Starting phenix.real_space_refine on Thu Feb 13 06:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7trq_26101/02_2025/7trq_26101.cif Found real_map, /net/cci-nas-00/data/ceres_data/7trq_26101/02_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_26101/02_2025/7trq_26101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7trq_26101/02_2025/7trq_26101.map" model { file = "/net/cci-nas-00/data/ceres_data/7trq_26101/02_2025/7trq_26101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7trq_26101/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 5.54, per 1000 atoms: 0.64 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: 2.27 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: 0.98 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: 2.68 Time building geometry restraints manager: 2.51 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: 1.820 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 22.970 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.850 ------------------------------------------------------------------------------- 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 8907 Z= 0.426 Angle : 0.831 10.254 12102 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 *********************** 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 : 1.038 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: 1.8616 time to fit residues: 342.1846 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 : 1.069 ------------------------------------------------------------------------------- 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: 4.9990 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 = 0.3472 r_free = 0.3472 target = 0.096135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.061995 restraints weight = 15295.161| |-----------------------------------------------------------------------------| r_work (start): 0.2795 rms_B_bonded: 2.36 r_work: 0.2650 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8907 Z= 0.189 Angle : 0.528 6.077 12102 Z= 0.288 Chirality : 0.042 0.135 1389 Planarity : 0.004 0.044 1520 Dihedral : 5.096 34.172 1246 Min Nonbonded Distance : 2.560 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: 0.72 (0.25), residues: 1113 helix: 1.63 (0.26), residues: 397 sheet: 0.50 (0.30), residues: 271 loop : -0.54 (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 *********************** 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 : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8269 (t-100) cc_final: 0.7834 (t-100) REVERT: R 121 MET cc_start: 0.8820 (mmm) cc_final: 0.8602 (mmp) REVERT: R 148 MET cc_start: 0.7927 (mmt) cc_final: 0.7683 (mmt) REVERT: R 152 MET cc_start: 0.8021 (mtm) cc_final: 0.7722 (mtp) REVERT: R 400 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7758 (mtm110) REVERT: B 15 LYS cc_start: 0.9164 (mtpp) cc_final: 0.8821 (mtmt) REVERT: B 215 GLU cc_start: 0.8883 (mp0) cc_final: 0.8518 (mp0) REVERT: G 17 GLU cc_start: 0.8926 (tp30) cc_final: 0.8197 (tp30) REVERT: G 20 LYS cc_start: 0.8692 (mttm) cc_final: 0.8453 (tmtt) REVERT: G 21 MET cc_start: 0.8944 (mmm) cc_final: 0.8452 (mmm) REVERT: G 42 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: H 73 ASP cc_start: 0.8613 (t0) cc_final: 0.8230 (t0) REVERT: A 24 ARG cc_start: 0.8128 (ttp-110) cc_final: 0.7653 (ttp-170) REVERT: A 35 LYS cc_start: 0.8947 (mttp) cc_final: 0.8723 (mtpp) REVERT: A 197 LYS cc_start: 0.9127 (mttt) cc_final: 0.8815 (mttp) REVERT: A 247 MET cc_start: 0.9152 (mtp) cc_final: 0.8855 (mtm) outliers start: 12 outliers final: 3 residues processed: 151 average time/residue: 1.7590 time to fit residues: 278.2350 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 : 0.995 ------------------------------------------------------------------------------- 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: 4.9990 chunk 93 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.096193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.062028 restraints weight = 15574.514| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.37 r_work: 0.2650 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8907 Z= 0.172 Angle : 0.505 7.795 12102 Z= 0.273 Chirality : 0.041 0.132 1389 Planarity : 0.004 0.040 1520 Dihedral : 4.675 31.112 1246 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.61 % Allowed : 11.63 % Favored : 86.76 % 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: 1.11 (0.25), residues: 