Starting phenix.real_space_refine on Sat Jun 7 12:42:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trq_26101/06_2025/7trq_26101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trq_26101/06_2025/7trq_26101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7trq_26101/06_2025/7trq_26101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trq_26101/06_2025/7trq_26101.map" model { file = "/net/cci-nas-00/data/ceres_data/7trq_26101/06_2025/7trq_26101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trq_26101/06_2025/7trq_26101.cif" } resolution = 2.5 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= 0.002 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: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5558 2.51 5 N 1471 2.21 5 O 1626 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8723 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2114 Classifications: {'peptide': 274} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2597 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 419 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1786 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1764 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'IUI': 1, 'IXO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.87, per 1000 atoms: 0.67 Number of scatterers: 8723 At special positions: 0 Unit cell: (92.13, 121.18, 126.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 3 9.00 O 1626 8.00 N 1471 7.00 C 5558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 185 " distance=2.03 Simple disulfide: pdb=" SG CYS R 426 " - pdb=" SG CYS R 429 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.37 Conformation dependent library (CDL) restraints added in 1.1 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: 29 helices and 13 sheets defined 39.2% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'R' and resid 31 through 60 removed outlier: 4.184A pdb=" N ILE R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA R 36 " --> pdb=" O MET R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 84 removed outlier: 3.522A pdb=" N TYR R 69 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU R 71 " --> pdb=" O ASN R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 3.512A pdb=" N LEU R 88 " --> pdb=" O PHE R 84 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 136 Processing helix chain 'R' and resid 145 through 176 Proline residue: R 166 - end of helix removed outlier: 5.189A pdb=" N GLN R 172 " --> pdb=" O ILE R 168 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N PHE R 173 " --> pdb=" O LEU R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 191 removed outlier: 3.578A pdb=" N LEU R 190 " --> pdb=" O ILE R 187 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER R 191 " --> pdb=" O GLN R 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 187 through 191' Processing helix chain 'R' and resid 192 through 204 Processing helix chain 'R' and resid 206 through 223 removed outlier: 4.072A pdb=" N ARG R 223 " --> pdb=" O SER R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 393 through 426 Proline residue: R 415 - end of helix removed outlier: 3.684A pdb=" N LEU R 421 " --> pdb=" O ASN R 417 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N PHE R 425 " --> pdb=" O LEU R 421 " (cutoff:3.500A) Processing helix chain 'R' and resid 431 through 453 removed outlier: 3.971A pdb=" N SER R 446 " --> pdb=" O CYS R 442 " (cutoff:3.500A) Proline residue: R 450 - end of helix Processing helix chain 'R' and resid 457 through 469 removed outlier: 3.566A pdb=" N LYS R 461 " --> pdb=" O ASN R 457 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU R 469 " --> pdb=" O ARG R 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.575A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.645A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 220 through 224 removed outlier: 4.040A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.605A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.668A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 231 removed outlier: 4.165A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 228 through 231' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.832A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.849A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.830A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.512A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.657A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.992A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.096A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.611A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.662A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.993A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.993A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 140 through 141 removed outlier: 3.848A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 146 through 148 removed outlier: 3.592A pdb=" N GLU H 246 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.242A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1281 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: 2.80 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1416 1.32 - 1.45: 2599 1.45 - 1.58: 4797 1.58 - 1.72: 0 1.72 - 1.85: 95 Bond restraints: 8907 Sorted by residual: bond pdb=" C10 IXO R 601 " pdb=" N11 IXO R 601 " ideal model delta sigma weight residual 1.270 1.469 -0.199 2.00e-02 2.50e+03 9.89e+01 bond pdb=" C10 IXO R 601 " pdb=" C14 IXO R 601 " ideal model delta sigma weight residual 1.492 1.324 0.168 2.00e-02 2.50e+03 7.07e+01 bond pdb=" C13 IXO R 601 " pdb=" O12 IXO R 601 " ideal model delta sigma weight residual 1.439 1.546 -0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" C05 IXO R 601 " pdb=" C06 IXO R 601 " ideal model delta sigma weight residual 1.450 1.529 -0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C07 IXO R 601 " pdb=" C08 IXO R 601 " ideal model delta sigma weight residual 1.454 1.528 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 8902 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 11698 2.05 - 4.10: 338 4.10 - 6.15: 57 6.15 - 8.20: 8 8.20 - 10.25: 1 Bond angle restraints: 12102 Sorted by residual: angle pdb=" CA TYR B 105 " pdb=" CB TYR B 105 " pdb=" CG TYR B 105 " ideal model delta sigma weight residual 113.90 119.30 -5.40 1.80e+00 3.09e-01 9.00e+00 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.80e+00 angle pdb=" CA TRP B 82 " pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 113.60 119.19 -5.59 1.90e+00 2.77e-01 8.66e+00 angle pdb=" CA TYR R 439 " pdb=" CB TYR R 439 " pdb=" CG TYR R 439 " ideal model delta sigma weight residual 113.90 119.20 -5.30 1.80e+00 3.09e-01 8.66e+00 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 126.55 -10.25 3.50e+00 8.16e-02 8.58e+00 ... (remaining 12097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4888 16.94 - 33.88: 299 33.88 - 50.82: 69 50.82 - 67.75: 8 67.75 - 84.69: 3 Dihedral angle restraints: 5267 sinusoidal: 1986 harmonic: 3281 Sorted by residual: dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 160.13 19.87 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA PHE A 196 " pdb=" C PHE A 196 " pdb=" N LYS A 197 " pdb=" CA LYS A 197 " ideal model delta harmonic sigma weight residual 180.00 160.99 19.01 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE H 32 " pdb=" C PHE H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta harmonic sigma weight residual 180.00 161.85 18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1139 0.067 - 0.134: 206 0.134 - 0.201: 40 0.201 - 0.268: 3 0.268 - 0.335: 1 Chirality restraints: 1389 Sorted by residual: chirality pdb=" CB VAL R 444 " pdb=" CA VAL R 444 " pdb=" CG1 VAL R 444 " pdb=" CG2 VAL R 444 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB ILE A 184 " pdb=" CA ILE A 184 " pdb=" CG1 ILE A 184 " pdb=" CG2 ILE A 184 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1386 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N IUI R 602 " -0.005 2.00e-02 2.50e+03 3.15e-02 3.23e+01 pdb=" C IUI R 602 " -0.044 2.00e-02 2.50e+03 pdb=" C1 IUI R 602 " -0.011 2.00e-02 2.50e+03 pdb=" C16 IUI R 602 " 0.077 2.00e-02 2.50e+03 pdb=" C2 IUI R 602 " 0.005 2.00e-02 2.50e+03 pdb=" C3 IUI R 602 " -0.022 2.00e-02 2.50e+03 pdb=" C4 IUI R 602 " -0.020 2.00e-02 2.50e+03 pdb=" C5 IUI R 602 " -0.006 2.00e-02 2.50e+03 pdb=" C6 IUI R 602 " -0.000 2.00e-02 2.50e+03 pdb=" C7 IUI R 602 " 0.058 2.00e-02 2.50e+03 pdb=" N1 IUI R 602 " -0.021 2.00e-02 2.50e+03 pdb=" N3 IUI R 602 " 0.000 2.00e-02 2.50e+03 pdb=" S IUI R 602 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" O IUI R 602 " -0.007 2.00e-02 2.50e+03 4.03e-02 2.03e+01 pdb=" C6 IUI R 602 " 0.039 2.00e-02 2.50e+03 pdb=" C7 IUI R 602 " -0.018 