Starting phenix.real_space_refine on Mon Jun 9 23:07:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bfq_44503/06_2025/9bfq_44503.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bfq_44503/06_2025/9bfq_44503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bfq_44503/06_2025/9bfq_44503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bfq_44503/06_2025/9bfq_44503.map" model { file = "/net/cci-nas-00/data/ceres_data/9bfq_44503/06_2025/9bfq_44503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bfq_44503/06_2025/9bfq_44503.cif" } resolution = 3.09 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= 0.003 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 6985 2.51 5 N 1884 2.21 5 O 2036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10958 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7992 Classifications: {'peptide': 1000} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 927} Chain breaks: 11 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2896 Classifications: {'peptide': 365} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 355} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 3, 'HIS:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 7.59, per 1000 atoms: 0.69 Number of scatterers: 10958 At special positions: 0 Unit cell: (85.49, 112.88, 162.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2036 8.00 N 1884 7.00 C 6985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 257 " distance=2.03 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 253 " distance=2.02 Simple disulfide: pdb=" SG CYS A 239 " - pdb=" SG CYS A 248 " distance=2.03 Simple disulfide: pdb=" SG CYS A 270 " - pdb=" SG CYS A 290 " distance=2.04 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 286 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 981 " - pdb=" SG CYS A 991 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 501 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 403 " 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 Links applied NAG-ASN " NAG A2601 " - " ASN A 966 " " NAG A2602 " - " ASN A 505 " " NAG B 601 " - " ASN B 183 " " NAG B 602 " - " ASN B 474 " " NAG B 603 " - " ASN B 485 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2578 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 23 sheets defined 16.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 208 through 227 Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.540A pdb=" N ARG A 252 " --> pdb=" O CYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 266 removed outlier: 3.562A pdb=" N LEU A 264 " --> pdb=" O TRP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 274 Processing helix chain 'A' and resid 283 through 305 removed outlier: 3.886A pdb=" N ILE A 305 " --> pdb=" O GLN A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.520A pdb=" N VAL A 309 " --> pdb=" O ILE A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.629A pdb=" N GLU A1069 " --> pdb=" O THR A1066 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA A1070 " --> pdb=" O PRO A1067 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1066 through 1070' Processing helix chain 'A' and resid 1172 through 1176 removed outlier: 3.979A pdb=" N SER A1176 " --> pdb=" O ASP A1173 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 151 through 166 removed outlier: 4.155A pdb=" N ALA B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 201 removed outlier: 3.684A pdb=" N LEU B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 218 through 226 Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.694A pdb=" N ALA B 237 " --> pdb=" O GLY B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 249 Processing helix chain 'B' and resid 265 through 278 removed outlier: 3.858A pdb=" N TYR B 269 " --> pdb=" O THR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 326 removed outlier: 3.504A pdb=" N LEU B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 388 removed outlier: 4.463A pdb=" N SER B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.029A pdb=" N TRP B 413 " --> pdb=" O ILE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 431 Processing helix chain 'B' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317 removed outlier: 4.050A pdb=" N LEU A 329 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 379 through 381 Processing sheet with id=AA3, first strand: chain 'A' and resid 379 through 381 Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 448 removed outlier: 6.667A pdb=" N HIS A 457 " --> pdb=" O GLU A 444 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU A 446 " --> pdb=" O ALA A 455 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ALA A 455 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 489 removed outlier: 3.504A pdb=" N GLY A 524 " --> pdb=" O LEU A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 568 removed outlier: 6.707A pdb=" N VAL A 552 " --> pdb=" O ILE A 566 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 810 " --> pdb=" O VAL A 547 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 576 through 578 removed outlier: 4.031A pdb=" N LEU A 594 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 624 through 631 removed outlier: 6.164A pdb=" N GLU A 642 " --> pdb=" O PRO A 625 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE A 653 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLU A 668 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N SER A 655 