1113 helix: 2.13 (0.26), residues: 395 sheet: 0.54 (0.30), residues: 274 loop : -0.37 (0.29), residues: 444 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 0.011 0.001 PHE B 199 TYR 0.015 0.001 TYR H 190 ARG 0.009 0.000 ARG B 197 *********************** 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 160 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8280 (t-100) cc_final: 0.7838 (t-100) REVERT: R 148 MET cc_start: 0.7877 (mmt) cc_final: 0.7605 (mmt) REVERT: R 152 MET cc_start: 0.8040 (mtm) cc_final: 0.7772 (mtp) REVERT: R 400 ARG cc_start: 0.8105 (ttp-170) cc_final: 0.7767 (mtm110) REVERT: B 15 LYS cc_start: 0.9166 (mtpp) cc_final: 0.8832 (mtmt) REVERT: B 19 ARG cc_start: 0.8447 (ttp80) cc_final: 0.8239 (ttp80) REVERT: B 215 GLU cc_start: 0.8886 (mp0) cc_final: 0.8546 (mp0) REVERT: G 17 GLU cc_start: 0.8915 (tp30) cc_final: 0.8045 (tp30) REVERT: G 20 LYS cc_start: 0.8697 (mttm) cc_final: 0.8495 (tmtt) REVERT: G 21 MET cc_start: 0.8970 (mmm) cc_final: 0.8437 (mmm) REVERT: G 42 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: G 58 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8791 (mp0) REVERT: H 73 ASP cc_start: 0.8607 (t0) cc_final: 0.8251 (t0) REVERT: A 24 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7645 (ttp-170) REVERT: A 35 LYS cc_start: 0.8947 (mttp) cc_final: 0.8722 (mtpp) REVERT: A 197 LYS cc_start: 0.9140 (mttt) cc_final: 0.8770 (mttp) outliers start: 15 outliers final: 6 residues processed: 151 average time/residue: 1.7344 time to fit residues: 273.8534 Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 48 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 80 optimal weight: 0.0050 chunk 91 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 33 optimal weight: 6.9990 chunk 15 optimal weight: 0.0020 chunk 86 optimal weight: 7.9990 chunk 25 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.096675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.062942 restraints weight = 15779.801| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.36 r_work: 0.2698 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8907 Z= 0.204 Angle : 0.510 8.313 12102 Z= 0.274 Chirality : 0.042 0.132 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.517 29.737 1246 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.05 % Allowed : 12.16 % Favored : 85.79 % 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: 1.19 (0.25), residues: 1113 helix: 2.19 (0.26), residues: 400 sheet: 0.53 (0.30), residues: 271 loop : -0.29 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** 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 157 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8265 (t-100) cc_final: 0.7834 (t-100) REVERT: R 148 MET cc_start: 0.7942 (mmt) cc_final: 0.7653 (mmt) REVERT: R 152 MET cc_start: 0.8180 (mtm) cc_final: 0.7877 (mtp) REVERT: R 400 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7806 (mtm110) REVERT: B 15 LYS cc_start: 0.9221 (mtpp) cc_final: 0.8879 (mtmt) REVERT: B 215 GLU cc_start: 0.8895 (mp0) cc_final: 0.8524 (mp0) REVERT: G 17 GLU cc_start: 0.8916 (tp30) cc_final: 0.8063 (tp30) REVERT: G 21 MET cc_start: 0.9002 (mmm) cc_final: 0.8453 (mmm) REVERT: G 42 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: G 58 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8862 (mp0) REVERT: A 24 ARG cc_start: 0.8268 (ttp-110) cc_final: 0.7782 (ttp-170) REVERT: A 197 LYS cc_start: 0.9201 (mttt) cc_final: 0.8871 (mttp) outliers start: 19 outliers final: 7 residues processed: 145 average time/residue: 1.7478 time to fit residues: 265.6316 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.975 ------------------------------------------------------------------------------- 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 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 A residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 56 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.096771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.063112 restraints weight = 15691.824| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.34 r_work: 0.2697 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8907 Z= 0.204 Angle : 0.511 8.313 12102 Z= 0.274 Chirality : 0.042 0.132 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.517 29.737 1246 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.86 % Allowed : 13.78 % 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: 1.19 (0.25), residues: 1113 helix: 2.19 (0.26), residues: 400 sheet: 0.53 (0.30), residues: 271 loop : -0.29 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** 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 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8259 (t-100) cc_final: 0.7828 (t-100) REVERT: R 148 MET cc_start: 0.7925 (mmt) cc_final: 0.7638 (mmt) REVERT: R 152 MET cc_start: 0.8160 (mtm) cc_final: 0.7858 (mtp) REVERT: R 400 ARG cc_start: 0.8165 (ttp-170) cc_final: 0.7801 (mtm110) REVERT: B 15 LYS cc_start: 0.9207 (mtpp) cc_final: 0.8870 (mtmt) REVERT: B 215 GLU cc_start: 0.8883 (mp0) cc_final: 0.8489 (mp0) REVERT: G 17 GLU cc_start: 0.8861 (tp30) cc_final: 0.8045 (tp30) REVERT: G 21 MET cc_start: 0.8951 (mmm) cc_final: 0.8413 (mmm) REVERT: G 42 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8110 (mp0) REVERT: G 58 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8848 (mp0) REVERT: A 24 ARG cc_start: 0.8249 (ttp-110) cc_final: 0.7760 (ttp-170) REVERT: A 197 LYS cc_start: 0.9188 (mttt) cc_final: 0.8854 (mttp) outliers start: 8 outliers final: 7 residues processed: 137 average time/residue: 1.7762 time to fit residues: 254.9580 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.024 ------------------------------------------------------------------------------- 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 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 A residue 48 THR 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: 4.9990 chunk 103 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.096770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063167 restraints weight = 15662.115| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.33 r_work: 0.2698 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2584 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8907 Z= 0.204 Angle : 0.511 8.313 12102 Z= 0.274 Chirality : 0.042 0.132 1389 Planarity : 0.003 0.042 1520 Dihedral : 4.517 29.737 1246 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.86 % Allowed : 13.78 % 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: 1.19 (0.25), residues: 1113 helix: 2.19 (0.26), residues: 400 sheet: 0.53 (0.30), residues: 271 loop : -0.29 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS H 35 PHE 0.022 0.001 PHE R 84 TYR 0.014 0.001 TYR H 190 ARG 0.006 0.000 ARG B 214 *********************** 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 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8261 (t-100) cc_final: 0.7826 (t-100) REVERT: R 148 MET cc_start: 0.7926 (mmt) cc_final: 0.7641 (mmt) REVERT: R 152 MET cc_start: 0.8156 (mtm) cc_final: 0.7854 (mtp) REVERT: R 400 ARG cc_start: 0.8169 (ttp-170) cc_final: 0.7807 (mtm110) REVERT: B 15 LYS cc_start: 0.9199 (mtpp) cc_final: 0.8858 (mtmt) REVERT: B 215 GLU cc_start: 0.8883 (mp0) cc_final: 0.8494 (mp0) REVERT: G 17 GLU cc_start: 0.8860 (tp30) cc_final: 0.8040 (tp30) REVERT: G 21 MET cc_start: 0.8958 (mmm) cc_final: 0.8416 (mmm) REVERT: G 42 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: G 58 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8861 (mp0) REVERT: A 24 ARG cc_start: 0.8256 (ttp-110) cc_final: 0.7768 (ttp-170) REVERT: A 197 LYS cc_start: 0.9192 (mttt) cc_final: 0.8862 (mttp) outliers start: 8 outliers final: 7 residues processed: 137 average time/residue: 1.7276 time to fit residues: 247.8792 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 135 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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 A residue 48 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 40 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 79 optimal weight: 7.9990 chunk 38 optimal weight: 0.2980 chunk 99 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 2.8386 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.094460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.060130 restraints weight = 15526.738| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 2.35 r_work: 0.2603 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8907 Z= 0.323 Angle : 0.576 10.325 12102 Z= 0.306 Chirality : 0.043 0.133 1389 Planarity : 0.004 0.044 1520 Dihedral : 4.614 30.215 1246 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.72 % Allowed : 13.02 % 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: 1.25 (0.25), residues: 1113 helix: 2.23 (0.26), residues: 401 sheet: 0.54 (0.30), residues: 276 loop : -0.24 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS H 35 PHE 0.030 0.002 PHE R 84 TYR 0.012 0.001 TYR R 89 ARG 0.006 0.001 ARG B 197 *********************** 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 153 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8320 (t-100) cc_final: 0.7769 (t-100) REVERT: R 121 MET cc_start: 0.8823 (mmm) cc_final: 0.8621 (mmp) REVERT: R 148 MET cc_start: 0.7813 (mmt) cc_final: 0.7528 (mmt) REVERT: R 152 MET cc_start: 0.8012 (mtm) cc_final: 0.7698 (mtp) REVERT: R 400 ARG cc_start: 0.8124 (ttp-170) cc_final: 0.7736 (mtm110) REVERT: B 215 GLU cc_start: 0.8874 (mp0) cc_final: 0.8411 (mp0) REVERT: G 17 GLU cc_start: 0.8784 (tp30) cc_final: 0.8085 (tp30) REVERT: G 20 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8414 (tptt) REVERT: G 21 MET cc_start: 0.8957 (mmm) cc_final: 0.8499 (mmm) REVERT: G 24 ASN cc_start: 0.8760 (m110) cc_final: 0.8074 (m-40) REVERT: G 42 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: G 58 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8774 (mp0) REVERT: H 73 ASP cc_start: 0.8562 (t0) cc_final: 0.8248 (t0) REVERT: A 24 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7662 (ttp-170) REVERT: A 197 LYS cc_start: 0.9132 (mttt) cc_final: 0.8753 (mttp) outliers start: 16 outliers final: 9 residues processed: 143 average time/residue: 1.7574 time to fit residues: 263.0637 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 32 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 57 optimal weight: 0.3980 chunk 27 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.060057 restraints weight = 15704.709| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.41 r_work: 0.2603 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2476 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8907 Z= 0.323 Angle : 0.576 10.325 12102 Z= 0.306 Chirality : 0.043 0.133 1389 Planarity : 0.004 0.044 1520 Dihedral : 4.614 30.215 1246 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 14.42 % Favored : 84.50 % 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: 1.25 (0.25), residues: 1113 helix: 2.23 (0.26), residues: 401 sheet: 0.54 (0.30), residues: 276 loop : -0.24 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS H 35 PHE 0.030 0.002 PHE R 84 TYR 0.012 0.001 TYR R 89 ARG 0.006 0.001 ARG B 197 *********************** 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 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8321 (t-100) cc_final: 0.7768 (t-100) REVERT: R 121 MET cc_start: 0.8802 (mmm) cc_final: 0.8600 (mmp) REVERT: R 148 MET cc_start: 0.7793 (mmt) cc_final: 0.7509 (mmt) REVERT: R 152 MET cc_start: 0.7981 (mtm) cc_final: 0.7669 (mtp) REVERT: R 400 ARG cc_start: 0.8115 (ttp-170) cc_final: 0.7726 (mtm110) REVERT: B 215 GLU cc_start: 0.8889 (mp0) cc_final: 0.8412 (mp0) REVERT: G 17 GLU cc_start: 0.8784 (tp30) cc_final: 0.8084 (tp30) REVERT: G 20 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8412 (tptt) REVERT: G 21 MET cc_start: 0.8953 (mmm) cc_final: 0.8494 (mmm) REVERT: G 24 ASN cc_start: 0.8756 (m110) cc_final: 0.8066 (m-40) REVERT: G 42 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: G 58 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8756 (mp0) REVERT: H 73 ASP cc_start: 0.8542 (t0) cc_final: 0.8193 (t0) REVERT: A 24 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7637 (ttp-170) REVERT: A 197 LYS cc_start: 0.9125 (mttt) cc_final: 0.8737 (mttp) outliers start: 10 outliers final: 9 residues processed: 136 average time/residue: 1.7799 time to fit residues: 253.4760 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.060086 restraints weight = 15592.352| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.40 r_work: 0.2603 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2477 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8907 Z= 0.323 Angle : 0.576 10.325 12102 Z= 0.306 Chirality : 0.043 0.133 1389 Planarity : 0.004 0.044 1520 Dihedral : 4.614 30.215 1246 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.08 % Allowed : 14.42 % Favored : 84.50 % 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: 1.25 (0.25), residues: 1113 helix: 2.23 (0.26), residues: 401 sheet: 0.54 (0.30), residues: 276 loop : -0.24 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.005 0.001 HIS H 35 PHE 0.030 0.002 PHE R 84 TYR 0.012 0.001 TYR R 89 ARG 0.006 0.001 ARG B 197 *********************** 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 