2.00e-02 2.50e+03 pdb=" C8 IUI R 602 " 0.049 2.00e-02 2.50e+03 pdb=" N2 IUI R 602 " -0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 193 " -0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO B 194 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 194 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 194 " -0.044 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2468 2.82 - 3.34: 7677 3.34 - 3.86: 14752 3.86 - 4.38: 17701 4.38 - 4.90: 30427 Nonbonded interactions: 73025 Sorted by model distance: nonbonded pdb=" O ASN R 87 " pdb=" OG1 THR R 90 " model vdw 2.295 3.040 nonbonded pdb=" OE1 GLU B 130 " pdb=" NH1 ARG B 134 " model vdw 2.345 3.120 nonbonded pdb=" O GLU R 395 " pdb=" OG1 THR R 399 " model vdw 2.350 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.359 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.364 3.040 ... (remaining 73020 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: 1.080 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.220 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:12.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 0.199 8911 Z= 0.304 Angle : 0.831 10.254 12110 Z= 0.467 Chirality : 0.056 0.335 1389 Planarity : 0.007 0.079 1520 Dihedral : 11.802 84.693 3137 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.50 (0.23), residues: 1113 helix: -0.01 (0.23), residues: 394 sheet: 0.20 (0.29), residues: 291 loop : -0.88 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.009 0.002 HIS A 322 PHE 0.029 0.003 PHE B 199 TYR 0.021 0.002 TYR R 439 ARG 0.009 0.001 ARG H 98 Details of bonding type rmsd hydrogen bonds : bond 0.13599 ( 453) hydrogen bonds : angle 5.83927 ( 1281) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.93081 ( 8) covalent geometry : bond 0.00640 ( 8907) covalent geometry : angle 0.83132 (12102) *********************** 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 176 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8133 (t-100) cc_final: 0.7748 (t-100) REVERT: R 148 MET cc_start: 0.7830 (mmt) cc_final: 0.7545 (mmt) REVERT: R 152 MET cc_start: 0.8152 (mtm) cc_final: 0.7825 (mtp) REVERT: R 400 ARG cc_start: 0.7846 (ttp-170) cc_final: 0.7533 (mtm110) REVERT: B 16 ASN cc_start: 0.9207 (m-40) cc_final: 0.8715 (m-40) REVERT: B 17 GLN cc_start: 0.9041 (tt0) cc_final: 0.8678 (tp-100) REVERT: H 73 ASP cc_start: 0.8398 (t0) cc_final: 0.8107 (t0) REVERT: H 87 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8157 (mtt180) REVERT: H 219 LEU cc_start: 0.9253 (tt) cc_final: 0.8919 (tt) REVERT: A 24 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7296 (mtm-85) REVERT: A 35 LYS cc_start: 0.8542 (mttp) cc_final: 0.8293 (mtpp) REVERT: A 197 LYS cc_start: 0.8841 (mttt) cc_final: 0.8460 (mttm) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 1.7501 time to fit residues: 322.0135 Evaluate side-chains 132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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: 6.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.0170 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 117 ASN B 32 GLN B 75 GLN A 294 ASN A 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.096105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.061940 restraints weight = 15298.190| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.37 r_work: 0.2649 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8911 Z= 0.133 Angle : 0.530 6.135 12110 Z= 0.289 Chirality : 0.042 0.136 1389 Planarity : 0.004 0.043 1520 Dihedral : 5.084 34.867 1246 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.29 % Allowed : 10.01 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 (0.25), residues: 1113 helix: 1.63 (0.26), residues: 397 sheet: 0.50 (0.30), residues: 271 loop : -0.55 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE A 189 TYR 0.016 0.001 TYR H 190 ARG 0.003 0.000 ARG H 38 Details of bonding type rmsd hydrogen bonds : bond 0.04396 ( 453) hydrogen bonds : angle 4.36569 ( 1281) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.56492 ( 8) covalent geometry : bond 0.00288 ( 8907) covalent geometry : angle 0.52850 (12102) *********************** 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 158 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8268 (t-100) cc_final: 0.7892 (t-100) REVERT: R 148 MET cc_start: 0.7917 (mmt) cc_final: 0.7674 (mmt) REVERT: R 152 MET cc_start: 0.8005 (mtm) cc_final: 0.7707 (mtp) REVERT: R 400 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7750 (mtm110) REVERT: B 15 LYS cc_start: 0.9159 (mtpp) cc_final: 0.8814 (mtmt) REVERT: B 215 GLU cc_start: 0.8872 (mp0) cc_final: 0.8510 (mp0) REVERT: G 17 GLU cc_start: 0.8908 (tp30) cc_final: 0.8178 (tp30) REVERT: G 20 LYS cc_start: 0.8687 (mttm) cc_final: 0.8445 (tmtt) REVERT: G 21 MET cc_start: 0.8940 (mmm) cc_final: 0.8453 (mmm) REVERT: G 42 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7858 (mp0) REVERT: H 73 ASP cc_start: 0.8599 (t0) cc_final: 0.8214 (t0) REVERT: A 24 ARG cc_start: 0.8118 (ttp-110) cc_final: 0.7643 (ttp-170) REVERT: A 35 LYS cc_start: 0.8934 (mttp) cc_final: 0.8704 (mtpp) REVERT: A 197 LYS cc_start: 0.9122 (mttt) cc_final: 0.8785 (mttp) REVERT: A 247 MET cc_start: 0.9144 (mtp) cc_final: 0.8852 (mtm) outliers start: 12 outliers final: 3 residues processed: 151 average time/residue: 1.6982 time to fit residues: 268.6056 Evaluate side-chains 139 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 62 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.062231 restraints weight = 15581.129| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.37 r_work: 0.2658 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2530 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8911 Z= 0.116 Angle : 0.507 7.542 12110 Z= 0.273 Chirality : 0.041 0.132 1389 Planarity : 0.004 0.044 1520 Dihedral : 4.675 31.851 1246 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.51 % Allowed : 11.63 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.06 (0.25), residues: 1113 helix: 2.09 (0.26), residues: 395 sheet: 0.50 (0.30), residues: 269 loop : -0.38 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE A 189 TYR 0.016 0.001 TYR H 190 ARG 0.007 0.001 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 453) hydrogen bonds : angle 4.19267 ( 1281) SS BOND : bond 0.00224 ( 4) SS BOND : angle 1.48866 ( 8) covalent geometry : bond 0.00250 ( 8907) covalent geometry : angle 0.50548 (12102) *********************** 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 159 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8266 (t-100) cc_final: 0.7831 (t-100) REVERT: R 121 MET cc_start: 0.8794 (mmm) cc_final: 0.8585 (mmp) REVERT: R 148 MET cc_start: 0.7920 (mmt) cc_final: 0.7649 (mmt) REVERT: R 152 MET cc_start: 0.8011 (mtm) cc_final: 0.7754 (mtp) REVERT: R 400 ARG cc_start: 0.8099 (ttp-170) cc_final: 0.7747 (mtm110) REVERT: B 15 LYS cc_start: 0.9149 (mtpp) cc_final: 0.8811 (mtmt) REVERT: B 19 ARG cc_start: 0.8441 (ttp80) cc_final: 0.8218 (ttp80) REVERT: B 215 GLU cc_start: 0.8862 (mp0) cc_final: 0.8541 (mp0) REVERT: G 17 GLU cc_start: 0.8913 (tp30) cc_final: 0.8033 (tp30) REVERT: G 18 GLN cc_start: 0.8702 (tp40) cc_final: 0.8490 (tp-100) REVERT: G 20 LYS cc_start: 0.8684 (mttm) cc_final: 0.8472 (tmtt) REVERT: G 21 MET cc_start: 0.8960 (mmm) cc_final: 0.8418 (mmm) REVERT: G 42 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.7973 (mp0) REVERT: G 58 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8767 (mp0) REVERT: H 73 ASP cc_start: 0.8605 (t0) cc_final: 0.8249 (t0) REVERT: A 24 ARG cc_start: 0.8135 (ttp-110) cc_final: 0.7651 (ttp-170) REVERT: A 35 LYS cc_start: 0.8942 (mttp) cc_final: 0.8713 (mtpp) REVERT: A 197 LYS cc_start: 0.9152 (mttt) cc_final: 0.8798 (mttp) outliers start: 14 outliers final: 5 residues processed: 150 average time/residue: 1.9263 time to fit residues: 302.7734 Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain A residue 33 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 4.9990 chunk 104 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.092646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.058111 restraints weight = 15565.413| |-----------------------------------------------------------------------------| r_work (start): 0.2703 rms_B_bonded: 2.35 r_work: 0.2562 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2437 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8880 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 8911 Z= 0.331 Angle : 0.617 7.785 12110 Z= 0.331 Chirality : 0.047 0.138 1389 Planarity : 0.004 0.042 1520 Dihedral : 5.009 33.290 1246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.26 % Allowed : 12.06 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.05 (0.25), residues: 1113 helix: 1.88 (0.26), residues: 406 sheet: 0.51 (0.29), residues: 292 loop : -0.28 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.007 0.002 HIS H 35 PHE 0.023 0.002 PHE R 84 TYR 0.016 0.002 TYR H 95 ARG 0.006 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.05140 ( 453) hydrogen bonds : angle 4.43658 ( 1281) SS BOND : bond 0.00348 ( 4) SS BOND : angle 1.84048 ( 8) covalent geometry : bond 0.00766 ( 8907) covalent geometry : angle 0.61544 (12102) *********************** 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 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8394 (t-100) cc_final: 0.7882 (t-100) REVERT: R 148 MET cc_start: 0.7884 (mmt) cc_final: 0.7583 (mmt) REVERT: R 152 MET cc_start: 0.8026 (mtm) cc_final: 0.7703 (mtp) REVERT: R 400 ARG cc_start: 0.8180 (ttp-170) cc_final: 0.7753 (mtm110) REVERT: B 215 GLU cc_start: 0.8859 (mp0) cc_final: 0.8397 (mp0) REVERT: G 17 GLU cc_start: 0.8911 (tp30) cc_final: 0.8021 (tp30) REVERT: G 20 LYS cc_start: 0.8723 (mttm) cc_final: 0.8496 (tmtt) REVERT: G 21 MET cc_start: 0.8982 (mmm) cc_final: 0.8447 (mmm) REVERT: G 42 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: G 57 SER cc_start: 0.9274 (p) cc_final: 0.9028 (p) REVERT: G 58 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8718 (mp0) REVERT: H 87 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7354 (mtt-85) REVERT: A 24 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7673 (ttp-170) REVERT: A 35 LYS cc_start: 0.9020 (mttp) cc_final: 0.8749 (mtpp) REVERT: A 197 LYS cc_start: 0.9147 (mttt) cc_final: 0.8767 (mttp) REVERT: A 208 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8329 (ttm-80) REVERT: A 234 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8699 (tt) outliers start: 21 outliers final: 10 residues processed: 142 average time/residue: 1.7463 time to fit residues: 259.7121 Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 87 ARG Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 15 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.0010 chunk 81 optimal weight: 0.8980 overall best weight: 0.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.061445 restraints weight = 15661.823| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.33 r_work: 0.2657 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8911 Z= 0.126 Angle : 0.567 7.745 12110 Z= 0.303 Chirality : 0.042 0.142 1389 Planarity : 0.004 0.043 1520 Dihedral : 4.966 32.916 1246 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.72 % Allowed : 12.70 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.25), residues: 1113 helix: 2.14 (0.26), residues: 399 sheet: 0.51 (0.29), residues: 281 loop : -0.22 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.023 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 453) hydrogen bonds : angle 4.35591 ( 1281) SS BOND : bond 0.01297 ( 4) SS BOND : angle 1.89231 ( 8) covalent geometry : bond 0.00265 ( 8907) covalent geometry : angle 0.56490 (12102) *********************** 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 150 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8342 (t-100) cc_final: 0.7881 (t-100) REVERT: R 148 MET cc_start: 0.7976 (mmt) cc_final: 0.7675 (mmt) REVERT: R 152 MET cc_start: 0.8177 (mtm) cc_final: 0.7892 (mtp) REVERT: R 177 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8183 (pptt) REVERT: R 400 ARG cc_start: 0.8226 (ttp-170) cc_final: 0.7827 (mtm110) REVERT: B 15 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8892 (mtmt) REVERT: B 215 GLU cc_start: 0.8845 (mp0) cc_final: 0.8401 (mp0) REVERT: G 17 GLU cc_start: 0.8920 (tp30) cc_final: 0.8041 (tp30) REVERT: G 20 LYS cc_start: 0.8747 (mttm) cc_final: 0.8544 (tmtt) REVERT: G 21 MET cc_start: 0.9006 (mmm) cc_final: 0.8460 (mmm) REVERT: G 42 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8262 (mp0) REVERT: G 57 SER cc_start: 0.9292 (p) cc_final: 0.9061 (p) REVERT: G 58 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8783 (mp0) REVERT: A 24 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.7783 (ttp-170) REVERT: A 197 LYS cc_start: 0.9194 (mttt) cc_final: 0.8852 (mttp) REVERT: A 234 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8718 (tt) outliers start: 16 outliers final: 9 residues processed: 139 average time/residue: 1.9680 time to fit residues: 288.0175 Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 64 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 0.0470 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 overall best weight: 3.