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N VAL A 666 " --> pdb=" O SER A 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 676 through 680 removed outlier: 4.416A pdb=" N GLN A 676 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TRP A 688 " --> pdb=" O TRP A 695 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 694 " --> pdb=" O LEU A 707 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 716 through 719 removed outlier: 3.701A pdb=" N ILE A 724 " --> pdb=" O GLN A 719 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 735 " --> pdb=" O LEU A 748 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 776 through 779 removed outlier: 3.671A pdb=" N ALA A 798 " --> pdb=" O LEU A 786 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 832 through 835 Processing sheet with id=AB4, first strand: chain 'A' and resid 917 through 920 removed outlier: 5.876A pdb=" N TYR A 863 " --> pdb=" O ASN A 880 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE B 466 " --> pdb=" O TYR B 479 " (cutoff:3.500A) removed outlier: 10.058A pdb=" N TYR B 481 " --> pdb=" O ARG B 464 " (cutoff:3.500A) removed outlier: 12.349A pdb=" N ARG B 464 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N MET B 444 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 468 " --> pdb=" O PHE B 442 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE B 442 " --> pdb=" O SER B 468 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA B 330 " --> pdb=" O LYS B 447 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 310 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N LEU B 333 " --> pdb=" O LEU B 310 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N SER B 312 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N GLU B 335 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN B 291 " --> pdb=" O THR B 309 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N PHE B 311 " --> pdb=" O ASN B 291 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYR B 293 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N VAL B 313 " --> pdb=" O TYR B 293 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N MET B 295 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N SER B 258 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE B 294 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N GLU B 260 " --> pdb=" O ILE B 294 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N PHE B 296 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA B 262 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 949 through 954 removed outlier: 5.041A pdb=" N VAL A 938 " --> pdb=" O GLN A 951 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N SER A 937 " --> pdb=" O SER A 933 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A1180 " --> pdb=" O ALA A 932 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 963 through 964 Processing sheet with id=AB7, first strand: chain 'A' and resid 1000 through 1006 removed outlier: 4.649A pdb=" N SER A1002 " --> pdb=" O THR A1015 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A1015 " --> pdb=" O SER A1002 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1011 " --> pdb=" O ASP A1006 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1042 through 1045 removed outlier: 3.625A pdb=" N TYR A1074 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1081 through 1089 removed outlier: 6.537A pdb=" N LEU A1098 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1086 " --> pdb=" O PHE A1096 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A1096 " --> pdb=" O PHE A1086 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU A1088 " --> pdb=" O GLN A1094 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN A1094 " --> pdb=" O LEU A1088 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TRP A1097 " --> pdb=" O TYR A1108 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG A1109 " --> pdb=" O MET A1121 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N MET A1121 " --> pdb=" O ARG A1109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1137 through 1139 Processing sheet with id=AC2, first strand: chain 'A' and resid 1207 through 1208 Processing sheet with id=AC3, first strand: chain 'A' and resid 1242 through 1248 Processing sheet with id=AC4, first strand: chain 'B' and resid 136 through 139 removed outlier: 3.774A pdb=" N LEU B 139 " --> pdb=" O ILE B 176 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 143 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ARG B 177 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LEU B 145 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE B 179 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 147 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL B 144 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N PHE B 209 " --> pdb=" O VAL B 144 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER B 146 " --> pdb=" O PHE B 209 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 338 through 339 390 hydrogen bonds defined for protein. 