Starting phenix.real_space_refine on Fri Aug 22 20:23:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nov_49618/08_2025/9nov_49618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nov_49618/08_2025/9nov_49618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nov_49618/08_2025/9nov_49618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nov_49618/08_2025/9nov_49618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nov_49618/08_2025/9nov_49618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nov_49618/08_2025/9nov_49618.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.021 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 52 5.16 5 Cl 3 4.86 5 C 4873 2.51 5 N 1289 2.21 5 O 1430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7647 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3629 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 24, 'TRANS': 442} Chain breaks: 4 Chain: "A" Number of atoms: 3785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3785 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 21, 'TRANS': 447} Chain breaks: 3 Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'RRJ': 1, 'RRY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.14, per 1000 atoms: 0.28 Number of scatterers: 7647 At special positions: 0 Unit cell: (92.999, 88.884, 97.114, 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) Cl 3 17.00 S 52 16.00 O 1430 8.00 N 1289 7.00 C 4873 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 351 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 517 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 410 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 499 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 233 " - pdb=" SG CYS A 513 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 366 " distance=2.03 Simple disulfide: pdb=" SG CYS A 405 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 495 " - pdb=" SG CYS A 514 " distance=2.03 Simple disulfide: pdb=" SG CYS A 499 " - pdb=" SG CYS A 517 " 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 ?1-2 " RRY C 1 " - " RRJ C 2 " NAG-ASN " NAG A 601 " - " ASN A 487 " " NAG A 602 " - " ASN A 84 " " NAG A 603 " - " ASN A 428 " " NAG A 604 " - " ASN A 312 " " NAG A 605 " - " ASN A 248 " " NAG A 606 " - " ASN A 292 " " NAG A 607 " - " ASN A 368 " " NAG B 601 " - " ASN B 475 " " NAG B 602 " - " ASN B 285 " " NAG B 603 " - " ASN B 264 " " NAG B 604 " - " ASN B 411 " " NAG B 605 " - " ASN B 85 " " NAG B 606 " - " ASN B 130 " " NAG B 607 " - " ASN B 380 " " NAG B 608 " - " ASN B 432 " Time building additional restraints: 0.71 Conformation dependent library (CDL) restraints added in 454.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1772 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 42.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 66 through 86 removed outlier: 3.610A pdb=" N LEU B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 118 removed outlier: 3.852A pdb=" N ALA B 109 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.918A pdb=" N GLN B 133 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 158 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.536A pdb=" N LEU B 174 " --> pdb=" O MET B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 205 removed outlier: 3.898A pdb=" N GLN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 234 removed outlier: 3.597A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 266 removed outlier: 3.723A pdb=" N SER B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 290 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 314 through 318 Processing helix chain 'B' and resid 333 through 346 removed outlier: 3.720A pdb=" N THR B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 387 removed outlier: 3.625A pdb=" N LEU B 385 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN B 386 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 408 removed outlier: 3.608A pdb=" N SER B 392 " --> pdb=" O HIS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 425 through 431 removed outlier: 4.487A pdb=" N ASN B 429 " --> pdb=" O GLN B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.687A pdb=" N ILE B 485 " --> pdb=" O ARG B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 65 through 85 removed outlier: 3.738A pdb=" N TYR A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 116 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.541A pdb=" N LEU A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 201 Processing helix chain 'A' and resid 213 through 228 Processing helix chain 'A' and resid 250 through 267 Processing helix chain 'A' and resid 280 through 292 removed outlier: 4.478A pdb=" N PHE A 284 " --> pdb=" O THR A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 334 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.583A