Starting phenix.real_space_refine on Fri Jun 6 11:22:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nov_49618/06_2025/9nov_49618.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nov_49618/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9nov_49618/06_2025/9nov_49618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nov_49618/06_2025/9nov_49618.map" model { file = "/net/cci-nas-00/data/ceres_data/9nov_49618/06_2025/9nov_49618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nov_49618/06_2025/9nov_49618.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.07, per 1000 atoms: 0.79 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: 1.89 Conformation dependent library (CDL) restraints added in 975.8 milliseconds 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: 0.91 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: 2.25 Time building geometry restraints manager: 2.19 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: 8.890 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.100 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- 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 (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: 0.57 (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 TRP 0.007 0.001 TRP B 461 HIS 0.003 0.001 HIS A 400 PHE 0.011 0.001 PHE B 226 TYR 0.028 0.002 TYR A 69 ARG 0.002 0.000 ARG A 182 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 15) link_NAG-ASN : angle 1.87007 ( 45) hydrogen bonds : bond 0.17670 ( 285) hydrogen bonds : angle 6.16765 ( 789) SS BOND : bond 0.00217 ( 14) SS BOND : angle 0.98651 ( 28) glycosidic custom : bond 0.05120 ( 1) glycosidic custom : angle 3.37562 ( 3) covalent geometry : bond 0.00475 ( 7827) covalent geometry : angle 0.55837 (10642) *********************** 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 : 0.801 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: 0.1674 time to fit residues: 20.9927 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 : 0.866 ------------------------------------------------------------------------------- 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 77 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100572 restraints weight = 12367.832| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.86 r_work: 0.3170 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7857 Z= 0.140 Angle : 0.519 9.371 10718 Z= 0.254 Chirality : 0.043 0.251 1240 Planarity : 0.003 0.035 1338 Dihedral : 7.793 65.466 1400 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.65 % Allowed : 24.97 % 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 (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: 0.69 (0.29), residues: 918 helix: 1.57 (0.29), residues: 341 sheet: -1.73 (0.41), residues: 132 loop : 0.45 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.004 0.001 HIS A 400 PHE 0.008 0.001 PHE B 226 TYR 0.016 0.001 TYR A 69 ARG 0.002 0.000 ARG B 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 15) link_NAG-ASN : angle 1.92534 ( 45) hydrogen bonds : bond 0.03646 ( 285) hydrogen bonds : angle 4.31051 ( 789) SS BOND : bond 0.00190 ( 14) SS BOND : angle 0.82605 ( 28) glycosidic custom : bond 0.00473 ( 1) glycosidic custom : angle 3.71377 ( 3) covalent geometry : bond 0.00331 ( 7827) covalent geometry : angle 0.49960 (10642) *********************** 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 : 0.792 Fit side-chains REVERT: B 115 MET cc_start: 0.7636 (ttm) cc_final: 0.7237 (tmm) REVERT: B 258 ASP cc_start: 0.8602 (t0) cc_final: 0.8255 (t0) REVERT: A 198 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8329 (mtm) REVERT: A 365 ASN cc_start: 0.7168 (OUTLIER) cc_final: 0.6900 (t0) outliers start: 30 outliers final: 12 residues processed: 96 average time/residue: 0.1427 time to fit residues: 20.7014 Evaluate side-chains 84 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 138 VAL Chi-restraints excluded: chain A residue 142 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 365 ASN 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 25 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 89 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 2 optimal weight: 0.0270 chunk 38 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.3601 r_free = 0.3601 target = 0.123639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102450 restraints weight = 12350.637| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.98 r_work: 0.3179 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0928 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 : 0.462 9.488 10718 Z= 0.228 Chirality : 0.042 0.258 1240 Planarity : 0.003 0.032 1338 Dihedral : 6.470 55.040 1373 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.41 % Allowed : 25.09 % 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 (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: 0.87 (0.29), residues: 918 helix: 1.81 (0.29), residues: 342 sheet: -1.70 (0.39), residues: 132 loop : 0.48 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.004 0.000 HIS A 400 PHE 0.006 0.001 PHE A 515 TYR 0.014 0.001 TYR B 394 ARG 0.001 0.000 ARG A 256 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 15) link_NAG-ASN : angle 1.71418 ( 45) hydrogen bonds : bond 0.03124 ( 285) hydrogen bonds : angle 3.92368 ( 789) SS BOND : bond 0.00183 ( 14) SS BOND : angle 0.62921 ( 28) glycosidic custom : bond 0.00113 ( 1) glycosidic custom : angle 0.78668 ( 3) covalent geometry : bond 0.00213 ( 7827) covalent geometry : angle 0.44907 (10642) *********************** 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 105 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.802 Fit side-chains REVERT: B 115 MET cc_start: 0.7573 (ttm) cc_final: 