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.095361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.061525 restraints weight = 15648.686| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.35 r_work: 0.2658 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8911 Z= 0.133 Angle : 0.571 7.745 12110 Z= 0.305 Chirality : 0.042 0.142 1389 Planarity : 0.004 0.043 1520 Dihedral : 4.966 32.916 1246 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.29 % Allowed : 13.35 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.25), residues: 1113 helix: 2.14 (0.26), residues: 399 sheet: 0.51 (0.29), residues: 281 loop : -0.22 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.023 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 453) hydrogen bonds : angle 4.35591 ( 1281) SS BOND : bond 0.04264 ( 4) SS BOND : angle 3.16001 ( 8) covalent geometry : bond 0.00265 ( 8907) covalent geometry : angle 0.56507 (12102) *********************** 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 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8344 (t-100) cc_final: 0.7890 (t-100) REVERT: R 148 MET cc_start: 0.7989 (mmt) cc_final: 0.7683 (mmt) REVERT: R 152 MET cc_start: 0.8194 (mtm) cc_final: 0.7908 (mtp) REVERT: R 177 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8183 (pptt) REVERT: R 400 ARG cc_start: 0.8231 (ttp-170) cc_final: 0.7832 (mtm110) REVERT: B 15 LYS cc_start: 0.9197 (mtpp) cc_final: 0.8900 (mtmt) REVERT: B 215 GLU cc_start: 0.8860 (mp0) cc_final: 0.8414 (mp0) REVERT: G 17 GLU cc_start: 0.8919 (tp30) cc_final: 0.8041 (tp30) REVERT: G 21 MET cc_start: 0.8998 (mmm) cc_final: 0.8458 (mmm) REVERT: G 42 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: G 57 SER cc_start: 0.9291 (p) cc_final: 0.9058 (p) REVERT: G 58 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8781 (mp0) REVERT: A 24 ARG cc_start: 0.8300 (ttp-110) cc_final: 0.7796 (ttp-170) REVERT: A 197 LYS cc_start: 0.9192 (mttt) cc_final: 0.8858 (mttp) REVERT: A 234 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8720 (tt) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 2.1872 time to fit residues: 313.7594 Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 57 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.061541 restraints weight = 15799.774| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.35 r_work: 0.2658 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8911 Z= 0.133 Angle : 0.571 7.745 12110 Z= 0.305 Chirality : 0.042 0.142 1389 Planarity : 0.004 0.043 1520 Dihedral : 4.966 32.916 1246 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.29 % Allowed : 13.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.25), residues: 1113 helix: 2.14 (0.26), residues: 399 sheet: 0.51 (0.29), residues: 281 loop : -0.22 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.023 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 453) hydrogen bonds : angle 4.35591 ( 1281) SS BOND : bond 0.04264 ( 4) SS BOND : angle 3.16001 ( 8) covalent geometry : bond 0.00265 ( 8907) covalent geometry : angle 0.56507 (12102) *********************** 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 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.056 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8343 (t-100) cc_final: 0.7883 (t-100) REVERT: R 148 MET cc_start: 0.7980 (mmt) cc_final: 0.7675 (mmt) REVERT: R 152 MET cc_start: 0.8181 (mtm) cc_final: 0.7893 (mtp) REVERT: R 177 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8184 (pptt) REVERT: R 400 ARG cc_start: 0.8230 (ttp-170) cc_final: 0.7830 (mtm110) REVERT: B 15 LYS cc_start: 0.9188 (mtpp) cc_final: 0.8890 (mtmt) REVERT: B 215 GLU cc_start: 0.8859 (mp0) cc_final: 0.8410 (mp0) REVERT: G 17 GLU cc_start: 0.8860 (tp30) cc_final: 0.8021 (tp30) REVERT: G 21 MET cc_start: 0.8972 (mmm) cc_final: 0.8438 (mmm) REVERT: G 42 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: G 57 SER cc_start: 0.9292 (p) cc_final: 0.9059 (p) REVERT: G 58 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8778 (mp0) REVERT: A 24 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7782 (ttp-170) REVERT: A 197 LYS cc_start: 0.9189 (mttt) cc_final: 0.8851 (mttp) REVERT: A 234 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8718 (tt) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 1.7095 time to fit residues: 243.8318 Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 0.6980 chunk 99 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 24 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.095404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.061517 restraints weight = 15939.324| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.36 r_work: 0.2658 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 8911 Z= 0.133 Angle : 0.571 7.745 12110 Z= 0.305 Chirality : 0.042 0.142 1389 Planarity : 0.004 0.043 1520 Dihedral : 4.966 32.916 1246 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.29 % Allowed : 13.