Starting phenix.real_space_refine on Sat Aug 3 17:39:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/08_2024/8j6i_36005.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/08_2024/8j6i_36005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/08_2024/8j6i_36005.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/08_2024/8j6i_36005.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/08_2024/8j6i_36005.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j6i_36005/08_2024/8j6i_36005.cif" } resolution = 2.92 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= 0.002 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 65 5.16 5 C 5630 2.51 5 N 1501 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 267": "OE1" <-> "OE2" Residue "A GLU 8": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 195": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "H PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 223": "OD1" <-> "OD2" Residue "H TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8801 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1748 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: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 405 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'GLU%COO:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1737 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'FI7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.04, per 1000 atoms: 0.57 Number of scatterers: 8801 At special positions: 0 Unit cell: (107.12, 110.416, 129.368, 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 65 16.00 O 1605 8.00 N 1501 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 18 " - pdb=" SG CYS R 183 " distance=2.04 Simple disulfide: pdb=" SG CYS R 100 " - pdb=" SG CYS R 177 " distance=2.04 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " 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: 3.20 Conformation dependent library (CDL) restraints added in 1.4 seconds 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.5% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 25 through 55 removed outlier: 3.638A pdb=" N VAL R 29 " --> pdb=" O PHE R 25 " (cutoff:3.500A) Proline residue: R 31 - end of helix removed outlier: 3.843A pdb=" N GLY R 44 " --> pdb=" O PHE R 40 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU R 47 " --> pdb=" O LEU R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 79 removed outlier: 3.575A pdb=" N CYS R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 89 removed outlier: 4.193A pdb=" N LEU R 83 " --> pdb=" O CYS R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 130 Processing helix chain 'R' and resid 140 through 160 removed outlier: 3.577A pdb=" N THR R 155 " --> pdb=" O LEU R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 165 removed outlier: 4.016A pdb=" N LYS R 164 " --> pdb=" O HIS R 161 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS R 165 " --> pdb=" O LEU R 162 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 161 through 165' Processing helix chain 'R' and resid 187 through 219 removed outlier: 3.897A pdb=" N ALA R 191 " --> pdb=" O GLN R 187 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 200 - end of helix removed outlier: 4.420A pdb=" N ARG R 218 " --> pdb=" O SER R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 245 removed outlier: 3.772A pdb=" N PHE R 232 " --> pdb=" O ARG R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.639A pdb=" N ARG R 251 " --> pdb=" O SER R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 280 Processing helix chain 'R' and resid 280 through 295 removed outlier: 4.150A pdb=" N TYR R 284 " --> pdb=" O LEU R 280 " (cutoff:3.500A) Proline residue: R 291 - end of helix Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.955A pdb=" N ALA A 12 " --> pdb=" O GLU A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 53 removed outlier: 3.513A pdb=" N LYS A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 5.176A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.722A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS A 286 " --> pdb=" O LEU A 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 282 through 286' Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.911A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 Processing helix chain 'B' and resid 3 through 26 removed outlier: 4.537A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 12 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.520A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.545A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 169 through 170 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.956A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N ALA A 226 