdb=" OG1 THR R 57 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.241 2.440 ... (remaining 78188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.020 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 30.910 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 : 0.005 0.118 9697 Z= 0.356 Angle : 0.970 22.986 13144 Z= 0.501 Chirality : 0.060 0.365 1493 Planarity : 0.005 0.042 1654 Dihedral : 12.319 89.718 3536 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -1.13 (0.24), residues: 1183 helix: 0.52 (0.26), residues: 400 sheet: -1.09 (0.29), residues: 288 loop : -1.52 (0.27), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP L 57 HIS 0.009 0.002 HIS B 54 PHE 0.024 0.003 PHE D 68 TYR 0.024 0.003 TYR A 320 ARG 0.009 0.001 ARG D 148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 1.193 Fit side-chains REVERT: A 26 ASP cc_start: 0.7340 (m-30) cc_final: 0.6893 (m-30) REVERT: D 6 GLU cc_start: 0.7503 (mp0) cc_final: 0.7194 (mp0) REVERT: D 127 VAL cc_start: 0.8911 (p) cc_final: 0.8640 (t) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2478 time to fit residues: 59.7114 Evaluate side-chains 143 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9697 Z= 0.214 Angle : 0.582 7.638 13144 Z= 0.305 Chirality : 0.043 0.186 1493 Planarity : 0.003 0.038 1654 Dihedral : 5.008 36.695 1370 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.68 % Allowed : 8.97 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.86 (0.24), residues: 1183 helix: 0.90 (0.27), residues: 400 sheet: -1.04 (0.28), residues: 290 loop : -1.45 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 57 HIS 0.005 0.001 HIS R 245 PHE 0.029 0.002 PHE A 334 TYR 0.028 0.001 TYR R 92 ARG 0.003 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.133 Fit side-chains REVERT: A 26 ASP cc_start: 0.7311 (m-30) cc_final: 0.6929 (m-30) REVERT: A 52 GLN cc_start: 0.7012 (tm-30) cc_final: 0.6796 (tt0) REVERT: D 180 MET cc_start: 0.7744 (ptm) cc_final: 0.7427 (ptm) REVERT: R 191 GLU cc_start: 0.7608 (tt0) cc_final: 0.7349 (tt0) outliers start: 7 outliers final: 5 residues processed: 148 average time/residue: 0.2383 time to fit residues: 48.5774 Evaluate side-chains 138 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain R residue 38 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 72 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 9 ASN L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9697 Z= 0.174 Angle : 0.544 7.652 13144 Z= 0.286 Chirality : 0.042 0.229 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.847 36.893 1370 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.64 % Allowed : 9.93 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.70 (0.24), residues: 1183 helix: 1.14 (0.27), residues: 396 sheet: -0.97 (0.28), residues: 290 loop : -1.43 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.022 0.001 PHE A 334 TYR 0.028 0.001 TYR R 92 ARG 0.004 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 147 time to evaluate : 1.107 Fit side-chains REVERT: A 26 ASP cc_start: 0.7289 (m-30) cc_final: 0.6904 (m-30) REVERT: A 287 TYR cc_start: 0.6493 (m-80) cc_final: 0.5378 (m-80) REVERT: D 180 MET cc_start: 0.7787 (ptm) cc_final: 0.7416 (ptm) REVERT: R 191 GLU cc_start: 0.7618 (tt0) cc_final: 0.7313 (tt0) outliers start: 17 outliers final: 11 residues processed: 156 average time/residue: 0.2326 time to fit residues: 49.7169 Evaluate side-chains 145 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 8 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 0.0270 chunk 113 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 30 optimal weight: 0.0870 chunk 94 optimal weight: 0.8980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 45 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.168 Angle : 0.541 7.698 13144 Z= 0.282 Chirality : 0.042 0.275 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.757 36.413 1370 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.64 % Allowed : 10.70 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.58 (0.24), residues: 1183 helix: 1.23 (0.27), residues: 398 sheet: -0.82 (0.29), residues: 275 loop : -1.41 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.019 0.001 PHE A 334 TYR 0.030 0.001 TYR R 92 ARG 0.005 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 1.223 Fit side-chains REVERT: A 26 ASP cc_start: 0.7260 (m-30) cc_final: 0.6856 (m-30) REVERT: A 287 TYR cc_start: 0.6311 (m-80) cc_final: 0.4961 (m-80) REVERT: D 180 MET cc_start: 0.7841 (ptm) cc_final: 0.7438 (ptm) outliers start: 17 outliers final: 13 residues processed: 155 average time/residue: 0.2310 time to fit residues: 49.4772 Evaluate side-chains 147 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** D 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9697 Z= 0.325 Angle : 0.610 7.960 13144 Z= 0.319 Chirality : 0.044 0.227 1493 Planarity : 0.003 0.041 1654 Dihedral : 5.011 36.850 1370 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.22 % Allowed : 11.38 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.63 (0.24), residues: 1183 helix: 1.15 (0.27), residues: 399 sheet: -1.00 (0.28), residues: 290 loop : -1.31 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.006 0.001 HIS B 142 PHE 0.020 0.002 PHE A 334 TYR 0.032 0.002 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.150 Fit side-chains REVERT: A 26 ASP cc_start: 0.7364 (m-30) cc_final: 0.6930 (m-30) REVERT: D 180 MET cc_start: 0.8096 (ptm) cc_final: 0.7592 (ptm) REVERT: L 16 THR cc_start: 0.6580 (OUTLIER) cc_final: 0.6249 (p) REVERT: R 16 TYR cc_start: 0.6587 (p90) cc_final: 0.6383 (p90) REVERT: R 190 VAL cc_start: 0.9141 (OUTLIER) cc_final: 0.8921 (p) REVERT: R 191 GLU cc_start: 0.7769 (tt0) cc_final: 0.7436 (tt0) outliers start: 23 outliers final: 18 residues processed: 167 average time/residue: 0.2194 time to fit residues: 51.1271 Evaluate side-chains 162 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 109 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9697 Z= 0.191 Angle : 0.561 8.523 13144 Z= 0.292 Chirality : 0.042 0.231 1493 Planarity : 0.003 0.040 1654 Dihedral : 4.833 36.132 1370 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.41 % Allowed : 12.63 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.51 (0.24), residues: 1183 helix: 1.25 (0.27), residues: 398 sheet: -0.88 (0.28), residues: 291 loop : -1.28 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.018 0.001 PHE A 334 TYR 0.032 0.001 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7301 (m-30) cc_final: 0.6887 (m-30) REVERT: A 52 GLN cc_start: 0.6623 (tm-30) cc_final: 0.6405 (tt0) REVERT: A 287 TYR cc_start: 0.6455 (m-80) cc_final: 0.5200 (m-80) REVERT: C 25 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8528 (mt) REVERT: D 180 MET cc_start: 0.7993 (ptm) cc_final: 0.7559 (ptm) REVERT: L 16 THR cc_start: 0.6577 (OUTLIER) cc_final: 0.6371 (p) REVERT: R 190 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8899 (p) outliers start: 25 outliers final: 16 residues processed: 166 average time/residue: 0.2229 time to fit residues: 51.3669 Evaluate side-chains 160 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 112 optimal weight: 0.0570 chunk 70 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.188 Angle : 0.550 7.767 13144 Z= 0.286 Chirality : 0.042 0.192 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.735 35.610 1370 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.93 % Allowed : 13.79 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.44 (0.24), residues: 1183 helix: 1.31 (0.27), residues: 398 sheet: -0.80 (0.29), residues: 291 loop : -1.26 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.016 0.001 PHE A 334 TYR 0.033 0.001 TYR R 92 ARG 0.006 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7301 (m-30) cc_final: 0.6885 (m-30) REVERT: A 52 GLN cc_start: 0.6724 (tm-30) cc_final: 0.6463 (tt0) REVERT: A 287 TYR cc_start: 0.6395 (m-80) cc_final: 0.5187 (m-80) REVERT: C 25 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8543 (mt) REVERT: D 180 MET cc_start: 0.8017 (ptm) cc_final: 0.7592 (ptm) REVERT: R 16 TYR cc_start: 0.6713 (p90) cc_final: 0.6383 (p90) REVERT: R 190 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8881 (p) outliers start: 20 outliers final: 15 residues processed: 161 average time/residue: 0.2334 time to fit residues: 51.6902 Evaluate side-chains 159 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 190 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 88 optimal weight: 0.0170 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9697 Z= 0.208 Angle : 0.563 9.277 13144 Z= 0.292 Chirality : 0.042 0.236 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.745 35.477 1370 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.93 % Allowed : 15.33 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.45 (0.24), residues: 1183 helix: 1.29 (0.27), residues: 402 sheet: -0.82 (0.29), residues: 293 loop : -1.27 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.029 