1053 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: 4.70 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1815 1.29 - 1.42: 2950 1.42 - 1.55: 6355 1.55 - 1.69: 21 1.69 - 1.82: 84 Bond restraints: 11225 Sorted by residual: bond pdb=" CA SER B 488 " pdb=" CB SER B 488 " ideal model delta sigma weight residual 1.535 1.359 0.176 1.90e-02 2.77e+03 8.61e+01 bond pdb=" C HIS B 480 " pdb=" O HIS B 480 " ideal model delta sigma weight residual 1.235 1.159 0.076 1.23e-02 6.61e+03 3.85e+01 bond pdb=" C LEU B 489 " pdb=" O LEU B 489 " ideal model delta sigma weight residual 1.236 1.178 0.058 1.14e-02 7.69e+03 2.55e+01 bond pdb=" C SER B 488 " pdb=" O SER B 488 " ideal model delta sigma weight residual 1.234 1.171 0.062 1.24e-02 6.50e+03 2.53e+01 bond pdb=" C THR B 487 " pdb=" O THR B 487 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.29e-02 6.01e+03 1.33e+01 ... (remaining 11220 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 14999 4.12 - 8.24: 243 8.24 - 12.36: 16 12.36 - 16.48: 2 16.48 - 20.59: 2 Bond angle restraints: 15262 Sorted by residual: angle pdb=" C ASP B 484 " pdb=" CA ASP B 484 " pdb=" CB ASP B 484 " ideal model delta sigma weight residual 110.35 129.02 -18.67 1.91e+00 2.74e-01 9.56e+01 angle pdb=" CG1 ILE A 305 " pdb=" CB ILE A 305 " pdb=" CG2 ILE A 305 " ideal model delta sigma weight residual 110.70 90.11 20.59 3.00e+00 1.11e-01 4.71e+01 angle pdb=" CA HIS B 480 " pdb=" CB HIS B 480 " pdb=" CG HIS B 480 " ideal model delta sigma weight residual 113.80 120.41 -6.61 1.00e+00 1.00e+00 4.37e+01 angle pdb=" N ASP B 484 " pdb=" CA ASP B 484 " pdb=" C ASP B 484 " ideal model delta sigma weight residual 113.29 100.71 12.58 2.00e+00 2.50e-01 3.96e+01 angle pdb=" C ASN B 485 " pdb=" CA ASN B 485 " pdb=" CB ASN B 485 " ideal model delta sigma weight residual 111.89 120.61 -8.72 1.42e+00 4.96e-01 3.77e+01 ... (remaining 15257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6146 17.95 - 35.90: 542 35.90 - 53.85: 89 53.85 - 71.80: 18 71.80 - 89.75: 7 Dihedral angle restraints: 6802 sinusoidal: 2832 harmonic: 3970 Sorted by residual: dihedral pdb=" C ASP B 484 " pdb=" N ASP B 484 " pdb=" CA ASP B 484 " pdb=" CB ASP B 484 " ideal model delta harmonic sigma weight residual -122.60 -141.03 18.43 0 2.50e+00 1.60e-01 5.44e+01 dihedral pdb=" CB CYS B 282 " pdb=" SG CYS B 282 " pdb=" SG CYS B 501 " pdb=" CB CYS B 501 " ideal model delta sinusoidal sigma weight residual 93.00 35.28 57.72 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" C ASN B 485 " pdb=" N ASN B 485 " pdb=" CA ASN B 485 " pdb=" CB ASN B 485 " ideal model delta harmonic sigma weight residual -122.60 -136.50 13.90 0 2.50e+00 1.60e-01 3.09e+01 ... (remaining 6799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1548 0.112 - 0.224: 124 0.224 - 0.336: 14 0.336 - 0.448: 4 0.448 - 0.560: 3 Chirality restraints: 1693 Sorted by residual: chirality pdb=" CA ASP B 484 " pdb=" N ASP B 484 " pdb=" C ASP B 484 " pdb=" CB ASP B 484 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" CA ASN B 485 " pdb=" N ASN B 485 " pdb=" C ASN B 485 " pdb=" CB ASN B 485 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CB VAL B 162 " pdb=" CA VAL B 162 " pdb=" CG1 VAL B 162 " pdb=" CG2 VAL B 162 " both_signs ideal model delta sigma weight residual False -2.63 -2.17 -0.46 2.00e-01 2.50e+01 5.29e+00 ... (remaining 1690 not shown) Planarity restraints: 1974 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2602 " -0.335 2.00e-02 2.50e+03 2.85e-01 1.02e+03 pdb=" C7 NAG A2602 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG A2602 " -0.004 2.00e-02 2.50e+03 pdb=" N2 NAG A2602 " 0.487 2.00e-02 2.50e+03 pdb=" O7 NAG A2602 " -0.227 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 230 " 0.034 2.00e-02 2.50e+03 3.01e-02 2.26e+01 pdb=" CG TRP B 230 " -0.080 2.00e-02 2.50e+03 pdb=" CD1 TRP B 230 " 0.038 2.00e-02 2.50e+03 pdb=" CD2 TRP B 230 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 230 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 230 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 230 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 230 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP B 230 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 370 " -0.023 2.00e-02 2.50e+03 3.15e-02 1.73e+01 pdb=" CG PHE B 370 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 PHE B 370 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 370 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 PHE B 370 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 370 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 370 " 0.004 2.00e-02 2.50e+03 ... (remaining 1971 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 3442 2.85 - 3.36: 7947 3.36 - 3.88: 18363 3.88 - 4.39: 20217 4.39 - 4.90: 35711 Nonbonded interactions: 85680 Sorted by model distance: nonbonded pdb=" O LEU B 246 " pdb=" OH TYR B 478 " model vdw 2.341 3.040 nonbonded pdb=" O LYS A 250 " pdb=" OG1 THR A 254 " model vdw 2.365 3.040 nonbonded pdb=" O GLY B 253 " pdb=" OG1 THR B 493 " model vdw 2.371 3.040 nonbonded pdb=" OG SER A1225 " pdb=" O GLY A1227 " model vdw 2.384 3.040 nonbonded pdb=" O MET A1199 " pdb=" OG SER A1223 " model vdw 2.385 3.040 ... (remaining 85675 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: 4.930 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.000 Find NCS groups from input model: 0.110 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 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 : 0.008 0.176 11240 Z= 0.381 Angle : 1.244 20.595 15297 Z= 0.675 Chirality : 0.071 0.560 1693 Planarity : 0.012 0.285 1969 Dihedral : 13.922 89.751 4194 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.08 % Allowed : 0.51 % Favored : 99.41 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.20), residues: 1333 helix: -4.06 (0.17), residues: 209 sheet: -0.65 (0.23), residues: 496 loop : -1.86 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP B 230 HIS 0.024 0.003 HIS A 529 PHE 0.072 0.005 PHE B 370 TYR 0.024 0.003 TYR A1013 ARG 0.020 0.001 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.00883 ( 5) link_NAG-ASN : angle 4.21321 ( 15) hydrogen bonds : bond 0.22441 ( 382) hydrogen bonds : angle 9.45304 ( 1053) SS BOND : bond 0.00528 ( 10) SS BOND : angle 1.36674 ( 20) covalent geometry : bond 0.00762 (11225) covalent geometry : angle 1.23767 (15262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 194 time to evaluate : 1.233 Fit side-chains revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6894 (m-30) cc_final: 0.6623 (m-30) REVERT: A 550 ARG cc_start: 0.8199 (mtt-85) cc_final: 0.7570 (mtp180) REVERT: A 565 MET cc_start: 0.7978 (tpp) cc_final: 0.7683 (mmm) REVERT: A 642 GLU cc_start: 0.6978 (tt0) cc_final: 0.6344 (tm-30) REVERT: A 682 LEU cc_start: 0.8626 (tp) cc_final: 0.8393 (tt) REVERT: A 890 ARG cc_start: 0.8110 (ttm170) cc_final: 0.7745 (mtp180) REVERT: A 928 ARG cc_start: 0.8020 (mtt180) cc_final: 0.7564 (mtm110) REVERT: A 935 GLN cc_start: 0.7972 (tt0) cc_final: 0.7680 (mp-120) REVERT: A 949 GLU cc_start: 0.7693 (tt0) cc_final: 0.7274 (mt-10) REVERT: A 1194 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7532 (mp0) REVERT: A 1264 GLN cc_start: 0.8170 (mt0) cc_final: 0.7160 (tt0) REVERT: B 164 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7487 (mm-40) REVERT: B 266 LEU cc_start: 0.7846 (tp) cc_final: 0.7545 (tt) REVERT: B 277 ARG cc_start: 0.7300 (mtm110) cc_final: 0.7012 (ttp80) REVERT: B 447 LYS cc_start: 0.7669 (tttt) cc_final: 0.7364 (ttpp) outliers start: 1 outliers final: 0 residues processed: 194 average time/residue: 0.2570 time to fit residues: 68.5410 Evaluate side-chains 159 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 41 optimal weight: 0.1980 chunk 64 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 712 GLN A 726 HIS B 245 HIS B 291 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.169617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138500 restraints weight = 12064.029| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 1.87 r_work: 0.3323 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11240 Z= 0.184 Angle : 0.628 6.261 15297 Z= 0.317 Chirality : 0.044 0.158 1693 Planarity : 0.006 0.056 1969 Dihedral : 5.712 59.333 1578 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.68 % Allowed : 7.05 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.71 (0.21), residues: 1333 helix: -1.79 (0.30), residues: 205 sheet: -0.38 (0.23), residues: 481 loop : -1.44 (0.21), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 688 HIS 0.009 0.001 HIS A 459 PHE 0.018 0.002 PHE B 495 TYR 0.015 0.002 TYR B 227 ARG 0.004 0.001 ARG B 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 2.63214 ( 15) hydrogen bonds : bond 0.04391 ( 382) hydrogen bonds : angle 6.19674 ( 1053) SS BOND : bond 0.00317 ( 10) SS BOND : angle 0.70768 ( 20) covalent geometry : bond 0.00436 (11225) covalent geometry : angle 0.62237 (15262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6999 (m-30) cc_final: 0.6796 (m-30) REVERT: A 549 ARG cc_start: 0.8102 (mmt180) cc_final: 0.7870 (mmp80) REVERT: A 550 ARG cc_start: 0.8021 (mtt-85) cc_final: 0.7675 (mtp180) REVERT: A 642 GLU cc_start: 0.6999 (tt0) cc_final: 0.6479 (tm-30) REVERT: A 682 LEU cc_start: 0.8650 (tp) cc_final: 0.8445 (tt) REVERT: A 890 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7631 (mtp180) REVERT: A 928 ARG cc_start: 0.7871 (mtt180) cc_final: 0.7584 (mtm110) REVERT: A 997 LEU cc_start: 0.8458 (mt) cc_final: 0.8226 (mp) REVERT: A 1046 ASP cc_start: 0.8197 (t0) cc_final: 0.7938 (t0) REVERT: A 1134 ASP cc_start: 0.7225 (t0) cc_final: 0.6954 (t70) REVERT: A 1264 GLN cc_start: 0.8237 (mt0) cc_final: 0.7208 (tt0) REVERT: B 266 LEU cc_start: 0.7741 (tp) cc_final: 0.7519 (tt) REVERT: B 434 ARG cc_start: 0.7801 (mtm180) cc_final: 0.7563 (mtm180) outliers start: 8 outliers final: 3 residues processed: 182 average time/residue: 0.2409 time to fit residues: 62.5207 Evaluate side-chains 155 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain B residue 291 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 64 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 75 optimal weight: 0.0670 chunk 29 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 33 optimal weight: 0.0870 chunk 115 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 52 optimal weight: 3.9990 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 712 GLN A 935 GLN B 298 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.170994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140488 restraints weight = 12177.151| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.84 r_work: 0.3371 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11240 Z= 0.110 Angle : 0.548 9.247 15297 Z= 0.273 Chirality : 0.041 0.174 1693 Planarity : 0.004 0.045 1969 Dihedral : 5.192 57.567 1578 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.76 % Allowed : 9.68 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -1.17 (0.21), residues: 1333 helix: -0.57 (0.35), residues: 205 sheet: -0.24 (0.23), residues: 481 loop : -1.20 (0.22), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 931 HIS 0.006 0.001 HIS A 459 PHE 0.017 0.001 PHE A 876 TYR 0.011 0.001 TYR A1013 ARG 0.004 0.000 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00249 ( 5) link_NAG-ASN : angle 