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.163A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.929A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.863A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.529A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.417A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.202A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.857A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.542A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.889A pdb=" N THR H 118 " --> pdb=" O GLY H 10 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.612A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.656A pdb=" N VAL H 155 " --> pdb=" O ILE H 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.883A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL H 226 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR H 175 " --> pdb=" O MET H 230 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1182 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: 2.49 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1407 1.31 - 1.44: 2526 1.44 - 1.57: 4967 1.57 - 1.70: 4 1.70 - 1.82: 92 Bond restraints: 8996 Sorted by residual: bond pdb=" C20 FI7 R 401 " pdb=" C21 FI7 R 401 " ideal model delta sigma weight residual 1.355 1.590 -0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " ideal model delta sigma weight residual 1.516 1.344 0.172 2.00e-02 2.50e+03 7.38e+01 bond pdb=" C13 FI7 R 401 " pdb=" N14 FI7 R 401 " ideal model delta sigma weight residual 1.320 1.474 -0.154 2.00e-02 2.50e+03 5.97e+01 bond pdb=" C08 FI7 R 401 " pdb=" C09 FI7 R 401 " ideal model delta sigma weight residual 1.393 1.542 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C08 FI7 R 401 " pdb=" N14 FI7 R 401 " ideal model delta sigma weight residual 1.327 1.469 -0.142 2.00e-02 2.50e+03 5.02e+01 ... (remaining 8991 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.83: 188 106.83 - 113.65: 4942 113.65 - 120.47: 3455 120.47 - 127.30: 3515 127.30 - 134.12: 96 Bond angle restraints: 12196 Sorted by residual: angle pdb=" N TYR R 269 " pdb=" CA TYR R 269 " pdb=" C TYR R 269 " ideal model delta sigma weight residual 111.11 104.72 6.39 1.20e+00 6.94e-01 2.83e+01 angle pdb=" C LEU R 80 " pdb=" N PRO R 81 " pdb=" CD PRO R 81 " ideal model delta sigma weight residual 125.00 105.29 19.71 4.10e+00 5.95e-02 2.31e+01 angle pdb=" C17 FI7 R 401 " pdb=" N19 FI7 R 401 " pdb=" C20 FI7 R 401 " ideal model delta sigma weight residual 130.45 116.24 14.21 3.00e+00 1.11e-01 2.25e+01 angle pdb=" CA PRO R 81 " pdb=" N PRO R 81 " pdb=" CD PRO R 81 " ideal model delta sigma weight residual 112.00 117.45 -5.45 1.40e+00 5.10e-01 1.51e+01 angle pdb=" C ILE R 13 " pdb=" N ASP R 14 " pdb=" CA ASP R 14 " ideal model delta sigma weight residual 123.91 117.63 6.28 1.66e+00 3.63e-01 1.43e+01 ... (remaining 12191 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.24: 4882 25.24 - 50.49: 390 50.49 - 75.73: 34 75.73 - 100.97: 4 100.97 - 126.21: 2 Dihedral angle restraints: 5312 sinusoidal: 2037 harmonic: 3275 Sorted by residual: dihedral pdb=" CB CYS R 100 " pdb=" SG CYS R 100 " pdb=" SG CYS R 177 " pdb=" CB CYS R 177 " ideal model delta sinusoidal sigma weight residual 93.00 132.79 -39.79 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" C25 FI7 R 401 " pdb=" C26 FI7 R 401 " pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " ideal model delta sinusoidal sigma weight residual 63.14 -63.07 126.21 1 3.00e+01 1.11e-03 1.70e+01 dihedral pdb=" C20 FI7 R 401 " pdb=" C27 FI7 R 401 " pdb=" C28 FI7 R 401 " pdb=" C26 FI7 R 401 " ideal model delta sinusoidal sigma weight residual 45.86 -56.98 102.84 1 3.00e+01 1.11e-03 1.30e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1205 0.054 - 0.108: 136 0.108 - 0.163: 38 0.163 - 0.217: 0 0.217 - 0.271: 2 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA TYR R 269 " pdb=" N TYR R 269 " pdb=" C TYR R 269 " pdb=" CB TYR R 269 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE R 13 " pdb=" N ILE R 13 " pdb=" C ILE R 13 " pdb=" CB ILE R 13 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA TYR H 235 " pdb=" N TYR H 235 " pdb=" C TYR H 235 " pdb=" CB TYR H 235 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1378 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 80 " 0.086 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO R 81 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO R 81 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO R 81 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.028 5.00e-02 4.00e+02 4.33e-02 2.99e+00 pdb=" N PRO B 236 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 239 " -0.008 2.00e-02 2.50e+03 1.14e-02 2.28e+00 pdb=" CG PHE H 239 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 PHE H 239 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE H 239 