Starting phenix.real_space_refine on Sun May 11 02:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dak_46691/05_2025/9dak_46691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dak_46691/05_2025/9dak_46691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dak_46691/05_2025/9dak_46691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dak_46691/05_2025/9dak_46691.map" model { file = "/net/cci-nas-00/data/ceres_data/9dak_46691/05_2025/9dak_46691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dak_46691/05_2025/9dak_46691.cif" } resolution = 2.4 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= 0.001 sd= 0.047 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 Zn 1 6.06 5 S 39 5.16 5 C 4589 2.51 5 N 1204 2.21 5 O 1470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 7303 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 707, 5544 Classifications: {'peptide': 707} Incomplete info: {'truncation_to_alanine': 94} Link IDs: {'PTRANS': 28, 'TRANS': 678} Unresolved non-hydrogen bonds: 271 Unresolved non-hydrogen angles: 329 Unresolved non-hydrogen dihedrals: 213 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 21, 'ASN:plan1': 5, 'ARG:plan': 2, 'ASP:plan': 16} Unresolved non-hydrogen planarities: 173 Chain: "B" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1320 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 176} Chain breaks: 2 Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 87 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 5.47, per 1000 atoms: 0.75 Number of scatterers: 7303 At special positions: 0 Unit cell: (117.129, 99.1089, 105.115, 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) Zn 1 29.99 S 39 16.00 O 1470 8.00 N 1204 7.00 C 4589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.10 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS B 426 " - pdb=" SG CYS B 479 " distance=2.15 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 534 " distance=2.28 Simple disulfide: pdb=" SG CYS B 507 " - pdb=" SG CYS B 516 " distance=2.09 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 BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " NAG-ASN " NAG A 901 " - " ASN A 91 " " NAG A 902 " - " ASN A 322 " " NAG A 903 " - " ASN A 329 " " NAG B 701 " - " ASN B 546 " " NAG C 1 " - " ASN A 104 " " NAG D 1 " - " ASN A 216 " " NAG E 1 " - " ASN A 280 " " NAG F 1 " - " ASN A 534 " " NAG G 1 " - " ASN A 546 " " NAG H 1 " - " ASN A 689 " " NAG I 1 " - " ASN B 497 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 894.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 374 " 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1704 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 59.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 21 through 53 Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 91 through 102 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.509A pdb=" N SER A 107 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.898A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.706A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 326 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.504A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.647A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.725A pdb=" N ASN A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.820A pdb=" N MET A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.744A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'A' and resid 623 through 628 Processing helix chain 'A' and resid 629 through 631 No H-bonds generated for 'chain 'A' and resid 629 through 631' Processing helix chain 'A' and resid 635 through 658 Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 695 through 706 Processing helix chain 'A' and resid 706 through 714 removed outlier: 3.590A pdb=" N PHE A 714 " --> pdb=" O ILE A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 400 removed outlier: 4.144A pdb=" N PHE B 400 " --> pdb=" O PRO B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 416 Processing helix chain 'B' and resid 430 through 436 Processing helix chain 'B' and resid 450 through 458 removed outlier: 5.111A pdb=" N SER B 455 " --> pdb=" O ALA B 452 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU B 458 " --> pdb=" O SER B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 469 Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 531 through 543 removed outlier: 3.816A pdb=" N ILE B 537 " --> pdb=" O