pdb=" N ASN A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER A 372 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 removed outlier: 3.696A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.717A pdb=" N SER A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 removed outlier: 3.723A pdb=" N TRP A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA3, first strand: chain 'B' and resid 124 through 126 Processing sheet with id=AA4, first strand: chain 'B' and resid 141 through 143 removed outlier: 6.385A pdb=" N GLN B 164 " --> pdb=" O PHE B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 240 removed outlier: 7.926A pdb=" N VAL B 209 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N GLU B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA B 211 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N VAL B 270 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL B 271 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TRP B 297 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N PHE B 324 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ALA B 299 " --> pdb=" O PHE B 324 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N GLN B 326 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N VAL B 321 " --> pdb=" O TRP B 459 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TYR B 454 " --> pdb=" O ARG B 473 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG B 473 " --> pdb=" O TYR B 454 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 456 " --> pdb=" O VAL B 471 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AA7, first strand: chain 'B' and resid 511 through 512 removed outlier: 3.569A pdb=" N LYS B 512 " --> pdb=" O CYS B 518 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 28 through 29 removed outlier: 6.150A pdb=" N LEU A 35 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A 99 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY A 37 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU A 34 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N ILE A 139 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY A 36 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N ILE A 162 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N VAL A 138 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN A 161 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.732A pdb=" N GLU A 63 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 233 through 240 removed outlier: 7.734A pdb=" N ILE A 206 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N GLN A 237 " --> pdb=" O ILE A 206 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL A 208 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N THR A 239 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL A 210 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 272 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA A 296 " --> pdb=" O THR A 321 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N LEU A 323 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TRP A 298 " --> pdb=" O LEU A 323 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE A 325 " --> pdb=" O TRP A 298 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA A 300 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 9.924A pdb=" N ILE A 327 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N PHE A 322 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 448 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER A 467 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A 450 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN A 474 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 429 through 430 Processing sheet with id=AB3, first strand: chain 'A' and resid 506 through 507 removed outlier: 3.619A pdb=" N LYS A 506 " --> pdb=" O GLU A 516 " (cutoff:3.500A) 285 hydrogen bonds defined for protein. 789 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: 1.30 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2430 1.34 - 1.46: 1653 1.46 - 1.58: 3666 1.58 - 1.70: 0 1.70 - 1.82: 78 Bond restraints: 7827 Sorted by residual: bond pdb=" C2 RRY C 1 " pdb=" O5 RRY C 1 " ideal model delta sigma weight residual 1.410 1.467 -0.057 2.00e-02 2.50e+03 8.13e+00 bond pdb=" C2 RRY C 1 " pdb=" C3 RRY C 1 " ideal model delta sigma weight residual 1.541 1.490 0.051 2.00e-02 2.50e+03 6.45e+00 bond pdb=" C4 RRY C 1 " pdb=" C5 RRY C 1 " ideal model delta sigma weight residual 1.535 1.486 0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C5 RRY C 1 " pdb=" O5 RRY C 1 " ideal model delta sigma weight residual 1.421 1.467 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C3 RRY C 1 " pdb=" C4 RRY C 1 " ideal model delta sigma weight residual 1.519 1.473 0.046 2.00e-02 2.50e+03 5.30e+00 ... (remaining 