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.20 (0.25), residues: 1113 helix: 2.14 (0.26), residues: 399 sheet: 0.51 (0.29), residues: 281 loop : -0.22 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 213 PHE 0.023 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.007 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 453) hydrogen bonds : angle 4.35591 ( 1281) SS BOND : bond 0.04264 ( 4) SS BOND : angle 3.16001 ( 8) covalent geometry : bond 0.00265 ( 8907) covalent geometry : angle 0.56507 (12102) *********************** 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 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8343 (t-100) cc_final: 0.7886 (t-100) REVERT: R 148 MET cc_start: 0.7979 (mmt) cc_final: 0.7674 (mmt) REVERT: R 152 MET cc_start: 0.8184 (mtm) cc_final: 0.7896 (mtp) REVERT: R 177 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8183 (pptt) REVERT: R 400 ARG cc_start: 0.8229 (ttp-170) cc_final: 0.7829 (mtm110) REVERT: B 15 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8894 (mtmt) REVERT: B 215 GLU cc_start: 0.8862 (mp0) cc_final: 0.8412 (mp0) REVERT: G 17 GLU cc_start: 0.8863 (tp30) cc_final: 0.8025 (tp30) REVERT: G 21 MET cc_start: 0.8974 (mmm) cc_final: 0.8440 (mmm) REVERT: G 42 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8249 (mp0) REVERT: G 57 SER cc_start: 0.9289 (p) cc_final: 0.9054 (p) REVERT: G 58 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8775 (mp0) REVERT: A 24 ARG cc_start: 0.8287 (ttp-110) cc_final: 0.7781 (ttp-170) REVERT: A 197 LYS cc_start: 0.9189 (mttt) cc_final: 0.8851 (mttp) REVERT: A 234 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8720 (tt) outliers start: 12 outliers final: 9 residues processed: 136 average time/residue: 1.6447 time to fit residues: 234.5145 Evaluate side-chains 144 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 132 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.062612 restraints weight = 15818.860| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.35 r_work: 0.2683 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8911 Z= 0.114 Angle : 0.561 10.693 12110 Z= 0.297 Chirality : 0.041 0.133 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.629 30.550 1246 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.51 % Allowed : 13.13 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.34 (0.25), residues: 1113 helix: 2.25 (0.26), residues: 401 sheet: 0.66 (0.30), residues: 264 loop : -0.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.035 0.001 PHE R 84 TYR 0.017 0.001 TYR H 190 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 453) hydrogen bonds : angle 4.18566 ( 1281) SS BOND : bond 0.00255 ( 4) SS BOND : angle 1.54233 ( 8) covalent geometry : bond 0.00242 ( 8907) covalent geometry : angle 0.55987 (12102) *********************** 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 154 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8325 (t-100) cc_final: 0.7853 (t-100) REVERT: R 148 MET cc_start: 0.7940 (mmt) cc_final: 0.7728 (mmt) REVERT: R 152 MET cc_start: 0.8187 (mtm) cc_final: 0.7890 (mtp) REVERT: R 177 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8181 (pptt) REVERT: R 400 ARG cc_start: 0.8218 (ttp-170) cc_final: 0.7828 (mtm110) REVERT: B 15 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8922 (mtmt) REVERT: B 215 GLU cc_start: 0.8884 (mp0) cc_final: 0.8460 (mp0) REVERT: G 17 GLU cc_start: 0.8768 (tp30) cc_final: 0.8210 (tp30) REVERT: G 20 LYS cc_start: 0.8826 (tmtt) cc_final: 0.8560 (ttmt) REVERT: G 21 MET cc_start: 0.8970 (mmm) cc_final: 0.8498 (mmm) REVERT: G 42 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8231 (mp0) REVERT: G 57 SER cc_start: 0.9294 (p) cc_final: 0.9063 (p) REVERT: G 58 