SER B 533 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 134 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.089A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.113A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 669 through 672 removed outlier: 12.858A pdb=" N PHE A 682 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 11.073A pdb=" N ILE A 693 " --> pdb=" O PHE A 682 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N VAL A 684 " --> pdb=" O SER A 691 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N SER A 691 " --> pdb=" O VAL A 684 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 669 through 672 Processing sheet with id=AA6, first strand: chain 'B' and resid 401 through 403 removed outlier: 6.887A pdb=" N TYR B 484 " --> pdb=" O VAL B 421 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N VAL B 421 " --> pdb=" O TYR B 484 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 515 through 521 removed outlier: 10.761A pdb=" N GLU B 518 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 11.427A pdb=" N VAL B 508 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N PHE B 520 " --> pdb=" O GLY B 506 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N THR B 499 " --> pdb=" O LYS B 574 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS B 574 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU B 501 " --> pdb=" O GLN B 572 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N GLN B 572 " --> pdb=" O LEU B 501 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1092 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: 2.15 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1279 1.32 - 1.45: 2003 1.45 - 1.58: 3999 1.58 - 1.71: 2 1.71 - 1.84: 64 Bond restraints: 7347 Sorted by residual: bond pdb=" CB LEU B 517 " pdb=" CG LEU B 517 " ideal model delta sigma weight residual 1.530 1.614 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C CYS B 507 " pdb=" O CYS B 507 " ideal model delta sigma weight residual 1.234 1.192 0.042 1.18e-02 7.18e+03 1.26e+01 bond pdb=" C5 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.413 1.475 -0.062 2.00e-02 2.50e+03 9.51e+00 bond pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sigma weight residual 1.417 1.476 -0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" C5 NAG C 1 " pdb=" O5 NAG C 1 " ideal model delta sigma weight residual 1.413 1.472 -0.059 2.00e-02 2.50e+03 8.63e+00 ... (remaining 7342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.38: 9889 4.38 - 8.76: 116 8.76 - 13.14: 0 13.14 - 17.52: 0 17.52 - 21.90: 1 Bond angle restraints: 10006 Sorted by residual: angle pdb=" CD1 LEU B 517 " pdb=" CG LEU B 517 " pdb=" CD2 LEU B 517 " ideal model delta sigma weight residual 110.80 132.70 -21.90 2.20e+00 2.07e-01 9.91e+01 angle pdb=" C ASN A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 119.56 127.51 -7.95 1.02e+00 9.61e-01 6.08e+01 angle pdb=" C SER A 257 " pdb=" N PRO A 258 " pdb=" CA PRO A 258 " ideal model delta sigma weight residual 119.56 127.20 -7.64 1.02e+00 9.61e-01 5.61e+01 angle pdb=" C GLY B 392 " pdb=" N PRO B 393 " pdb=" CA PRO B 393 " ideal model delta sigma weight residual 119.78 127.44 -7.66 1.03e+00 9.43e-01 5.53e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 127.26 -7.50 1.03e+00 9.43e-01 5.31e+01 ... (remaining 10001 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.55: 4434 21.55 - 43.10: 124 43.10 - 64.65: 25 64.65 - 86.20: 20 86.20 - 107.75: 8 Dihedral angle restraints: 4611 sinusoidal: 1972 harmonic: 2639 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual -86.00 -117.36 31.36 1 1.00e+01 1.00e-02 1.40e+01 dihedral pdb=" O4 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual -71.29 -179.04 107.75 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C3 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C5 BMA G 3 " pdb=" O5 BMA G 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.30 105.92 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 4608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 1056 0.150 - 0.300: 76 0.300 - 0.450: 10 0.450 - 0.600: 0 0.600 - 0.750: 2 Chirality restraints: 1144 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-02 2.50e+03 1.41e+03 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.30e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.06e+02 ... (remaining 1141 not shown) Planarity restraints: 1269 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 