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE H 239 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE H 239 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE H 239 " -0.004 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 341 2.71 - 3.26: 8845 3.26 - 3.81: 14116 3.81 - 4.35: 17311 4.35 - 4.90: 29677 Nonbonded interactions: 70290 Sorted by model distance: nonbonded pdb=" O ILE R 278 " pdb=" OG SER R 281 " model vdw 2.167 3.040 nonbonded pdb=" O ASP B 66 " pdb=" OG SER B 67 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.248 3.040 nonbonded pdb=" O TYR B 145 " pdb=" N GLY B 162 " model vdw 2.262 3.120 nonbonded pdb=" O ASP B 247 " pdb=" OD1 ASP B 247 " model vdw 2.264 3.040 ... (remaining 70285 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=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: 0.780 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 24.810 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 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 : 0.006 0.235 8996 Z= 0.458 Angle : 0.626 19.710 12196 Z= 0.313 Chirality : 0.040 0.271 1381 Planarity : 0.005 0.146 1538 Dihedral : 16.601 126.213 3185 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 25.99 % Favored : 74.01 % 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: 1.37 (0.27), residues: 1113 helix: 2.35 (0.28), residues: 365 sheet: 1.30 (0.34), residues: 252 loop : -0.41 (0.30), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 93 HIS 0.004 0.000 HIS R 189 PHE 0.023 0.001 PHE H 239 TYR 0.015 0.001 TYR H 235 ARG 0.005 0.000 ARG R 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.891 Fit side-chains REVERT: R 23 ASP cc_start: 0.5249 (t70) cc_final: 0.4522 (t0) REVERT: R 86 ASN cc_start: 0.5355 (t0) cc_final: 0.4945 (m110) REVERT: R 112 GLN cc_start: 0.6961 (tp40) cc_final: 0.6564 (mm-40) REVERT: R 141 ASN cc_start: 0.5635 (m110) cc_final: 0.5373 (m-40) REVERT: R 227 LYS cc_start: 0.5514 (mtmm) cc_final: 0.5206 (mtpt) REVERT: R 285 MET cc_start: 0.6969 (ttp) cc_final: 0.6581 (ttp) REVERT: R 290 ASP cc_start: 0.7039 (m-30) cc_final: 0.6710 (t70) REVERT: A 195 HIS cc_start: 0.7710 (t70) cc_final: 0.7358 (t-170) REVERT: A 197 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7432 (mttt) REVERT: A 198 MET cc_start: 0.8481 (ttm) cc_final: 0.8246 (ttp) REVERT: A 276 GLU cc_start: 0.6616 (mm-30) cc_final: 0.5968 (mt-10) REVERT: A 305 CYS cc_start: 0.7644 (m) cc_final: 0.6602 (t) REVERT: A 321 THR cc_start: 0.8904 (t) cc_final: 0.8517 (m) REVERT: A 330 LYS cc_start: 0.7417 (mttt) cc_final: 0.7047 (tptt) REVERT: A 349 LYS cc_start: 0.7152 (ttmm) cc_final: 0.6352 (tppt) REVERT: B 46 ARG cc_start: 0.7402 (mtp85) cc_final: 0.7057 (mtp-110) REVERT: B 217 MET cc_start: 0.6776 (pmm) cc_final: 0.5839 (pp-130) REVERT: B 220 GLN cc_start: 0.8300 (mp10) cc_final: 0.8063 (mt0) REVERT: B 230 ASN cc_start: 0.7390 (t0) cc_final: 0.7149 (m-40) REVERT: B 295 ASN cc_start: 0.7403 (m-40) cc_final: 0.7037 (m110) REVERT: B 325 MET cc_start: 0.8172 (tpp) cc_final: 0.7875 (mmm) REVERT: H 69 THR cc_start: 0.6352 (t) cc_final: 0.5795 (m) REVERT: H 82 GLN cc_start: 0.7600 (tp40) cc_final: 0.7339 (tp40) REVERT: H 195 LEU cc_start: 0.7729 (mp) cc_final: 0.7501 (mt) REVERT: H 230 MET cc_start: 0.7464 (tpp) cc_final: 0.6981 (mmm) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 1.0160 time to fit residues: 204.1150 Evaluate side-chains 117 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 99 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: R 137 ASN A 347 ASN B 32 GLN B 175 GLN B 176 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 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 0.042 8996 Z= 0.231 Angle : 0.619 8.119 12196 Z= 0.320 Chirality : 0.043 0.199 1381 Planarity : 0.004 0.045 1538 Dihedral : 6.074 71.353 1244 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.68 % Favored : 96.23 % Rotamer: Outliers : 4.81 % Allowed : 24.06 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.26), residues: 1113 helix: 2.09 (0.27), residues: 369 sheet: 0.96 (0.33), residues: 278 loop : -0.44 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS R 189 PHE 0.015 0.002 PHE A 196 TYR 0.023 0.001 TYR H 235 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 126 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 25 PHE cc_start: 0.6599 (OUTLIER) cc_final: 0.6066 (t80) REVERT: R 86 ASN cc_start: 0.5538 (t0) cc_final: 0.5276 (m110) REVERT: R 94 LYS cc_start: 0.4679 (OUTLIER) cc_final: 0.4201 (mtmm) REVERT: R 112 GLN cc_start: 0.7192 (tp40) cc_final: 0.6883 (mm-40) REVERT: R 227 LYS cc_start: 0.5684 (mtmm) cc_final: 0.5299 (pttt) REVERT: R 238 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.5862 (mt) REVERT: R 285 MET cc_start: 0.6912 (ttp) cc_final: 0.6690 (ttp) REVERT: A 18 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6498 (mmm) REVERT: A 195 HIS cc_start: 0.7667 (t70) cc_final: 0.7381 (t-90) REVERT: A 198 MET cc_start: 0.8730 (ttm) cc_final: 0.8469 (ttp) REVERT: A 207 GLU cc_start: 0.6986 (tt0) cc_final: 0.6760 (tt0) REVERT: A 276 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6276 (mt-10) REVERT: A 305 CYS cc_start: 0.7544 (m) cc_final: 0.6437 (t) REVERT: A 321 THR cc_start: 0.8917 (t) cc_final: 0.8578 (m) REVERT: A 349 LYS cc_start: 0.7292 (ttmm) cc_final: 0.6547 (tppt) REVERT: B 50 THR cc_start: 0.8765 (t) cc_final: 0.8470 (m) REVERT: B 134 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7204 (ptt-90) REVERT: B 234 PHE cc_start: 0.9105 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: B 251 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.6197 (mtm-85) REVERT: B 325 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8108 (mmm) REVERT: H 30 SER cc_start: 0.7873 (t) cc_final: 0.7490 (p) REVERT: H 82 GLN cc_start: 0.7915 (tp40) cc_final: 0.7680 (tp40) REVERT: H 195 LEU cc_start: 0.7846 (mp) cc_final: 0.7520 (mt) REVERT: H 230 MET cc_start: 0.7665 (tpp) cc_final: 0.7186 (mmm) outliers start: 45 outliers final: 15 residues processed: 155 average time/residue: 0.9537 time to fit residues: 160.4692 Evaluate side-chains 129 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 194 LEU Chi-restraints excluded: chain R residue 238 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 254 CYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 0.0060 chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 322 HIS B 176 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN H 82 GLN H 142 GLN H 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8996 Z= 0.228 Angle : 0.596 8.508 12196 Z= 0.308 Chirality : 0.043 0.190 1381 Planarity : 0.004 0.044 1538 Dihedral : 5.616 53.133 1244 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 5.13 % Allowed : 24.28 % Favored : 70.59 % 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: 0.92 (0.26), residues: 1113 helix: 1.95 (0.28), residues: 373 sheet: 0.68 (0.32), residues: 292 loop : -0.55 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.002 PHE A 267 TYR 0.026 0.001 TYR H 235 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 133 time to evaluate : 0.956 Fit side-chains revert: symmetry clash REVERT: R 23 ASP cc_start: 0.6147 (OUTLIER) cc_final: 0.5689 (m-30) REVERT: R 25 PHE cc_start: 0.6772 (OUTLIER) cc_final: 0.6270 (t80) REVERT: R 84 MET cc_start: 0.4822 (tpt) cc_final: 0.4576 (tpt) REVERT: R 86 ASN cc_start: 0.5257 (t0) cc_final: 0.5030 (m110) REVERT: R 112 GLN cc_start: 0.7332 (tp40) cc_final: 0.7010 (mm-40) REVERT: R 214 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8472 (t) REVERT: R 227 LYS cc_start: 0.5980 (mtmm) cc_final: 0.5422 (pttt) REVERT: R 258 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6094 (mt) REVERT: A 18 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.6986 (mmm) REVERT: A 22 ASN cc_start: 0.7720 (m-40) cc_final: 0.7317 (m-40) REVERT: A 33 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6549 (tt0) REVERT: A 197 LYS cc_start: 0.8619 (mtmt) cc_final: 0.7842 (mttt) REVERT: A 198 MET cc_start: 0.8855 (ttm) cc_final: 0.8618 (ttp) REVERT: A 207 GLU cc_start: 0.7066 (tt0) cc_final: 0.6571 (mt-10) REVERT: A 247 MET cc_start: 0.8079 (mtp) cc_final: 0.7835 (mtm) REVERT: A 276 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6568 (mt-10) REVERT: A 305 CYS cc_start: 0.7566 (m) cc_final: 0.6469 (t) REVERT: A 309 ASP cc_start: 0.7634 (m-30) cc_final: 0.7315 (m-30) REVERT: A 312 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7718 (mptm) REVERT: A 321 THR cc_start: 0.8944 (t) cc_final: 0.8626 (m) REVERT: A 349 LYS cc_start: 0.7655 (ttmm) cc_final: 0.6818 (tppt) REVERT: B 50 THR cc_start: 0.8764 (t) cc_final: 0.8480 (m) REVERT: B 120 ILE cc_start: 0.7790 (OUTLIER) cc_final: 0.7205 (mm) REVERT: B 134 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7456 (ptt-90) REVERT: B 234 PHE cc_start: 0.9075 (OUTLIER) cc_final: 0.8568 (m-80) REVERT: B 262 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8077 (mtm) REVERT: H 30 SER cc_start: 0.8065 (t) cc_final: 0.7707 (p) REVERT: H 82 GLN cc_start: 0.8024 (tp-100) cc_final: 0.7771 (tp40) REVERT: H 195 LEU cc_start: 0.7842 (mp) cc_final: 0.7529 (mt) REVERT: H 230 MET cc_start: 0.7674 (tpp) cc_final: 0.7287 (mmm) outliers start: 48 outliers final: 14 residues processed: 165 average time/residue: 0.9846 time to fit residues: 175.6513 Evaluate side-chains 138 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 25 PHE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 351 CYS Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 75 GLN B 175 GLN B 230 ASN B 237 ASN B 259 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 8996 Z= 0.406 Angle : 0.710 11.428 12196 Z= 0.366 