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8322 (t-100) cc_final: 0.7766 (t-100) REVERT: R 121 MET cc_start: 0.8794 (mmm) cc_final: 0.8591 (mmp) REVERT: R 148 MET cc_start: 0.7789 (mmt) cc_final: 0.7506 (mmt) REVERT: R 152 MET cc_start: 0.7978 (mtm) cc_final: 0.7664 (mtp) REVERT: R 400 ARG cc_start: 0.8111 (ttp-170) cc_final: 0.7723 (mtm110) REVERT: B 215 GLU cc_start: 0.8888 (mp0) cc_final: 0.8413 (mp0) REVERT: G 17 GLU cc_start: 0.8780 (tp30) cc_final: 0.8080 (tp30) REVERT: G 20 LYS cc_start: 0.8769 (tmtt) cc_final: 0.8409 (tptt) REVERT: G 21 MET cc_start: 0.8950 (mmm) cc_final: 0.8490 (mmm) REVERT: G 24 ASN cc_start: 0.8756 (m110) cc_final: 0.8067 (m-40) REVERT: G 42 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8148 (mp0) REVERT: G 58 GLU cc_start: 0.9071 (mt-10) cc_final: 0.8757 (mp0) REVERT: H 73 ASP cc_start: 0.8543 (t0) cc_final: 0.8197 (t0) REVERT: A 24 ARG cc_start: 0.8133 (ttp-110) cc_final: 0.7635 (ttp-170) REVERT: A 197 LYS cc_start: 0.9122 (mttt) cc_final: 0.8734 (mttp) outliers start: 10 outliers final: 9 residues processed: 136 average time/residue: 1.7597 time to fit residues: 250.6361 Evaluate side-chains 143 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 104 optimal weight: 10.0000 chunk 107 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 77 optimal weight: 0.0770 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.096581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.063285 restraints weight = 15928.069| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.33 r_work: 0.2695 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8907 Z= 0.167 Angle : 0.567 9.778 12102 Z= 0.299 Chirality : 0.042 0.133 1389 Planarity : 0.003 0.041 1520 Dihedral : 4.540 29.417 1246 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.18 % Allowed : 14.42 % Favored : 84.39 % 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: 1.31 (0.25), residues: 1113 helix: 2.27 (0.26), residues: 401 sheet: 0.56 (0.30), residues: 271 loop : -0.19 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.037 0.001 PHE R 84 TYR 0.016 0.001 TYR H 190 ARG 0.008 0.000 ARG B 19 ********************** 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 149 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 98 TRP cc_start: 0.8302 (t-100) cc_final: 0.7784 (t-100) REVERT: R 148 MET cc_start: 0.7949 (mmt) cc_final: 0.7666 (mmt) REVERT: R 152 MET cc_start: 0.8182 (mtm) cc_final: 0.7914 (mtp) REVERT: R 400 ARG cc_start: 0.8196 (ttp-170) cc_final: 0.7827 (mtm110) REVERT: B 15 LYS cc_start: 0.9207 (mtpp) cc_final: 0.8950 (mtmt) REVERT: B 215 GLU cc_start: 0.8876 (mp0) cc_final: 0.8467 (mp0) REVERT: G 17 GLU cc_start: 0.8824 (tp30) cc_final: 0.8097 (tp30) REVERT: G 20 LYS cc_start: 0.8819 (tmtt) cc_final: 0.8437 (tptt) REVERT: G 21 MET cc_start: 0.9005 (mmm) cc_final: 0.8556 (mmm) REVERT: G 24 ASN cc_start: 0.8667 (m110) cc_final: 0.7826 (m-40) REVERT: G 42 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8183 (mp0) REVERT: G 58 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8837 (mp0) REVERT: H 73 ASP cc_start: 0.8577 (t0) cc_final: 0.8293 (t0) REVERT: A 24 ARG cc_start: 0.8290 (ttp-110) cc_final: 0.7792 (ttp-170) REVERT: A 197 LYS cc_start: 0.9176 (mttt) cc_final: 0.8846 (mttp) outliers start: 11 outliers final: 7 residues processed: 140 average time/residue: 1.7263 time to fit residues: 253.4621 Evaluate side-chains 145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 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 192 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 0.4980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.063173 restraints weight = 15826.735| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.33 r_work: 0.2694 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8907 Z= 0.167 Angle : 0.567 9.778 12102 Z= 0.299 Chirality : 0.042 0.133 1389 Planarity : 0.003 0.041 1520 Dihedral : 4.540 29.417 1246 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.86 % Allowed : 14.85 % Favored : 84.28 % 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: 1.31 (0.25), residues: 1113 helix: 2.27 (0.26), residues: 401 sheet: 0.56 (0.30), residues: 271 loop : -0.19 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.037 0.001 PHE R 84 TYR 0.016 0.001 TYR H 190 ARG 0.008 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8700.35 seconds wall clock time: 153 minutes 45.61 seconds (9225.61 seconds total)