0.002 PHE D 68 TYR 0.033 0.001 TYR R 92 ARG 0.007 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7315 (m-30) cc_final: 0.6890 (m-30) REVERT: A 287 TYR cc_start: 0.6476 (m-80) cc_final: 0.5419 (m-80) REVERT: C 25 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (mt) REVERT: D 180 MET cc_start: 0.7996 (ptm) cc_final: 0.7581 (ptm) REVERT: R 16 TYR cc_start: 0.6731 (p90) cc_final: 0.6392 (p90) outliers start: 20 outliers final: 16 residues processed: 157 average time/residue: 0.2384 time to fit residues: 51.6625 Evaluate side-chains 161 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.0270 chunk 32 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.1980 chunk 69 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9697 Z= 0.171 Angle : 0.549 7.615 13144 Z= 0.287 Chirality : 0.041 0.227 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.651 34.693 1370 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.74 % Allowed : 15.72 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.41 (0.24), residues: 1183 helix: 1.32 (0.27), residues: 406 sheet: -0.69 (0.29), residues: 288 loop : -1.34 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS R 245 PHE 0.023 0.001 PHE D 68 TYR 0.032 0.001 TYR R 92 ARG 0.008 0.000 ARG D 206 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 153 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7306 (m-30) cc_final: 0.6894 (m-30) REVERT: A 52 GLN cc_start: 0.6510 (tm-30) cc_final: 0.6105 (tt0) REVERT: A 287 TYR cc_start: 0.6412 (m-80) cc_final: 0.5214 (m-80) REVERT: C 25 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8545 (mt) REVERT: D 180 MET cc_start: 0.7908 (ptm) cc_final: 0.7513 (ptm) REVERT: R 16 TYR cc_start: 0.6761 (p90) cc_final: 0.6457 (p90) outliers start: 18 outliers final: 14 residues processed: 163 average time/residue: 0.2337 time to fit residues: 52.5432 Evaluate side-chains 162 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9697 Z= 0.238 Angle : 0.599 9.281 13144 Z= 0.310 Chirality : 0.043 0.379 1493 Planarity : 0.003 0.039 1654 Dihedral : 4.744 35.166 1370 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.45 % Allowed : 16.39 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.38 (0.25), residues: 1183 helix: 1.34 (0.27), residues: 402 sheet: -0.78 (0.29), residues: 294 loop : -1.20 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.025 0.002 PHE D 68 TYR 0.033 0.001 TYR R 92 ARG 0.004 0.000 ARG D 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2366 Ramachandran restraints generated. 1183 Oldfield, 0 Emsley, 1183 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.192 Fit side-chains REVERT: A 26 ASP cc_start: 0.7332 (m-30) cc_final: 0.6913 (m-30) REVERT: A 52 GLN cc_start: 0.6639 (tm-30) cc_final: 0.6126 (tt0) REVERT: C 25 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8544 (mt) REVERT: D 180 MET cc_start: 0.7972 (ptm) cc_final: 0.7551 (ptm) REVERT: R 16 TYR cc_start: 0.6868 (p90) cc_final: 0.6570 (p90) outliers start: 15 outliers final: 13 residues processed: 158 average time/residue: 0.2415 time to fit residues: 51.7462 Evaluate side-chains 161 residues out of total 1040 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 129 THR Chi-restraints excluded: chain D residue 226 THR Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain R residue 38 PHE Chi-restraints excluded: chain R residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 85 optimal weight: 0.0060 chunk 13 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 GLN ** L 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.114772 restraints weight = 19058.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114745 restraints weight = 18917.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115869 restraints weight = 18339.654| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9697 Z= 0.189 Angle : 0.584 8.813 13144 Z= 0.301 Chirality : 0.043 0.362 1493 Planarity : 0.003 0.038 1654 Dihedral : 4.696 34.756 1370 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.45 % Allowed : 16.97 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: -0.33 (0.25), residues: 1183 helix: 1.38 (0.27), residues: 402 sheet: -0.74 (0.29), residues: 288 loop : -1.18 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS R 245 PHE 0.024 0.001 PHE D 68 TYR 0.032 0.001 TYR R 92 ARG 0.006 0.000 ARG D 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2200.83 seconds wall clock time: 41 minutes 15.63 seconds (2475.63 seconds total)