Chirality : 0.047 0.245 1381 Planarity : 0.005 0.051 1538 Dihedral : 6.084 52.316 1244 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 6.52 % Allowed : 21.82 % Favored : 71.66 % 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: 0.64 (0.26), residues: 1113 helix: 1.69 (0.27), residues: 364 sheet: 0.52 (0.31), residues: 291 loop : -0.64 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.005 0.001 HIS R 131 PHE 0.023 0.003 PHE A 267 TYR 0.033 0.002 TYR H 235 ARG 0.006 0.001 ARG R 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 121 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: R 94 LYS cc_start: 0.5238 (OUTLIER) cc_final: 0.4999 (mtmm) REVERT: R 103 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5498 (ttp) REVERT: R 112 GLN cc_start: 0.7480 (tp40) cc_final: 0.6824 (tp-100) REVERT: R 162 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5601 (pp) REVERT: R 214 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.8381 (t) REVERT: R 227 LYS cc_start: 0.6465 (mtmm) cc_final: 0.6185 (mtmt) REVERT: R 258 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6112 (mt) REVERT: A 18 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7227 (mmm) REVERT: A 22 ASN cc_start: 0.7840 (m-40) cc_final: 0.7468 (m-40) REVERT: A 33 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6891 (tt0) REVERT: A 52 GLN cc_start: 0.7279 (OUTLIER) cc_final: 0.6858 (tp40) REVERT: A 184 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8721 (tt) REVERT: A 197 LYS cc_start: 0.8682 (mtmt) cc_final: 0.7987 (mttt) REVERT: A 198 MET cc_start: 0.8830 (ttm) cc_final: 0.8620 (ttm) REVERT: A 207 GLU cc_start: 0.7391 (tt0) cc_final: 0.6577 (mt-10) REVERT: A 208 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7485 (mtm-85) REVERT: A 247 MET cc_start: 0.8228 (mtp) cc_final: 0.8021 (mtp) REVERT: A 276 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6937 (mt-10) REVERT: A 305 CYS cc_start: 0.7653 (m) cc_final: 0.6923 (t) REVERT: A 312 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7390 (mptm) REVERT: A 321 THR cc_start: 0.8917 (t) cc_final: 0.8650 (m) REVERT: A 349 LYS cc_start: 0.7756 (ttmm) cc_final: 0.6975 (tppt) REVERT: B 50 THR cc_start: 0.8835 (t) cc_final: 0.8625 (m) REVERT: B 120 ILE cc_start: 0.7689 (OUTLIER) cc_final: 0.7106 (mm) REVERT: B 134 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7477 (ptt-90) REVERT: H 30 SER cc_start: 0.8270 (t) cc_final: 0.7962 (p) REVERT: H 195 LEU cc_start: 0.7934 (mp) cc_final: 0.7470 (mt) outliers start: 61 outliers final: 20 residues processed: 162 average time/residue: 1.0461 time to fit residues: 182.3405 Evaluate side-chains 142 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 45 ASN Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 103 MET Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 258 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 184 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 ASN R 217 GLN ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 ASN B 237 ASN H 82 GLN H 142 GLN H 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8996 Z= 0.254 Angle : 0.599 8.367 12196 Z= 0.311 Chirality : 0.043 0.205 1381 Planarity : 0.004 0.049 1538 Dihedral : 5.370 48.048 1244 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 6.31 % Allowed : 22.03 % Favored : 71.66 % 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: 0.58 (0.26), residues: 1113 helix: 1.62 (0.28), residues: 373 sheet: 0.47 (0.31), residues: 288 loop : -0.68 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.013 0.002 PHE R 180 TYR 0.030 0.001 TYR H 235 ARG 0.004 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: R 64 ILE cc_start: 0.6728 (OUTLIER) cc_final: 0.6488 (mp) REVERT: R 94 LYS cc_start: 0.5089 (OUTLIER) cc_final: 0.4799 (mtmm) REVERT: R 162 LEU cc_start: 0.6018 (OUTLIER) cc_final: 0.5458 (pp) REVERT: R 227 LYS cc_start: 0.6488 (mtmm) cc_final: 0.6255 (mtmt) REVERT: A 18 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7177 (mmm) REVERT: A 22 ASN cc_start: 0.7787 (m-40) cc_final: 0.7412 (m-40) REVERT: A 33 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: A 184 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8718 (tt) REVERT: A 197 LYS cc_start: 0.8634 (mtmt) cc_final: 0.7895 (mttt) REVERT: A 198 MET cc_start: 0.8802 (ttm) cc_final: 0.8574 (ttm) REVERT: A 207 GLU cc_start: 0.7379 (tt0) cc_final: 0.6578 (mt-10) REVERT: A 276 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6868 (mt-10) REVERT: A 305 CYS cc_start: 0.7716 (m) cc_final: 0.6966 (t) REVERT: A 312 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7534 (mptm) REVERT: A 349 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7076 (tppt) REVERT: B 50 THR cc_start: 0.8826 (t) cc_final: 0.8620 (m) REVERT: B 120 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.6975 (mm) REVERT: B 134 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7374 (ptt-90) REVERT: B 251 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8272 (ttm170) REVERT: H 30 SER cc_start: 0.8274 (t) cc_final: 0.7968 (p) REVERT: H 34 MET cc_start: 0.8126 (mmp) cc_final: 0.7887 (mmm) REVERT: H 82 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7867 (tp40) REVERT: H 142 GLN cc_start: 0.5589 (OUTLIER) cc_final: 0.4994 (mt0) REVERT: H 195 LEU cc_start: 0.7885 (mp) cc_final: 0.7441 (mt) REVERT: H 233 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7137 (mt) outliers start: 59 outliers final: 22 residues processed: 163 average time/residue: 1.0001 time to fit residues: 175.7828 Evaluate side-chains 146 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 230 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 251 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 233 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8996 Z= 0.343 Angle : 0.644 10.224 12196 Z= 0.335 Chirality : 0.045 0.224 1381 Planarity : 0.005 0.052 1538 Dihedral : 5.621 47.181 1244 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer: Outliers : 6.52 % Allowed : 22.78 % Favored : 70.70 % 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: 0.54 (0.26), residues: 1113 helix: 1.61 (0.28), residues: 365 sheet: 0.27 (0.31), residues: 297 loop : -0.55 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.004 0.001 HIS R 131 PHE 0.016 0.002 PHE B 292 TYR 0.031 0.002 TYR H 235 ARG 0.005 0.001 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 114 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: R 64 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6534 (mp) REVERT: R 94 LYS cc_start: 0.5078 (OUTLIER) cc_final: 0.4872 (mtmm) REVERT: R 112 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7132 (tt0) REVERT: R 162 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5557 (pp) REVERT: A 18 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7304 (mmm) REVERT: A 22 ASN cc_start: 0.7784 (m-40) cc_final: 0.7411 (m-40) REVERT: A 33 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: A 197 LYS cc_start: 0.8647 (mtmt) cc_final: 0.7875 (mttt) REVERT: A 207 GLU cc_start: 0.7338 (tt0) cc_final: 0.6548 (mt-10) REVERT: A 276 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6933 (mt-10) REVERT: A 305 CYS cc_start: 0.7715 (m) cc_final: 0.6947 (t) REVERT: A 312 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7441 (mptm) REVERT: A 349 LYS cc_start: 0.7875 (ttmm) cc_final: 0.7096 (tppt) REVERT: B 50 THR cc_start: 0.8809 (t) cc_final: 0.8601 (m) REVERT: B 120 ILE cc_start: 0.7765 (OUTLIER) cc_final: 0.7204 (mm) REVERT: B 134 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7474 (ptt-90) REVERT: B 234 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8055 (m-80) REVERT: H 30 SER cc_start: 0.8270 (t) cc_final: 0.7974 (p) REVERT: H 34 MET cc_start: 0.8214 (mmp) cc_final: 0.7963 (mmm) REVERT: H 142 GLN cc_start: 0.5381 (OUTLIER) cc_final: 0.4862 (mt0) REVERT: H 195 LEU cc_start: 0.7920 (mp) cc_final: 0.7470 (mt) outliers start: 61 outliers final: 28 residues processed: 157 average time/residue: 0.9242 time to fit residues: 157.3291 Evaluate side-chains 150 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 111 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0570 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 237 ASN H 82 GLN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8996 Z= 0.187 Angle : 0.559 6.576 12196 Z= 0.292 Chirality : 0.042 0.185 1381 Planarity : 0.004 0.051 1538 Dihedral : 5.279 45.828 1244 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.32 % Rotamer: Outliers : 5.67 % Allowed : 24.28 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1113 helix: 1.76 (0.28), residues: 367 sheet: 0.44 (0.31), residues: 290 loop : -0.48 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 195 PHE 0.011 0.001 PHE A 189 TYR 0.027 0.001 TYR H 235 ARG 0.006 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 116 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: R 64 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6568 (mp) REVERT: R 93 TRP cc_start: 0.4897 (t-100) cc_final: 0.4678 (t-100) REVERT: R 94 LYS cc_start: 0.4869 (OUTLIER) cc_final: 0.4657 (mtmm) REVERT: R 103 MET cc_start: 0.5882 (ttp) cc_final: 0.5404 (ttt) REVERT: R 107 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6087 (tt) REVERT: R 112 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7363 (mm-40) REVERT: R 162 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5397 (pp) REVERT: R 189 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5843 (p90) REVERT: R 252 ILE cc_start: 0.7750 (OUTLIER) cc_final: 0.7132 (mt) REVERT: A 24 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6542 (ttm110) REVERT: A 25 GLU