0.7193 (tmm) REVERT: B 258 ASP cc_start: 0.8579 (t0) cc_final: 0.8195 (t0) REVERT: B 458 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8252 (pt) REVERT: A 55 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7040 (pm20) outliers start: 28 outliers final: 9 residues processed: 99 average time/residue: 0.1558 time to fit residues: 23.1172 Evaluate side-chains 80 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 146 SER Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 289 SER 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 142 ASP 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.122289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.101201 restraints weight = 12341.189| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.96 r_work: 0.3164 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7857 Z= 0.121 Angle : 0.485 9.234 10718 Z= 0.237 Chirality : 0.043 0.254 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.336 56.294 1367 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.17 % Allowed : 25.46 % 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 (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: 0.86 (0.29), residues: 918 helix: 1.79 (0.29), residues: 342 sheet: -1.59 (0.40), residues: 132 loop : 0.45 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 PHE 0.008 0.001 PHE B 226 TYR 0.019 0.001 TYR A 69 ARG 0.001 0.000 ARG B 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 15) link_NAG-ASN : angle 1.73358 ( 45) hydrogen bonds : bond 0.03181 ( 285) hydrogen bonds : angle 3.84883 ( 789) SS BOND : bond 0.00163 ( 14) SS BOND : angle 0.67051 ( 28) glycosidic custom : bond 0.00065 ( 1) glycosidic custom : angle 0.58378 ( 3) covalent geometry : bond 0.00289 ( 7827) covalent geometry : angle 0.47192 (10642) *********************** 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 99 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 1.648 Fit side-chains REVERT: B 115 MET cc_start: 0.7545 (ttm) cc_final: 0.7193 (tmm) REVERT: B 258 ASP cc_start: 0.8592 (t0) cc_final: 0.8220 (t0) REVERT: A 55 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: A 365 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6876 (t0) outliers start: 26 outliers final: 17 residues processed: 94 average time/residue: 0.2474 time to fit residues: 33.3701 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 : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR 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 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 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 Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 33 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.122419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101310 restraints weight = 12262.253| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.96 r_work: 0.3162 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7857 Z= 0.121 Angle : 0.486 9.361 10718 Z= 0.238 Chirality : 0.043 0.255 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.329 56.320 1367 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.65 % Allowed : 25.70 % 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 (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: 0.86 (0.29), residues: 918 helix: 1.78 (0.29), residues: 342 sheet: -1.53 (0.40), residues: 132 loop : 0.44 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 PHE 0.008 0.001 PHE B 226 TYR 0.013 0.001 TYR B 394 ARG 0.001 0.000 ARG B 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 15) link_NAG-ASN : angle 1.74633 ( 45) hydrogen bonds : bond 0.03149 ( 285) hydrogen bonds : angle 3.77626 ( 789) SS BOND : bond 0.00222 ( 14) SS BOND : angle 0.57325 ( 28) glycosidic custom : bond 0.00077 ( 1) glycosidic custom : angle 0.53303 ( 3) covalent geometry : bond 0.00289 ( 7827) covalent geometry : angle 0.47326 (10642) *********************** 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 104 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: B 115 MET cc_start: 0.7590 (ttm) cc_final: 0.7268 (tmm) REVERT: B 258 ASP cc_start: 0.8591 (t0) cc_final: 0.8196 (t0) REVERT: B 291 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7159 (mtp-110) REVERT: A 55 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: A 365 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.7006 (t0) outliers start: 30 outliers final: 20 residues processed: 98 average time/residue: 0.2146 time to fit residues: 31.6800 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 : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 THR 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 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 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 22 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 37 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 46 optimal weight: 0.0030 chunk 91 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- 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 = 0.3597 r_free = 0.3597 target = 0.123437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.102362 restraints weight = 12312.729| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.95 r_work: 0.3162 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1186 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= 0.098 Angle : 0.469 9.419 10718 Z= 0.230 Chirality : 0.042 0.258 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.235 55.249 1367 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.92 % Allowed : 26.07 % Favored : 71.