2.29667 ( 15) hydrogen bonds : bond 0.03506 ( 382) hydrogen bonds : angle 5.57832 ( 1053) SS BOND : bond 0.00250 ( 10) SS BOND : angle 0.55793 ( 20) covalent geometry : bond 0.00255 (11225) covalent geometry : angle 0.54336 (15262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6987 (m-30) cc_final: 0.6711 (m-30) REVERT: A 228 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6933 (pt0) REVERT: A 549 ARG cc_start: 0.8093 (mmt180) cc_final: 0.7787 (mmp80) REVERT: A 550 ARG cc_start: 0.7848 (mtt-85) cc_final: 0.7619 (mtp180) REVERT: A 642 GLU cc_start: 0.6810 (tt0) cc_final: 0.6508 (tm-30) REVERT: A 890 ARG cc_start: 0.7991 (ttm170) cc_final: 0.7613 (mtp180) REVERT: A 928 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7508 (mtm110) REVERT: A 1134 ASP cc_start: 0.7178 (t0) cc_final: 0.6924 (t0) REVERT: A 1156 ARG cc_start: 0.8024 (mmt90) cc_final: 0.7757 (mmt-90) REVERT: A 1264 GLN cc_start: 0.8197 (mt0) cc_final: 0.7139 (tt0) outliers start: 9 outliers final: 4 residues processed: 171 average time/residue: 0.2373 time to fit residues: 57.9876 Evaluate side-chains 160 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain B residue 278 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 82 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 124 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 78 optimal weight: 0.0170 chunk 2 optimal weight: 0.5980 chunk 76 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 chunk 125 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 700 HIS A 712 GLN A 719 GLN A 940 HIS A 951 GLN A1229 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.172192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.140630 restraints weight = 12029.451| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.90 r_work: 0.3356 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11240 Z= 0.102 Angle : 0.528 7.283 15297 Z= 0.261 Chirality : 0.041 0.172 1693 Planarity : 0.004 0.040 1969 Dihedral : 4.857 57.084 1578 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.02 % Allowed : 10.87 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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 (0.22), residues: 1333 helix: 0.22 (0.36), residues: 211 sheet: -0.14 (0.23), residues: 490 loop : -0.91 (0.23), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1014 HIS 0.007 0.001 HIS A 459 PHE 0.013 0.001 PHE A 876 TYR 0.010 0.001 TYR A1054 ARG 0.005 0.000 ARG B 483 Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 5) link_NAG-ASN : angle 2.01054 ( 15) hydrogen bonds : bond 0.03146 ( 382) hydrogen bonds : angle 5.19200 ( 1053) SS BOND : bond 0.00237 ( 10) SS BOND : angle 0.52610 ( 20) covalent geometry : bond 0.00235 (11225) covalent geometry : angle 0.52407 (15262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 169 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6957 (m-30) cc_final: 0.6626 (m-30) REVERT: A 228 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6763 (pt0) REVERT: A 549 ARG cc_start: 0.8067 (mmt180) cc_final: 0.7842 (mmp80) REVERT: A 642 GLU cc_start: 0.6522 (tt0) cc_final: 0.6256 (tm-30) REVERT: A 715 TRP cc_start: 0.8800 (t-100) cc_final: 0.8555 (t-100) REVERT: A 821 LEU cc_start: 0.7254 (mm) cc_final: 0.6905 (mt) REVERT: A 890 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7560 (mtt180) REVERT: A 928 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7452 (mtm110) REVERT: A 1134 ASP cc_start: 0.7124 (t0) cc_final: 0.6881 (t0) REVERT: A 1156 ARG cc_start: 0.8025 (mmt90) cc_final: 0.7722 (mmt-90) REVERT: A 1264 GLN cc_start: 0.8142 (mt0) cc_final: 0.7088 (tt0) REVERT: B 190 LEU cc_start: 0.6655 (mt) cc_final: 0.6397 (mp) REVERT: B 206 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.7015 (mtm) outliers start: 12 outliers final: 5 residues processed: 175 average time/residue: 0.2439 time to fit residues: 59.7653 Evaluate side-chains 165 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 278 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 72 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 65 optimal weight: 0.0980 chunk 121 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 589 ASN A 697 GLN A 712 GLN A1284 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.169312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137326 restraints weight = 12136.667| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.90 r_work: 0.3335 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11240 Z= 0.147 Angle : 0.554 9.063 15297 Z= 0.275 Chirality : 0.042 0.157 1693 Planarity : 0.004 0.035 1969 Dihedral : 4.915 57.303 1578 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.19 % Allowed : 12.31 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.60 (0.23), residues: 1333 helix: 0.48 (0.36), residues: 211 sheet: -0.27 (0.22), residues: 514 loop : -0.72 (0.24), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 809 HIS 0.007 0.001 HIS A 459 PHE 0.019 0.002 PHE B 495 TYR 0.013 0.001 TYR A 261 ARG 0.012 0.000 ARG A 550 Details of bonding type rmsd link_NAG-ASN : bond 0.00258 ( 5) link_NAG-ASN : angle 2.05012 ( 15) hydrogen bonds : bond 0.03267 ( 382) hydrogen bonds : angle 5.18924 ( 1053) SS BOND : bond 0.00246 ( 10) SS BOND : angle 0.65064 ( 20) covalent geometry : bond 0.00357 (11225) covalent geometry : angle 0.55069 (15262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 1.185 Fit side-chains REVERT: A 219 ASP cc_start: 0.7013 (m-30) cc_final: 0.6676 (m-30) REVERT: A 228 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.6878 (pt0) REVERT: A 419 GLU cc_start: 0.7626 (tp30) cc_final: 0.7307 (mm-30) REVERT: A 549 ARG cc_start: 0.8084 (mmt180) cc_final: 0.7843 (mmp80) REVERT: A 642 GLU cc_start: 0.6549 (tt0) cc_final: 0.6226 (tm-30) REVERT: A 890 ARG cc_start: 0.8005 (ttm170) cc_final: 0.7623 (mtp180) REVERT: A 928 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7418 (mtm110) REVERT: A 998 GLN cc_start: 0.8277 (mt0) cc_final: 0.7922 (mp10) REVERT: A 1134 ASP cc_start: 0.7198 (t0) cc_final: 0.6955 (t0) REVERT: A 1150 ARG cc_start: 0.7747 (mtm-85) cc_final: 0.7482 (mtp-110) REVERT: A 1156 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7740 (mmt-90) REVERT: A 1264 GLN cc_start: 0.8159 (mt0) cc_final: 0.7078 (tt0) REVERT: B 190 LEU cc_start: 0.6689 (mt) cc_final: 0.6356 (mp) REVERT: B 206 MET cc_start: 0.7353 (OUTLIER) cc_final: 0.7104 (mtm) REVERT: B 274 GLU cc_start: 0.7550 (tp30) cc_final: 0.6888 (tp30) REVERT: B 278 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: B 290 ASP cc_start: 0.6041 (m-30) cc_final: 0.5797 (t0) REVERT: B 447 LYS cc_start: 0.7577 (tttt) cc_final: 0.7329 (ttpp) outliers start: 14 outliers final: 8 residues processed: 175 average time/residue: 0.2497 time to fit residues: 61.9545 Evaluate side-chains 178 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 529 HIS Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 80 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 106 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 712 GLN A1284 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.167890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135251 restraints weight = 12171.432| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.95 r_work: 0.3311 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11240 Z= 0.170 Angle : 0.569 9.529 15297 Z= 0.282 Chirality : 0.043 0.180 1693 Planarity : 0.004 0.036 1969 Dihedral : 4.997 57.472 1578 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.36 % Allowed : 12.99 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.55 (0.23), residues: 1333 helix: 0.64 (0.36), residues: 217 sheet: -0.36 (0.23), residues: 511 loop : -0.60 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 809 HIS 0.006 0.001 HIS A 459 PHE 0.020 0.002 PHE B 495 TYR 0.012 0.001 TYR A1054 ARG 0.004 0.000 ARG A1192 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 5) link_NAG-ASN : angle 2.17069 ( 15) hydrogen bonds : bond 0.03284 ( 382) hydrogen bonds : angle 5.20624 ( 1053) SS BOND : bond 0.00263 ( 10) SS BOND : angle 0.73765 ( 20) covalent geometry : bond 0.00412 (11225) covalent geometry : angle 0.56508 (15262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 171 time to evaluate : 1.174 Fit side-chains REVERT: A 219 ASP cc_start: 0.6975 (m-30) cc_final: 0.6665 (m-30) REVERT: A 549 ARG cc_start: 0.8027 (mmt180) cc_final: 0.7712 (mmp80) REVERT: A 642 GLU cc_start: 0.6504 (tt0) cc_final: 0.6198 (tm-30) REVERT: A 928 ARG cc_start: 0.7637 (mtt180) cc_final: 0.7392 (mtm180) REVERT: A 1134 ASP cc_start: 0.7229 (t0) cc_final: 0.6991 (t0) REVERT: A 1150 ARG cc_start: 0.7706 (mtm-85) cc_final: 0.7432 (mtp-110) REVERT: A 1264 GLN cc_start: 0.8157 (mt0) cc_final: 0.7104 (tt0) REVERT: B 190 LEU cc_start: 0.6781 (mt) cc_final: 0.6563 (mp) REVERT: B 206 MET cc_start: 0.7466 (OUTLIER) cc_final: 0.7233 (mtm) REVERT: B 264 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6628 (mt-10) REVERT: B 278 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7738 (mp10) REVERT: B 290 ASP cc_start: 0.5943 (m-30) cc_final: 0.5675 (t0) REVERT: B 447 LYS cc_start: 0.7576 (tttt) cc_final: 0.7325 (ttpp) outliers start: 16 outliers final: 12 residues processed: 179 average time/residue: 0.2403 time to fit residues: 61.3104 Evaluate side-chains 175 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 529 HIS Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 278 GLN Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 132 optimal weight: 0.0870 chunk 92 optimal weight: 0.6980 chunk 120 optimal weight: 0.0570 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 697 GLN A 712 GLN A 999 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.168900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.136828 restraints weight = 12306.128| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.90 r_work: 0.3322 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11240 Z= 0.140 Angle : 0.548 9.096 15297 Z= 0.272 Chirality : 0.042 0.187 1693 Planarity : 0.004 0.033 1969 Dihedral : 4.895 57.393 1578 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.53 % Allowed : 13.92 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.48 (0.23), residues: 1333 helix: 0.87 (0.36), residues: 217 sheet: -0.35 (0.23), residues: 515 loop : -0.61 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 809 HIS 0.006 0.001 HIS A 459 PHE 0.018 0.001 PHE B 495 TYR 0.017 0.001 TYR A 261 ARG 0.004 0.000 ARG A1156 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 5) link_NAG-ASN : angle 2.05891 ( 15) hydrogen bonds : bond 0.03127 ( 382) hydrogen bonds : angle 5.13470 ( 1053) SS BOND : bond 0.00260 ( 10) SS BOND : angle 0.67751 ( 20) covalent geometry : bond 0.00337 (11225) covalent geometry : angle 0.54465 (15262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.237 Fit side-chains REVERT: A 219 ASP cc_start: 0.6968 (m-30) cc_final: 0.6597 (m-30) REVERT: A 228 