7822 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 10473 1.85 - 3.70: 152 3.70 - 5.56: 13 5.56 - 7.41: 3 7.41 - 9.26: 1 Bond angle restraints: 10642 Sorted by residual: angle pdb=" C2 NAG A 604 " pdb=" N2 NAG A 604 " pdb=" C7 NAG A 604 " ideal model delta sigma weight residual 124.56 133.82 -9.26 3.00e+00 1.11e-01 9.52e+00 angle pdb=" CA VAL A 465 " pdb=" C VAL A 465 " pdb=" N ALA A 466 " ideal model delta sigma weight residual 116.60 119.98 -3.38 1.45e+00 4.76e-01 5.42e+00 angle pdb=" C ILE A 104 " pdb=" N SER A 105 " pdb=" CA SER A 105 " ideal model delta sigma weight residual 121.19 124.86 -3.67 1.59e+00 3.96e-01 5.33e+00 angle pdb=" C2 RRY C 1 " pdb=" C3 RRY C 1 " pdb=" O3 RRY C 1 " ideal model delta sigma weight residual 116.21 109.64 6.57 3.00e+00 1.11e-01 4.80e+00 angle pdb=" N SER A 105 " pdb=" CA SER A 105 " pdb=" C SER A 105 " ideal model delta sigma weight residual 111.37 114.81 -3.44 1.64e+00 3.72e-01 4.40e+00 ... (remaining 10637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.31: 4350 22.31 - 44.61: 443 44.61 - 66.92: 91 66.92 - 89.23: 15 89.23 - 111.54: 3 Dihedral angle restraints: 4902 sinusoidal: 2171 harmonic: 2731 Sorted by residual: dihedral pdb=" CB CYS A 495 " pdb=" SG CYS A 495 " pdb=" SG CYS A 514 " pdb=" CB CYS A 514 " ideal model delta sinusoidal sigma weight residual -86.00 -173.91 87.91 1 1.00e+01 1.00e-02 9.25e+01 dihedral pdb=" CB CYS A 233 " pdb=" SG CYS A 233 " pdb=" SG CYS A 513 " pdb=" CB CYS A 513 " ideal model delta sinusoidal sigma weight residual -86.00 -166.67 80.67 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS A 102 " pdb=" CB CYS A 102 " ideal model delta sinusoidal sigma weight residual -86.00 -152.24 66.24 1 1.00e+01 1.00e-02 5.73e+01 ... (remaining 4899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 980 0.052 - 0.104: 220 0.104 - 0.155: 33 0.155 - 0.207: 6 0.207 - 0.259: 1 Chirality restraints: 1240 Sorted by residual: chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 84 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C2 NAG A 604 " pdb=" C1 NAG A 604 " pdb=" C3 NAG A 604 " pdb=" N2 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.49 -2.29 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C1 NAG B 608 " pdb=" ND2 ASN B 432 " pdb=" C2 NAG B 608 " pdb=" O5 NAG B 608 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.76e-01 ... (remaining 1237 not shown) Planarity restraints: 1353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 69 " -0.008 2.00e-02 2.50e+03 1.13e-02 2.56e+00 pdb=" CG TYR A 69 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 69 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR A 69 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 69 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 69 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 69 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 69 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 111 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO B 112 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 439 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 440 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.016 5.00e-02 4.00e+02 ... (remaining 1350 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3413 2.94 - 3.43: 7383 3.43 - 3.92: 12444 3.92 - 4.41: 14100 4.41 - 4.90: 23678 Nonbonded interactions: 61018 Sorted by model distance: nonbonded pdb=" O2 RRY C 1 " pdb=" O2 RRJ C 2 " model vdw 2.451 2.432 nonbonded pdb=" O2 RRY C 1 " pdb=" O3 RRY C 1 " model vdw 2.453 2.432 nonbonded pdb=" O5 RRY C 1 " pdb=" C1 RRJ C 2 " model vdw 2.467 2.776 nonbonded pdb=" O5 NAG A 602 " pdb=" O6 NAG A 602 " model vdw 2.563 2.432 nonbonded pdb=" N GLN A 244 " pdb=" OE1 GLN A 244 " model vdw 2.591 3.120 ... (remaining 61013 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: 6.130 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7857 Z= 0.208 Angle : 0.574 9.258 10718 Z= 0.282 Chirality : 0.045 0.259 1240 Planarity : 0.003 0.035 1338 Dihedral : 17.379 111.537 3088 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.05 % Allowed : 25.82 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.28), residues: 918 helix: 1.54 (0.29), residues: 330 sheet: -1.85 (0.41), residues: 137 loop : 0.39 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 182 TYR 0.028 0.002 TYR A 69 PHE 0.011 0.001 PHE B 226 TRP 0.007 0.001 TRP B 461 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00475 ( 7827) covalent geometry : angle 0.55837 (10642) SS BOND : bond 0.00217 ( 14) SS BOND : angle 0.98651 ( 28) hydrogen bonds : bond 0.17670 ( 285) hydrogen bonds : angle 6.16765 ( 789) glycosidic custom : bond 0.05120 ( 1) glycosidic custom : angle 3.37562 ( 3) link_NAG-ASN : bond 0.00221 ( 15) link_NAG-ASN : angle 1.87007 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 