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.29), residues: 918 helix: 1.96 (0.29), residues: 336 sheet: -1.16 (0.39), residues: 145 loop : 0.46 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 PHE 0.006 0.001 PHE B 226 TYR 0.022 0.001 TYR A 69 ARG 0.001 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 15) link_NAG-ASN : angle 1.67327 ( 45) hydrogen bonds : bond 0.02932 ( 285) hydrogen bonds : angle 3.69065 ( 789) SS BOND : bond 0.00172 ( 14) SS BOND : angle 0.43066 ( 28) glycosidic custom : bond 0.00066 ( 1) glycosidic custom : angle 0.50079 ( 3) covalent geometry : bond 0.00229 ( 7827) covalent geometry : angle 0.45736 (10642) *********************** 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 101 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.876 Fit side-chains REVERT: B 115 MET cc_start: 0.7565 (ttm) cc_final: 0.7163 (tmm) REVERT: B 258 ASP cc_start: 0.8597 (t0) cc_final: 0.8126 (t0) REVERT: B 458 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8116 (pt) REVERT: A 55 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7008 (pm20) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.1510 time to fit residues: 22.0044 Evaluate side-chains 89 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 280 THR Chi-restraints excluded: chain A residue 390 SER 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 510 ILE Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 1 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 31 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 60 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.123198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101832 restraints weight = 12326.992| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.98 r_work: 0.3170 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7857 Z= 0.104 Angle : 0.476 9.351 10718 Z= 0.233 Chirality : 0.043 0.258 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.215 55.512 1366 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.78 % Allowed : 25.94 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 918 helix: 1.83 (0.29), residues: 342 sheet: -1.14 (0.39), residues: 142 loop : 0.41 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 PHE 0.007 0.001 PHE B 226 TYR 0.014 0.001 TYR B 394 ARG 0.001 0.000 ARG B 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00290 ( 15) link_NAG-ASN : angle 1.66140 ( 45) hydrogen bonds : bond 0.02968 ( 285) hydrogen bonds : angle 3.67692 ( 789) SS BOND : bond 0.00195 ( 14) SS BOND : angle 0.42759 ( 28) glycosidic custom : bond 0.00056 ( 1) glycosidic custom : angle 0.47578 ( 3) covalent geometry : bond 0.00246 ( 7827) covalent geometry : angle 0.46465 (10642) *********************** 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 105 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 74 time to evaluate : 0.797 Fit side-chains revert: symmetry clash REVERT: B 115 MET cc_start: 0.7565 (ttm) cc_final: 0.7205 (tmm) REVERT: B 258 ASP cc_start: 0.8585 (t0) cc_final: 0.8170 (t0) REVERT: A 55 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7048 (pm20) REVERT: A 365 ASN cc_start: 0.7207 (OUTLIER) cc_final: 0.6996 (t0) outliers start: 31 outliers final: 20 residues processed: 99 average time/residue: 0.1411 time to fit residues: 21.0681 Evaluate side-chains 91 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 125 ILE 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 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 142 ASP 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 1 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.0670 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.124199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.103175 restraints weight = 12391.053| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 2.95 r_work: 0.3190 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7857 Z= 0.093 Angle : 0.476 9.371 10718 Z= 0.233 Chirality : 0.042 0.261 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.152 54.800 1366 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.29 % Allowed : 26.43 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 918 helix: 1.85 (0.28), residues: 342 sheet: -1.36 (0.40), residues: 132 loop : 0.44 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.003 0.000 HIS A 400 PHE 0.006 0.001 PHE A 236 TYR 0.024 0.001 TYR A 69 ARG 0.001 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00304 ( 15) link_NAG-ASN : angle 1.61689 ( 45) hydrogen bonds : bond 0.02848 ( 285) hydrogen bonds : angle 3.64533 ( 789) SS BOND : bond 0.00157 ( 14) SS BOND : angle 0.40343 ( 28) glycosidic custom : bond 0.00056 ( 1) glycosidic custom : angle 0.47417 ( 3) covalent geometry : bond 0.00219 ( 7827) covalent geometry : angle 0.46501 (10642) *********************** 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 103 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.830 Fit side-chains REVERT: B 115 MET cc_start: 0.7477 (ttm) cc_final: 0.7076 (tmm) REVERT: B 191 ARG cc_start: 0.7247 (OUTLIER) cc_final: 0.6283 (ttp80) REVERT: B 258 ASP cc_start: 0.8562 (t0) cc_final: 0.8105 (t0) REVERT: B 291 ARG cc_start: 0.8091 (OUTLIER) cc_final: 0.7210 (mtp-110) REVERT: A 55 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.6963 (pm20) outliers start: 27 outliers final: 20 residues processed: 96 average time/residue: 0.1824 time to fit residues: 24.8293 Evaluate side-chains 94 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 191 ARG 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 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 280 THR Chi-restraints excluded: chain A residue 390 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 70 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3584 r_free = 0.3584 target = 0.122487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101045 restraints weight = 12622.442| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.02 