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6936 (pt0) REVERT: A 331 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 549 ARG cc_start: 0.7984 (mmt180) cc_final: 0.7756 (mmp80) REVERT: A 642 GLU cc_start: 0.6581 (tt0) cc_final: 0.6296 (tm-30) REVERT: A 928 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7363 (mtm180) REVERT: A 1134 ASP cc_start: 0.7247 (t0) cc_final: 0.6995 (t0) REVERT: A 1150 ARG cc_start: 0.7707 (mtm-85) cc_final: 0.7436 (mtp-110) REVERT: A 1157 LEU cc_start: 0.8046 (mp) cc_final: 0.7684 (mp) REVERT: A 1264 GLN cc_start: 0.8152 (mt0) cc_final: 0.6853 (tm-30) REVERT: B 190 LEU cc_start: 0.6804 (mt) cc_final: 0.6586 (mp) REVERT: B 206 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7262 (mtm) REVERT: B 264 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6617 (mt-10) outliers start: 18 outliers final: 10 residues processed: 175 average time/residue: 0.2492 time to fit residues: 62.2582 Evaluate side-chains 171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 424 THR Chi-restraints excluded: chain B residue 487 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 81 optimal weight: 0.9980 chunk 133 optimal weight: 0.0870 chunk 53 optimal weight: 0.7980 chunk 7 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 712 GLN A 889 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136275 restraints weight = 12224.775| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.91 r_work: 0.3402 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11240 Z= 0.131 Angle : 0.549 10.338 15297 Z= 0.271 Chirality : 0.042 0.183 1693 Planarity : 0.004 0.076 1969 Dihedral : 4.833 57.376 1578 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.61 % Allowed : 14.35 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.37 (0.23), residues: 1333 helix: 1.02 (0.37), residues: 217 sheet: -0.30 (0.23), residues: 512 loop : -0.53 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 809 HIS 0.006 0.001 HIS A 459 PHE 0.017 0.001 PHE B 495 TYR 0.012 0.001 TYR A1054 ARG 0.004 0.000 ARG A1156 Details of bonding type rmsd link_NAG-ASN : bond 0.00243 ( 5) link_NAG-ASN : angle 1.99713 ( 15) hydrogen bonds : bond 0.03065 ( 382) hydrogen bonds : angle 5.12967 ( 1053) SS BOND : bond 0.00256 ( 10) SS BOND : angle 0.67282 ( 20) covalent geometry : bond 0.00317 (11225) covalent geometry : angle 0.54585 (15262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.110 Fit side-chains revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6980 (m-30) cc_final: 0.6606 (m-30) REVERT: A 228 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.6990 (pt0) REVERT: A 331 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7825 (mm) REVERT: A 529 HIS cc_start: 0.5268 (OUTLIER) cc_final: 0.5047 (m170) REVERT: A 738 ILE cc_start: 0.7380 (mp) cc_final: 0.7132 (mm) REVERT: A 928 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7391 (mtm180) REVERT: A 1134 ASP cc_start: 0.7285 (t0) cc_final: 0.7024 (t0) REVERT: A 1150 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7456 (mtp-110) REVERT: A 1264 GLN cc_start: 0.8092 (mt0) cc_final: 0.6878 (tm-30) REVERT: B 190 LEU cc_start: 0.6852 (mt) cc_final: 0.6598 (mp) REVERT: B 206 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7247 (mtm) REVERT: B 264 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6600 (mt-10) REVERT: B 447 LYS cc_start: 0.7589 (tttt) cc_final: 0.7337 (ttpp) outliers start: 19 outliers final: 13 residues processed: 177 average time/residue: 0.2304 time to fit residues: 57.9104 Evaluate side-chains 173 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 529 HIS Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 424 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.0070 chunk 86 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 0.0170 chunk 7 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN A 712 GLN A 719 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.168757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.136785 restraints weight = 12238.251| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 1.89 r_work: 0.3353 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11240 Z= 0.119 Angle : 0.534 6.216 15297 Z= 0.267 Chirality : 0.042 0.157 1693 Planarity : 0.004 0.067 1969 Dihedral : 4.760 57.379 1578 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.70 % Allowed : 14.26 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.27 (0.23), residues: 1333 helix: 1.19 (0.37), residues: 217 sheet: -0.24 (0.23), residues: 512 loop : -0.51 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP A 809 HIS 0.006 0.001 HIS A 459 PHE 0.016 0.001 PHE B 495 TYR 0.012 0.001 TYR A1054 ARG 0.006 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 5) link_NAG-ASN : angle 1.92519 ( 15) hydrogen bonds : bond 0.03052 ( 382) hydrogen bonds : angle 5.05289 ( 1053) SS BOND : bond 0.00251 ( 10) SS BOND : angle 0.64293 ( 20) covalent geometry : bond 0.00284 (11225) covalent geometry : angle 0.53100 (15262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 219 ASP cc_start: 0.6951 (m-30) cc_final: 0.6577 (m-30) REVERT: A 228 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: A 317 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6703 (mt-10) REVERT: A 331 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7810 (mm) REVERT: A 549 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7571 (mmp80) REVERT: A 599 PHE cc_start: 0.6587 (p90) cc_final: 0.6243 (p90) REVERT: A 928 