68 time to evaluate : 0.328 Fit side-chains REVERT: B 115 MET cc_start: 0.7652 (ttm) cc_final: 0.7365 (tmm) REVERT: B 258 ASP cc_start: 0.8607 (t0) cc_final: 0.8282 (t0) REVERT: B 317 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7915 (mm110) REVERT: B 498 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8406 (ttp80) REVERT: A 198 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8329 (mtm) outliers start: 25 outliers final: 20 residues processed: 87 average time/residue: 0.0794 time to fit residues: 10.0397 Evaluate side-chains 90 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 67 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 317 GLN Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 233 CYS Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 364 ASP Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 458 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.121684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100977 restraints weight = 12417.689| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.00 r_work: 0.3178 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.0720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7857 Z= 0.115 Angle : 0.502 9.426 10718 Z= 0.245 Chirality : 0.043 0.254 1240 Planarity : 0.003 0.034 1338 Dihedral : 7.665 64.837 1400 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.65 % Allowed : 24.85 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.29), residues: 918 helix: 1.65 (0.29), residues: 342 sheet: -1.69 (0.41), residues: 132 loop : 0.47 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 177 TYR 0.017 0.001 TYR A 69 PHE 0.007 0.001 PHE B 284 TRP 0.006 0.001 TRP B 303 HIS 0.004 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 7827) covalent geometry : angle 0.48362 (10642) SS BOND : bond 0.00164 ( 14) SS BOND : angle 0.75996 ( 28) hydrogen bonds : bond 0.03483 ( 285) hydrogen bonds : angle 4.25045 ( 789) glycosidic custom : bond 0.00340 ( 1) glycosidic custom : angle 3.61075 ( 3) link_NAG-ASN : bond 0.00294 ( 15) link_NAG-ASN : angle 1.84581 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.319 Fit side-chains REVERT: B 115 MET cc_start: 0.7627 (ttm) cc_final: 0.7229 (tmm) REVERT: B 258 ASP cc_start: 0.8604 (t0) cc_final: 0.8263 (t0) REVERT: A 198 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8554 (mtm) outliers start: 30 outliers final: 11 residues processed: 97 average time/residue: 0.0676 time to fit residues: 9.8673 Evaluate side-chains 82 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 80 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.101587 restraints weight = 12371.518| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.99 r_work: 0.3149 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7857 Z= 0.128 Angle : 0.485 9.360 10718 Z= 0.239 Chirality : 0.043 0.253 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.614 56.883 1373 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 4.14 % Allowed : 24.48 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.29), residues: 918 helix: 1.71 (0.29), residues: 342 sheet: -1.67 (0.40), residues: 132 loop : 0.45 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.015 0.001 TYR B 394 PHE 0.008 0.001 PHE B 226 TRP 0.006 0.001 TRP B 208 HIS 0.003 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7827) covalent geometry : angle 0.47018 (10642) SS BOND : bond 0.00161 ( 14) SS BOND : angle 0.76286 ( 28) hydrogen bonds : bond 0.03418 ( 285) hydrogen bonds : angle 4.02721 ( 789) glycosidic custom : bond 0.00139 ( 1) glycosidic custom : angle 0.70350 ( 3) link_NAG-ASN : bond 0.00268 ( 15) link_NAG-ASN : angle 1.80436 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 75 time to evaluate : 0.301 Fit side-chains REVERT: B 115 MET cc_start: 0.7661 (ttm) cc_final: 0.7299 (tmm) REVERT: B 258 ASP cc_start: 0.8573 (t0) cc_final: 0.8242 (t0) REVERT: A 55 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7084 (pm20) REVERT: A 365 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6927 (t0) outliers start: 34 outliers final: 17 residues processed: 103 average time/residue: 0.0630 time to fit residues: 9.9707 Evaluate side-chains 88 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 434 HIS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 41 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3609 r_free = 0.3609 target = 0.124672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.103535 restraints weight = 12492.662| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.03 r_work: 0.3169 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7857 Z= 0.096 Angle : 0.469 9.248 10718 Z= 0.230 Chirality : 0.043 0.258 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.280 55.398 1370 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.80 % Allowed : 25.70 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.29), residues: 918 helix: 1.82 (0.29), residues: 342 sheet: -1.59 (0.40), residues: 132 loop : 0.47 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 177 TYR 0.019 0.001 TYR A 69 PHE 0.006 0.001 PHE B 284 TRP 0.006 0.001 TRP B 208 HIS 0.004 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 7827) covalent geometry : angle 0.45702 (10642) SS BOND : bond 0.00131 ( 14) SS BOND : angle 0.59120 ( 28) hydrogen bonds : bond 0.02986 ( 285) hydrogen bonds : angle 3.79865 ( 789) glycosidic custom : bond 0.00086 ( 1) glycosidic custom : angle 0.54422 ( 3) link_NAG-ASN : bond 0.00305 ( 15) link_NAG-ASN : angle 1.69312 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.299 Fit side-chains REVERT: B 115 MET cc_start: 0.7559 (ttm) cc_final: 0.7216 (tmm) REVERT: B 258 ASP cc_start: 0.8585 (t0) cc_final: 0.8211 (t0) REVERT: B 458 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8299 (pt) REVERT: A 55 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7040 (pm20) REVERT: A 365 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6948 (t0) REVERT: A 439 ASP cc_start: 0.7878 (m-30) cc_final: 0.7663 (m-30) outliers start: 23 outliers final: 12 residues processed: 94 average time/residue: 0.0729 time to fit residues: 10.3861 Evaluate side-chains 84 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3534 r_free = 0.3534 target = 0.118731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097689 restraints weight = 12601.969| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.89 r_work: 0.3106 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 7857 Z= 0.231 Angle : 0.572 9.071 10718 Z= 0.283 Chirality : 0.045 0.245 1240 Planarity : 0.003 0.035 1338 Dihedral : 6.749 59.998 1367 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.26 % Allowed : 25.09 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.29), residues: 918 helix: 1.54 (0.29), residues: 342 sheet: -1.62 (0.40), residues: 132 loop : 0.33 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 177 TYR 0.018 0.002 TYR A 389 PHE 0.013 0.001 PHE B 226 TRP 0.007 0.001 TRP A 205 HIS 0.003 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00553 ( 7827) covalent geometry : angle 0.55705 (10642) SS BOND : bond 0.00496 ( 14) SS BOND : angle 0.69403 ( 28) hydrogen bonds : bond 0.03876 ( 285) hydrogen bonds : angle 4.06600 ( 789) glycosidic custom : bond 0.00016 ( 1) glycosidic custom : angle 0.68404 ( 3) link_NAG-ASN : bond 0.00221 ( 15) link_NAG-ASN : angle 2.04213 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 115 MET cc_start: 0.7711 (ttm) cc_final: 0.7307 (tmm) REVERT: B 258 ASP cc_start: 0.8623 (t0) cc_final: 0.8287 (t0) REVERT: B 291 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7086 (mtp180) REVERT: A 55 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: A 365 ASN cc_start: 0.7244 (OUTLIER) cc_final: 0.6979 (t0) outliers start: 35 outliers final: 21 residues processed: 95 average time/residue: 0.0892 time to fit residues: 12.1609 Evaluate side-chains 91 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 236 CYS Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 103 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 72 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 74 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 86 optimal weight: 0.2980 chunk 3 optimal weight: 4.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- 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 = 0.3564 r_free = 0.3564 target = 0.120941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099867 restraints weight = 12564.218| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.95 r_work: 0.3133 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7857 Z= 0.136 Angle : 0.502 9.383 10718 Z= 0.247 Chirality : 0.043 0.251 1240 Planarity : 0.003 0.034 1338 Dihedral : 6.439 57.561 1365 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.92 % Allowed : 26.19 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.28), residues: 918 helix: 1.60 (0.28), residues: 342 sheet: -1.60 (0.40), residues: 132 loop : 0.33 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 177 TYR 0.022 0.001 TYR A 69 PHE 0.008 0.001 PHE B 226 TRP 0.007 0.001 TRP B 303 HIS 0.003 0.001 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 7827) covalent geometry : angle 0.48717 (10642) SS BOND : bond 0.00219 ( 14) SS BOND : angle 0.57479 ( 28) hydrogen bonds : bond 0.03292 ( 285) hydrogen bonds : angle 3.86838 ( 789) glycosidic custom : bond 0.00046 ( 1) glycosidic custom : angle 0.50981 ( 3) link_NAG-ASN : bond 0.00264 ( 15) link_NAG-ASN : angle 1.92093 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.305 Fit side-chains REVERT: B 115 MET cc_start: 0.7685 (ttm) cc_final: 0.7225 (tmm) REVERT: B 258 ASP cc_start: 0.8610 (t0) cc_final: 0.8244 (t0) REVERT: A 55 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6957 (pm20) REVERT: A 365 ASN cc_start: 0.7199 (OUTLIER) cc_final: 0.6962 (t0) outliers start: 24 outliers final: 15 residues processed: 95 average time/residue: 0.0704 time to fit residues: 10.0954 Evaluate side-chains 86 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.121457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100379 restraints weight = 12402.523| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.94 r_work: 0.3143 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7857 Z= 0.117 Angle : 0.490 9.389 10718 Z= 0.239 Chirality : 0.043 0.256 1240 Planarity : 0.003 0.034 1338 Dihedral : 6.335 56.625 1365 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.92 % Allowed : 26.19 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.29), residues: 918 helix: 1.71 (0.29), residues: 342 sheet: -1.27 (0.39), residues: 142 loop : 0.33 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 177 TYR 0.015 0.001 TYR B 394 PHE 0.008 0.001 PHE B 226 TRP 0.007 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 7827) covalent geometry : angle 0.47612 (10642) SS BOND : bond 0.00198 ( 14) SS BOND : angle 0.52379 ( 28) hydrogen bonds : bond 0.03145 ( 285) hydrogen bonds : angle 3.77334 ( 789) glycosidic custom : bond 0.00060 ( 1) glycosidic custom : angle 0.49590 ( 3) link_NAG-ASN : bond 0.00272 ( 15) link_NAG-ASN : angle 1.82119 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.346 Fit side-chains REVERT: B 115 MET cc_start: 0.7613 (ttm) cc_final: 0.7184 (tmm) REVERT: B 258 ASP cc_start: 0.8587 (t0) cc_final: 0.8254 (t0) REVERT: A 55 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.6927 (pm20) REVERT: A 254 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7712 (mtp85) REVERT: A 365 ASN cc_start: 0.7191 (OUTLIER) cc_final: 0.6974 (t0) outliers start: 24 outliers final: 17 residues processed: 95 average time/residue: 0.0798 time to fit residues: 11.0110 Evaluate side-chains 88 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 69 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 58 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100603 restraints weight = 12488.027| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.96 r_work: 0.3146 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7857 Z= 0.118 Angle : 0.491 9.394 10718 Z= 0.240 Chirality : 0.043 0.258 1240 Planarity : 0.003 0.034 1338 Dihedral : 6.296 56.217 1365 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.29 % Allowed : 26.07 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.29), residues: 918 helix: 1.72 (0.29), residues: 342 sheet: -1.25 (0.39), residues: 142 loop : 0.32 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 254 TYR 0.023 0.001 TYR A 69 PHE 0.008 0.001 PHE B 226 TRP 0.007 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7827) covalent geometry : angle 0.47802 (10642) SS BOND : bond 0.00210 ( 14) SS BOND : angle 0.52874 ( 28) hydrogen bonds : bond 0.03131 ( 285) hydrogen bonds : angle 3.75736 ( 789) glycosidic custom : bond 0.00046 ( 1) glycosidic custom : angle 0.47673 ( 3) link_NAG-ASN : bond 0.00274 ( 15) link_NAG-ASN : angle 1.79694 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.301 Fit side-chains REVERT: B 115 MET cc_start: 0.7583 (ttm) cc_final: 0.7156 (tmm) REVERT: B 258 ASP cc_start: 0.8600 (t0) cc_final: 0.8247 (t0) REVERT: B 291 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7137 (mtp-110) REVERT: B 498 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8398 (ttp80) REVERT: A 55 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6885 (pm20) REVERT: A 198 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8238 (mtm) REVERT: A 365 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6945 (t0) outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 0.0847 time to fit residues: 11.3303 Evaluate side-chains 92 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 68 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 89 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.122105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.100984 restraints weight = 12379.662| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.95 r_work: 0.3152 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7857 Z= 0.111 Angle : 0.487 9.402 10718 Z= 0.238 Chirality : 0.043 0.259 1240 Planarity : 0.003 0.034 1338 Dihedral : 6.255 56.025 1365 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.56 % Allowed : 26.80 % Favored : 70.