cc_start: 0.7500 (tt0) cc_final: 0.7289 (mt-10) REVERT: A 33 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6584 (tt0) REVERT: A 197 LYS cc_start: 0.8556 (mtmt) cc_final: 0.7782 (mttt) REVERT: A 207 GLU cc_start: 0.7312 (tt0) cc_final: 0.6541 (mt-10) REVERT: A 276 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6913 (mt-10) REVERT: A 305 CYS cc_start: 0.7816 (m) cc_final: 0.7114 (t) REVERT: A 312 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7395 (mptm) REVERT: A 313 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.5976 (mtp85) REVERT: A 314 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6759 (mttm) REVERT: A 349 LYS cc_start: 0.7863 (ttmm) cc_final: 0.7074 (tppt) REVERT: B 50 THR cc_start: 0.8795 (t) cc_final: 0.8551 (m) REVERT: B 134 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7367 (ptt-90) REVERT: B 234 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8061 (m-80) REVERT: B 254 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.7836 (t70) REVERT: H 30 SER cc_start: 0.8241 (t) cc_final: 0.7934 (p) REVERT: H 34 MET cc_start: 0.8093 (mmp) cc_final: 0.7837 (mmm) REVERT: H 82 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7710 (tp-100) REVERT: H 142 GLN cc_start: 0.5490 (OUTLIER) cc_final: 0.4987 (mt0) REVERT: H 195 LEU cc_start: 0.7889 (mp) cc_final: 0.7450 (mt) outliers start: 53 outliers final: 20 residues processed: 150 average time/residue: 1.1277 time to fit residues: 181.3690 Evaluate side-chains 148 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 112 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 112 GLN Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 175 GLN B 237 ASN H 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8996 Z= 0.193 Angle : 0.554 6.637 12196 Z= 0.289 Chirality : 0.042 0.180 1381 Planarity : 0.004 0.055 1538 Dihedral : 5.276 41.044 1244 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.77 % Favored : 96.14 % Rotamer: Outliers : 5.24 % Allowed : 24.81 % Favored : 69.95 % 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: 0.77 (0.26), residues: 1113 helix: 1.82 (0.28), residues: 367 sheet: 0.42 (0.31), residues: 291 loop : -0.46 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 195 PHE 0.018 0.001 PHE R 82 TYR 0.026 0.001 TYR H 235 ARG 0.007 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: R 60 LYS cc_start: 0.5860 (pttt) cc_final: 0.5410 (pttm) REVERT: R 64 ILE cc_start: 0.6810 (OUTLIER) cc_final: 0.6539 (mp) REVERT: R 162 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5324 (pp) REVERT: R 189 HIS cc_start: 0.6123 (OUTLIER) cc_final: 0.5823 (p90) REVERT: R 214 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8326 (t) REVERT: R 252 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7100 (mt) REVERT: A 24 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6544 (ttm110) REVERT: A 25 GLU cc_start: 0.7493 (tt0) cc_final: 0.7289 (mt-10) REVERT: A 197 LYS cc_start: 0.8559 (mtmt) cc_final: 0.7798 (mttt) REVERT: A 207 GLU cc_start: 0.7324 (tt0) cc_final: 0.6517 (mt-10) REVERT: A 276 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6916 (mt-10) REVERT: A 305 CYS cc_start: 0.7814 (m) cc_final: 0.7117 (t) REVERT: A 312 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7373 (mptm) REVERT: A 313 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.5968 (mtp85) REVERT: A 314 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6760 (mttm) REVERT: A 349 LYS cc_start: 0.7831 (ttmm) cc_final: 0.7050 (tppt) REVERT: B 50 THR cc_start: 0.8781 (t) cc_final: 0.8536 (m) REVERT: B 134 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.7383 (ptt-90) REVERT: B 234 PHE cc_start: 0.8941 (OUTLIER) cc_final: 0.7970 (m-80) REVERT: B 254 ASP cc_start: 0.8417 (OUTLIER) cc_final: 0.7840 (t70) REVERT: B 256 ARG cc_start: 0.7623 (mtt90) cc_final: 0.7381 (mtt90) REVERT: H 30 SER cc_start: 0.8235 (t) cc_final: 0.7940 (p) REVERT: H 34 MET cc_start: 0.8094 (mmp) cc_final: 0.7864 (mmm) REVERT: H 195 LEU cc_start: 0.7941 (mp) cc_final: 0.7531 (mt) outliers start: 49 outliers final: 24 residues processed: 151 average time/residue: 1.0923 time to fit residues: 177.1151 Evaluate side-chains 145 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 109 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 64 ILE Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 286 ASN Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 230 MET Chi-restraints excluded: chain H residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.1980 chunk 64 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN H 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8996 Z= 0.253 Angle : 0.592 8.307 12196 Z= 0.309 Chirality : 0.043 0.191 1381 Planarity : 0.004 0.054 1538 Dihedral : 5.440 41.563 1244 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 5.35 % Allowed : 25.35 % Favored : 69.30 % 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: 0.71 (0.26), residues: 1113 helix: 1.73 (0.27), residues: 367 sheet: 0.38 (0.31), residues: 293 loop : -0.45 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS A 195 PHE 0.011 0.002 PHE A 189 TYR 0.027 0.002 TYR H 235 ARG 0.005 0.000 ARG B 129 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2226 Ramachandran restraints generated. 