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8851 (mp0) REVERT: H 73 ASP cc_start: 0.8473 (t0) cc_final: 0.8246 (t0) REVERT: A 24 ARG cc_start: 0.8289 (ttp-110) cc_final: 0.7796 (ttp-170) REVERT: A 52 GLN cc_start: 0.7685 (mt0) cc_final: 0.7469 (mt0) REVERT: A 197 LYS cc_start: 0.9194 (mttt) cc_final: 0.8859 (mttp) REVERT: A 234 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8747 (tt) outliers start: 14 outliers final: 8 residues processed: 145 average time/residue: 1.6426 time to fit residues: 249.8943 Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 0.0970 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.062678 restraints weight = 15922.752| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.35 r_work: 0.2683 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8911 Z= 0.114 Angle : 0.562 10.693 12110 Z= 0.297 Chirality : 0.041 0.133 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.630 30.550 1246 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 13.89 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.34 (0.25), residues: 1113 helix: 2.25 (0.26), residues: 401 sheet: 0.66 (0.30), residues: 264 loop : -0.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.035 0.001 PHE R 84 TYR 0.017 0.001 TYR H 190 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 453) hydrogen bonds : angle 4.18566 ( 1281) SS BOND : bond 0.00976 ( 4) SS BOND : angle 1.75725 ( 8) covalent geometry : bond 0.00242 ( 8907) covalent geometry : angle 0.55990 (12102) ********************** REFINEMENT MACRO_CYCLE 10 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 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8326 (t-100) cc_final: 0.7847 (t-100) REVERT: R 148 MET cc_start: 0.7912 (mmt) cc_final: 0.7702 (mmt) REVERT: R 152 MET cc_start: 0.8160 (mtm) cc_final: 0.7864 (mtp) REVERT: R 177 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8187 (pptt) REVERT: R 400 ARG cc_start: 0.8203 (ttp-170) cc_final: 0.7812 (mtm110) REVERT: B 15 LYS cc_start: 0.9203 (mtpp) cc_final: 0.8920 (mtmt) REVERT: B 215 GLU cc_start: 0.8874 (mp0) cc_final: 0.8432 (mp0) REVERT: G 17 GLU cc_start: 0.8766 (tp30) cc_final: 0.8208 (tp30) REVERT: G 21 MET cc_start: 0.8969 (mmm) cc_final: 0.8487 (mmm) REVERT: G 42 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8222 (mp0) REVERT: G 57 SER cc_start: 0.9281 (p) cc_final: 0.9042 (p) REVERT: G 58 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8837 (mp0) REVERT: H 73 ASP cc_start: 0.8460 (t0) cc_final: 0.8180 (t0) REVERT: A 24 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7769 (ttp-170) REVERT: A 52 GLN cc_start: 0.7668 (mt0) cc_final: 0.7450 (mt0) REVERT: A 197 LYS cc_start: 0.9189 (mttt) cc_final: 0.8845 (mttp) REVERT: A 234 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (tt) outliers start: 11 outliers final: 8 residues processed: 139 average time/residue: 1.6766 time to fit residues: 244.2375 Evaluate side-chains 147 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 LYS Chi-restraints excluded: chain R residue 159 LEU Chi-restraints excluded: chain R residue 177 LYS Chi-restraints excluded: chain R residue 429 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 144 THR Chi-restraints excluded: chain H residue 186 GLN Chi-restraints excluded: chain H residue 192 MET Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 234 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.062716 restraints weight = 15868.270| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.34 r_work: 0.2683 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 8911 Z= 0.114 Angle : 0.562 10.693 12110 Z= 0.297 Chirality : 0.041 0.133 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.629 30.550 1246 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 13.89 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: 1.34 (0.25), residues: 1113 helix: 2.25 (0.26), residues: 401 sheet: 0.66 (0.30), residues: 264 loop : -0.18 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.035 0.001 PHE R 84 TYR 0.017 0.001 TYR H 190 ARG 0.008 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04077 ( 453) hydrogen bonds : angle 4.18566 ( 1281) SS BOND : bond 0.00976 ( 4) SS BOND : angle 1.75725 ( 8) covalent geometry : bond 0.00242 ( 8907) covalent geometry : angle 0.55990 (12102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9923.59 seconds wall clock time: 173 minutes 2.93 seconds (10382.93 seconds total)