ARG cc_start: 0.7605 (mtt180) cc_final: 0.7341 (mtm180) REVERT: A 1049 GLN cc_start: 0.8328 (pm20) cc_final: 0.8052 (pm20) REVERT: A 1134 ASP cc_start: 0.7146 (t0) cc_final: 0.6908 (t0) REVERT: A 1150 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7428 (mtp-110) REVERT: A 1264 GLN cc_start: 0.8079 (mt0) cc_final: 0.6810 (tp40) REVERT: B 190 LEU cc_start: 0.6864 (mt) cc_final: 0.6611 (mp) REVERT: B 206 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7252 (mtm) REVERT: B 264 GLU cc_start: 0.7116 (mm-30) cc_final: 0.6557 (mt-10) REVERT: B 447 LYS cc_start: 0.7574 (tttt) cc_final: 0.7327 (ttpp) outliers start: 20 outliers final: 13 residues processed: 172 average time/residue: 0.2293 time to fit residues: 56.9306 Evaluate side-chains 171 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 549 ARG Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 861 TRP Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 134 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 697 GLN A 712 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.167383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.134669 restraints weight = 12150.664| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.96 r_work: 0.3368 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11240 Z= 0.149 Angle : 0.556 7.064 15297 Z= 0.277 Chirality : 0.042 0.156 1693 Planarity : 0.004 0.060 1969 Dihedral : 4.826 57.309 1578 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.78 % Allowed : 14.60 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.31 (0.23), residues: 1333 helix: 1.19 (0.37), residues: 217 sheet: -0.27 (0.23), residues: 521 loop : -0.54 (0.25), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 809 HIS 0.006 0.001 HIS A 459 PHE 0.019 0.001 PHE B 495 TYR 0.031 0.001 TYR A 351 ARG 0.005 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 5) link_NAG-ASN : angle 1.95815 ( 15) hydrogen bonds : bond 0.03159 ( 382) hydrogen bonds : angle 5.08714 ( 1053) SS BOND : bond 0.00261 ( 10) SS BOND : angle 0.72439 ( 20) covalent geometry : bond 0.00359 (11225) covalent geometry : angle 0.55245 (15262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2666 Ramachandran restraints generated. 1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.159 Fit side-chains REVERT: A 219 ASP cc_start: 0.7037 (m-30) cc_final: 0.6661 (m-30) REVERT: A 228 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7040 (pt0) REVERT: A 317 GLU cc_start: 0.7120 (mt-10) cc_final: 0.6795 (mt-10) REVERT: A 331 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.7893 (mm) REVERT: A 565 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7516 (mmm) REVERT: A 575 ASP cc_start: 0.6329 (t70) cc_final: 0.6024 (t70) REVERT: A 928 ARG cc_start: 0.7818 (mtt180) cc_final: 0.7450 (mtm180) REVERT: A 1134 ASP cc_start: 0.7319 (t0) cc_final: 0.7085 (t0) REVERT: A 1150 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7532 (mtp-110) REVERT: A 1264 GLN cc_start: 0.8092 (mt0) cc_final: 0.6872 (tp40) REVERT: B 190 LEU cc_start: 0.6960 (mt) cc_final: 0.6699 (mp) REVERT: B 206 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7335 (mtm) REVERT: B 264 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6594 (mt-10) REVERT: B 278 GLN cc_start: 0.7668 (mp10) cc_final: 0.7111 (mp10) REVERT: B 360 LYS cc_start: 0.6294 (OUTLIER) cc_final: 0.6092 (ttpt) REVERT: B 447 LYS cc_start: 0.7604 (tttt) cc_final: 0.7351 (ttpp) outliers start: 21 outliers final: 14 residues processed: 173 average time/residue: 0.2319 time to fit residues: 57.7523 Evaluate side-chains 177 residues out of total 1197 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 331 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 565 MET Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 861 TRP Chi-restraints excluded: chain A residue 870 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain B residue 166 ASN Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 360 LYS Chi-restraints excluded: chain B residue 424 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 130 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 ASN ** A 527 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.165318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.131941 restraints weight = 12148.570| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.93 r_work: 0.3257 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11240 Z= 0.190 Angle : 0.593 7.330 15297 Z= 0.296 Chirality : 0.044 0.204 1693 Planarity : 0.005 0.056 1969 Dihedral : 4.988 57.470 1578 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.78 % Allowed : 15.20 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % 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: -0.36 (0.23), residues: 1333 helix: 1.10 (0.37), residues: 217 sheet: -0.30 (0.23), residues: 515 loop : -0.56 (0.25), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 809 HIS 0.006 0.001 HIS B 248 PHE 0.022 0.002 PHE B 495 TYR 0.030 0.002 TYR A 351 ARG 0.004 0.000 ARG A 549 Details of bonding type rmsd link_NAG-ASN : bond 0.00307 ( 5) link_NAG-ASN : angle 2.03312 ( 15) hydrogen bonds : bond 0.03320 ( 382) hydrogen bonds : angle 5.23987 ( 1053) SS BOND : bond 0.00286 ( 10) SS BOND : angle 0.82571 ( 20) covalent geometry : bond 0.00462 (11225) covalent geometry : angle 0.58959 (15262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5759.12 seconds wall clock time: 99 minutes 16.27 seconds (5956.27 seconds total)