1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 108 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: R 103 MET cc_start: 0.5850 (ttp) cc_final: 0.5377 (ttt) REVERT: R 162 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5348 (pp) REVERT: R 189 HIS cc_start: 0.6141 (OUTLIER) cc_final: 0.5844 (p90) REVERT: R 214 SER cc_start: 0.8642 (OUTLIER) cc_final: 0.8313 (t) REVERT: R 252 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7108 (mt) REVERT: A 24 ARG cc_start: 0.7054 (OUTLIER) cc_final: 0.6535 (ttm110) REVERT: A 25 GLU cc_start: 0.7502 (tt0) cc_final: 0.7289 (mt-10) REVERT: A 207 GLU cc_start: 0.7309 (tt0) cc_final: 0.6521 (tt0) REVERT: A 276 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6935 (mt-10) REVERT: A 305 CYS cc_start: 0.7739 (m) cc_final: 0.7032 (t) REVERT: A 312 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7384 (mptm) REVERT: A 313 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6020 (mtp85) REVERT: A 314 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6744 (mttm) REVERT: A 349 LYS cc_start: 0.7835 (ttmm) cc_final: 0.7061 (tppt) REVERT: B 50 THR cc_start: 0.8793 (t) cc_final: 0.8541 (m) REVERT: B 134 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7463 (ptt-90) REVERT: B 234 PHE cc_start: 0.8966 (OUTLIER) cc_final: 0.7941 (m-80) REVERT: B 254 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7837 (t70) REVERT: B 256 ARG cc_start: 0.7643 (mtt90) cc_final: 0.7402 (mtt90) REVERT: G 37 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8408 (mp) REVERT: H 30 SER cc_start: 0.8241 (t) cc_final: 0.7953 (p) REVERT: H 34 MET cc_start: 0.8155 (mmp) cc_final: 0.7899 (mmm) REVERT: H 142 GLN cc_start: 0.5619 (OUTLIER) cc_final: 0.5225 (mt0) REVERT: H 195 LEU cc_start: 0.7951 (mp) cc_final: 0.7545 (mt) outliers start: 50 outliers final: 25 residues processed: 140 average time/residue: 1.0651 time to fit residues: 160.1909 Evaluate side-chains 146 residues out of total 977 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 108 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 71 VAL Chi-restraints excluded: chain R residue 94 LYS Chi-restraints excluded: chain R residue 102 LEU Chi-restraints excluded: chain R residue 107 LEU Chi-restraints excluded: chain R residue 160 VAL Chi-restraints excluded: chain R residue 162 LEU Chi-restraints excluded: chain R residue 189 HIS Chi-restraints excluded: chain R residue 214 SER Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 287 SER Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 205 ARG Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain H residue 142 GLN Chi-restraints excluded: chain H residue 184 SER Chi-restraints excluded: chain H residue 230 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.1671 > 50: distance: 42 - 85: 24.626 distance: 71 - 76: 7.262 distance: 76 - 77: 11.055 distance: 76 - 124: 18.265 distance: 77 - 78: 6.226 distance: 77 - 80: 11.179 distance: 78 - 79: 6.891 distance: 78 - 82: 13.621 distance: 80 - 81: 5.349 distance: 82 - 83: 17.672 distance: 83 - 84: 15.013 distance: 84 - 85: 16.742 distance: 84 - 86: 17.764 distance: 86 - 87: 13.064 distance: 87 - 88: 3.018 distance: 87 - 90: 3.570 distance: 88 - 89: 11.259 distance: 88 - 91: 6.971 distance: 91 - 92: 12.341 distance: 92 - 93: 8.923 distance: 92 - 95: 9.866 distance: 93 - 94: 15.841 distance: 93 - 97: 4.921 distance: 95 - 96: 25.359 distance: 97 - 98: 4.148 distance: 98 - 99: 8.256 distance: 98 - 101: 15.059 distance: 99 - 100: 30.816 distance: 99 - 105: 8.615 distance: 101 - 102: 14.613 distance: 102 - 103: 11.021 distance: 102 - 104: 21.743 distance: 105 - 106: 18.780 distance: 106 - 107: 10.878 distance: 106 - 109: 24.915 distance: 107 - 108: 27.928 distance: 107 - 110: 7.565 distance: 110 - 111: 8.500 distance: 111 - 112: 10.947 distance: 112 - 113: 13.779 distance: 112 - 116: 7.604 distance: 114 - 115: 10.305 distance: 116 - 117: 5.268 distance: 116 - 187: 6.815 distance: 117 - 118: 10.971 distance: 117 - 120: 10.770 distance: 118 - 119: 15.766 distance: 118 - 121: 18.971 distance: 119 - 184: 31.567 distance: 123 - 124: 11.511 distance: 123 - 130: 6.289 distance: 126 - 127: 4.776 distance: 127 - 128: 8.308 distance: 128 - 129: 8.164 distance: 130 - 131: 7.156 distance: 130 - 171: 9.662 distance: 131 - 134: 4.886 distance: 132 - 133: 4.419 distance: 134 - 135: 4.964 distance: 135 - 137: 3.154