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.81 (0.28), residues: 918 helix: 1.74 (0.28), residues: 342 sheet: -1.22 (0.39), residues: 142 loop : 0.32 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 254 TYR 0.015 0.001 TYR B 394 PHE 0.007 0.001 PHE B 226 TRP 0.007 0.001 TRP B 208 HIS 0.003 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7827) covalent geometry : angle 0.47506 (10642) SS BOND : bond 0.00186 ( 14) SS BOND : angle 0.51243 ( 28) hydrogen bonds : bond 0.03048 ( 285) hydrogen bonds : angle 3.71368 ( 789) glycosidic custom : bond 0.00065 ( 1) glycosidic custom : angle 0.50677 ( 3) link_NAG-ASN : bond 0.00278 ( 15) link_NAG-ASN : angle 1.74644 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.303 Fit side-chains REVERT: B 115 MET cc_start: 0.7627 (ttm) cc_final: 0.7247 (tmm) REVERT: B 258 ASP cc_start: 0.8587 (t0) cc_final: 0.8205 (t0) REVERT: B 291 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7125 (mtp-110) REVERT: B 498 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8422 (ttp80) REVERT: A 55 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.6939 (pm20) REVERT: A 198 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.8254 (mtm) outliers start: 21 outliers final: 16 residues processed: 91 average time/residue: 0.0968 time to fit residues: 12.2058 Evaluate side-chains 89 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.102552 restraints weight = 12375.764| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.94 r_work: 0.3179 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7857 Z= 0.093 Angle : 0.474 9.451 10718 Z= 0.231 Chirality : 0.042 0.266 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.125 54.699 1364 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.31 % Allowed : 27.28 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.29), residues: 918 helix: 1.78 (0.28), residues: 343 sheet: -1.16 (0.39), residues: 142 loop : 0.38 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 256 TYR 0.026 0.001 TYR A 69 PHE 0.006 0.001 PHE A 236 TRP 0.009 0.001 TRP B 208 HIS 0.003 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7827) covalent geometry : angle 0.46241 (10642) SS BOND : bond 0.00146 ( 14) SS BOND : angle 0.45399 ( 28) hydrogen bonds : bond 0.02832 ( 285) hydrogen bonds : angle 3.63083 ( 789) glycosidic custom : bond 0.00055 ( 1) glycosidic custom : angle 0.52651 ( 3) link_NAG-ASN : bond 0.00313 ( 15) link_NAG-ASN : angle 1.68966 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1836 Ramachandran restraints generated. 918 Oldfield, 0 Emsley, 918 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.311 Fit side-chains REVERT: B 115 MET cc_start: 0.7490 (ttm) cc_final: 0.7079 (tmm) REVERT: B 258 ASP cc_start: 0.8583 (t0) cc_final: 0.8130 (t0) REVERT: B 291 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7252 (mtp-110) REVERT: B 498 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8415 (ttp80) REVERT: A 55 GLN cc_start: 0.7639 (OUTLIER) cc_final: 0.6919 (pm20) REVERT: A 113 TYR cc_start: 0.9000 (t80) cc_final: 0.8720 (t80) REVERT: A 198 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8195 (mtm) REVERT: A 439 ASP cc_start: 0.7837 (m-30) cc_final: 0.7558 (m-30) outliers start: 19 outliers final: 14 residues processed: 95 average time/residue: 0.0847 time to fit residues: 11.4095 Evaluate side-chains 91 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 291 ARG Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 498 ARG Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 390 SER Chi-restraints excluded: chain A residue 405 CYS Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 60 optimal weight: 0.0270 chunk 25 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 = 0.3599 r_free = 0.3599 target = 0.123380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.102395 restraints weight = 12366.487| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.95 r_work: 0.3175 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7857 Z= 0.102 Angle : 0.483 9.405 10718 Z= 0.236 Chirality : 0.042 0.265 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.144 55.202 1364 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.68 % Allowed : 27.16 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.29), residues: 918 helix: 1.80 (0.28), residues: 343 sheet: -1.18 (0.39), residues: 147 loop : 0.39 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 256 TYR 0.014 0.001 TYR B 394 PHE 0.012 0.001 PHE B 160 TRP 0.007 0.001 TRP B 208 HIS 0.003 0.000 HIS A 400 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 7827) covalent geometry : angle 0.47161 (10642) SS BOND : bond 0.00168 ( 14) SS BOND : angle 0.47496 ( 28) hydrogen bonds : bond 0.02917 ( 285) hydrogen bonds : angle 3.63946 ( 789) glycosidic custom : bond 0.00064 ( 1) glycosidic custom : angle 0.48926 ( 3) link_NAG-ASN : bond 0.00294 ( 15) link_NAG-ASN : angle 1.68079 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.55 seconds wall clock time: 32 minutes 17.18 seconds (1937.18 seconds total)