r_work: 0.3154 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7857 Z= 0.124 Angle : 0.496 9.327 10718 Z= 0.244 Chirality : 0.043 0.253 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.268 56.161 1366 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.17 % Allowed : 26.43 % 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 (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: 0.87 (0.29), residues: 918 helix: 1.75 (0.28), residues: 343 sheet: -1.39 (0.40), residues: 137 loop : 0.46 (0.32), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 PHE 0.011 0.001 PHE B 160 TYR 0.015 0.001 TYR B 394 ARG 0.001 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00264 ( 15) link_NAG-ASN : angle 1.69375 ( 45) hydrogen bonds : bond 0.03127 ( 285) hydrogen bonds : angle 3.71593 ( 789) SS BOND : bond 0.00232 ( 14) SS BOND : angle 0.48519 ( 28) glycosidic custom : bond 0.00049 ( 1) glycosidic custom : angle 0.42526 ( 3) covalent geometry : bond 0.00296 ( 7827) covalent geometry : angle 0.48438 (10642) *********************** 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 98 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.876 Fit side-chains REVERT: B 115 MET cc_start: 0.7592 (ttm) cc_final: 0.7215 (tmm) REVERT: B 191 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6377 (ttp80) REVERT: B 258 ASP cc_start: 0.8572 (t0) cc_final: 0.8153 (t0) REVERT: B 291 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7213 (mtp-110) REVERT: A 55 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7060 (pm20) REVERT: A 365 ASN cc_start: 0.7217 (OUTLIER) cc_final: 0.7010 (t0) outliers start: 26 outliers final: 21 residues processed: 93 average time/residue: 0.1864 time to fit residues: 24.8761 Evaluate side-chains 97 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 191 ARG 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 449 ASN 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 183 THR Chi-restraints excluded: chain A residue 280 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 22 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3594 r_free = 0.3594 target = 0.123213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.102286 restraints weight = 12400.678| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.89 r_work: 0.3171 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1324 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= 0.108 Angle : 0.485 9.391 10718 Z= 0.238 Chirality : 0.043 0.256 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.227 55.668 1366 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.05 % Allowed : 26.67 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 918 helix: 1.75 (0.28), residues: 343 sheet: -1.30 (0.41), residues: 132 loop : 0.44 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 208 HIS 0.003 0.000 HIS A 400 PHE 0.012 0.001 PHE B 160 TYR 0.025 0.001 TYR A 69 ARG 0.001 0.000 ARG A 254 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 15) link_NAG-ASN : angle 1.68106 ( 45) hydrogen bonds : bond 0.03016 ( 285) hydrogen bonds : angle 3.67619 ( 789) SS BOND : bond 0.00194 ( 14) SS BOND : angle 0.45944 ( 28) glycosidic custom : bond 0.00048 ( 1) glycosidic custom : angle 0.45210 ( 3) covalent geometry : bond 0.00256 ( 7827) covalent geometry : angle 0.47329 (10642) ********************** 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 99 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.860 Fit side-chains REVERT: B 115 MET cc_start: 0.7517 (ttm) cc_final: 0.7109 (tmm) REVERT: B 191 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6296 (ttp80) REVERT: B 258 ASP cc_start: 0.8569 (t0) cc_final: 0.8133 (t0) REVERT: B 291 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7261 (mtp-110) REVERT: A 55 GLN cc_start: 0.7691 (OUTLIER) cc_final: 0.6984 (pm20) outliers start: 25 outliers final: 20 residues processed: 94 average time/residue: 0.1816 time to fit residues: 24.2479 Evaluate side-chains 95 residues out of total 821 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 63 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 191 ARG 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 449 ASN 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 280 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 0.4980 chunk 18 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3590 r_free = 0.3590 target = 0.122828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.101731 restraints weight = 12447.347| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.91 r_work: 0.3168 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7857 Z= 0.115 Angle : 0.487 9.372 10718 Z= 0.240 Chirality : 0.043 0.255 1240 Planarity : 0.003 0.033 1338 Dihedral : 6.247 55.970 1366 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.41 % Allowed : 26.43 % 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 (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: 0.89 (0.29), residues: 918 helix: 1.74 (0.28), residues: 343 sheet: -1.30 (0.41), residues: 132 loop : 0.44 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 303 HIS 0.003 0.000 HIS A 400 PHE 0.012 0.001 PHE B 160 TYR 0.014 0.001 TYR B 394 ARG 0.001 0.000 ARG B 177 Details of bonding type rmsd link_NAG-ASN : bond 0.00270 ( 15) link_NAG-ASN : angle 1.68564 ( 45) hydrogen bonds : bond 0.03073 ( 285) hydrogen bonds : angle 3.68344 ( 789) SS BOND : bond 0.00208 ( 14) SS BOND : angle 0.48404 ( 28) glycosidic custom : bond 0.00048 ( 1) glycosidic custom : angle 0.43471 ( 3) covalent geometry : bond 0.00274 ( 7827) covalent geometry : angle 0.47562 (10642) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4180.51 seconds wall clock time: 74 minutes 42.65 seconds (4482.65 seconds total)