322 " 0.036 2.00e-02 2.50e+03 3.83e-02 1.83e+01 pdb=" CG ASN A 322 " -0.017 2.00e-02 2.50e+03 pdb=" OD1 ASN A 322 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 322 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG A 902 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 321 " -0.016 2.00e-02 2.50e+03 3.13e-02 9.81e+00 pdb=" C HIS A 321 " 0.054 2.00e-02 2.50e+03 pdb=" O HIS A 321 " -0.020 2.00e-02 2.50e+03 pdb=" N ASN A 322 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 497 " 0.033 2.00e-02 2.50e+03 1.74e-02 6.08e+00 pdb=" CG TYR A 497 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR A 497 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 497 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 497 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A 497 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 497 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 497 " 0.025 2.00e-02 2.50e+03 ... (remaining 1266 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 24 2.53 - 3.12: 5445 3.12 - 3.71: 10881 3.71 - 4.31: 17070 4.31 - 4.90: 26398 Nonbonded interactions: 59818 Sorted by model distance: nonbonded pdb=" OD1 ASP A 350 " pdb=" O HOH A1001 " model vdw 1.935 3.040 nonbonded pdb=" O PHE B 523 " pdb=" O HOH B 801 " model vdw 2.098 3.040 nonbonded pdb=" O ASP A 269 " pdb=" O HOH A1002 " model vdw 2.114 3.040 nonbonded pdb=" O ASP A 608 " pdb=" O HOH A1003 " model vdw 2.120 3.040 nonbonded pdb=" O ASN A 397 " pdb=" O HOH A1004 " model vdw 2.214 3.040 ... (remaining 59813 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 1 through 2) selection = (chain 'F' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.030 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.014 0.517 7377 Z= 0.688 Angle : 1.291 21.895 10084 Z= 0.820 Chirality : 0.087 0.750 1144 Planarity : 0.005 0.034 1258 Dihedral : 13.166 107.747 2889 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.47 % Allowed : 1.25 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 0.51 (0.26), residues: 891 helix: 0.31 (0.22), residues: 445 sheet: 0.77 (0.55), residues: 83 loop : 0.54 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.013 0.003 PHE B 520 TYR 0.033 0.004 TYR A 497 ARG 0.008 0.000 ARG A 575 Details of bonding type rmsd link_NAG-ASN : bond 0.05386 ( 11) link_NAG-ASN : angle 5.11715 ( 33) link_BETA1-4 : bond 0.05413 ( 9) link_BETA1-4 : angle 5.30054 ( 27) hydrogen bonds : bond 0.22415 ( 386) hydrogen bonds : angle 6.73263 ( 1092) link_BETA1-6 : bond 0.04819 ( 2) link_BETA1-6 : angle 2.44087 ( 6) metal coordination : bond 0.37953 ( 2) SS BOND : bond 0.11921 ( 6) SS BOND : angle 4.68880 ( 12) covalent geometry : bond 0.01124 ( 7347) covalent geometry : angle 1.22000 (10006) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.852 Fit side-chains REVERT: A 270 MET cc_start: 0.8713 (tpp) cc_final: 0.8482 (tpt) REVERT: A 297 MET cc_start: 0.8920 (mtp) cc_final: 0.8720 (mtp) REVERT: A 480 MET cc_start: 0.8842 (mtp) cc_final: 0.8630 (mtp) outliers start: 3 outliers final: 1 residues processed: 127 average time/residue: 1.5226 time to fit residues: 201.9626 Evaluate side-chains 86 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.0470 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN A 64 ASN A 77 HIS A 97 GLN A 159 HIS A 553 GLN B 503 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.137521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.097745 restraints weight = 7467.653| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.49 r_work: 0.2960 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7377 Z= 0.152 Angle : 0.634 14.123 10084 Z= 0.324 Chirality : 0.043 0.196 1144 Planarity : 0.005 0.034 1258 Dihedral : 8.993 70.601 1422 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.19 % Allowed : 6.09 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.99 (0.27), residues: 891 helix: 2.08 (0.24), residues: 436 sheet: 1.09 (0.49), residues: 97 loop : 0.54 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 478 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.002 PHE A 516 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 482 Details of bonding type rmsd link_NAG-ASN : bond 0.00801 ( 11) link_NAG-ASN : angle 3.60101 ( 33) link_BETA1-4 : bond 0.00566 ( 9) link_BETA1-4 : angle 2.08120 ( 27) hydrogen bonds : bond 0.06873 ( 386) hydrogen bonds : angle 4.92648 ( 1092) link_BETA1-6 : bond 0.00510 ( 2) link_BETA1-6 : angle 1.36557 ( 6) metal coordination : bond 0.00911 ( 2) SS BOND : bond 0.00701 ( 6) SS BOND : angle 2.12910 ( 12) covalent geometry : bond 0.00300 ( 7347) covalent geometry : angle 0.58637 (10006) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8445 (tptp) cc_final: 0.8210 (tptp) REVERT: A 233 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 270 MET cc_start: 0.9081 (tpp) cc_final: 0.8802 (tpt) REVERT: A 289 GLN cc_start: 0.7941 (mm-40) cc_final: 0.7558 (mm-40) REVERT: A 323 MET cc_start: 0.8709 (mmp) cc_final: 0.8506 (mmm) REVERT: A 596 LYS cc_start: 0.8361 (tttt) cc_final: 0.8070 (ttpt) REVERT: A 696 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7401 (ttt-90) REVERT: B 558 LEU cc_start: 0.8506 (mp) cc_final: 0.8247 (mp) REVERT: B 570 VAL cc_start: 0.8445 (t) cc_final: 0.8211 (t) outliers start: 14 outliers final: 3 residues processed: 106 average time/residue: 1.3171 time to fit residues: 147.0665 Evaluate side-chains 86 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 696 ARG Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 84 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 159 HIS A 195 ASN A 553 GLN A 711 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.092476 restraints weight = 7478.217| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.50 r_work: 0.2886 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7377 Z= 0.183 Angle : 0.655 13.930 10084 Z= 0.336 Chirality : 0.046 0.265 1144 Planarity : 0.005 0.038 1258 Dihedral : 6.669 59.596 1422 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.03 % Allowed : 7.81 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.80 (0.28), residues: 891 helix: 1.95 (0.24), residues: 454 sheet: 0.87 (0.49), residues: 92 loop : 0.38 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 478 HIS 0.007 0.002 HIS A 241 PHE 0.020 0.002 PHE A 523 TYR 0.019 0.002 TYR A 385 ARG 0.004 0.001 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00692 ( 11) link_NAG-ASN : angle 3.41819 ( 33) link_BETA1-4 : bond 0.00666 ( 9) link_BETA1-4 : angle 2.09614 ( 27) hydrogen bonds : bond 0.07667 ( 386) hydrogen bonds : angle 4.65246 ( 1092) link_BETA1-6 : bond 0.00386 ( 2) link_BETA1-6 : angle 1.33244 ( 6) metal coordination : bond 0.00182 ( 2) SS BOND : bond 0.01164 ( 6) SS BOND : angle 3.47324 ( 12) covalent geometry : bond 0.00412 ( 7347) covalent geometry : angle 0.60486 (10006) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: A 115 LYS cc_start: 0.8548 (tptp) cc_final: 0.8299 (tptp) REVERT: A 233 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 270 MET cc_start: 0.9113 (tpp) cc_final: 0.8847 (tpt) REVERT: A 289 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7604 (mm-40) REVERT: A 596 LYS cc_start: 0.8512 (tttt) cc_final: 0.8248 (ttpt) REVERT: A 696 ARG cc_start: 0.7946 (ttm-80) cc_final: 0.7726 (ttt-90) outliers start: 13 outliers final: 2 residues processed: 97 average time/residue: 1.4509 time to fit residues: 147.6787 Evaluate side-chains 85 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 159 HIS A 195 ASN A 553 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.135501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.093698 restraints weight = 7668.783| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.31 r_work: 0.2943 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7377 Z= 0.143 Angle : 0.675 27.634 10084 Z= 0.338 Chirality : 0.046 0.433 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.835 57.005 1422 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.50 % Allowed : 8.12 % Favored : 89.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.83 (0.28), residues: 891 helix: 2.04 (0.24), residues: 452 sheet: 0.93 (0.52), residues: 84 loop : 0.30 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.014 0.002 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 11) link_NAG-ASN : angle 3.69139 ( 33) link_BETA1-4 : bond 0.00630 ( 9) link_BETA1-4 : angle 1.92896 ( 27) hydrogen bonds : bond 0.06636 ( 386) hydrogen bonds : angle 4.48654 ( 1092) link_BETA1-6 : bond 0.00467 ( 2) link_BETA1-6 : angle 1.26499 ( 6) metal coordination : bond 0.00132 ( 2) SS BOND : bond 0.01435 ( 6) SS BOND : angle 4.65864 ( 12) covalent geometry : bond 0.00299 ( 7347) covalent geometry : angle 0.61454 (10006) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8548 (tptp) cc_final: 0.8300 (tptp) REVERT: A 233 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 270 MET cc_start: 0.9107 (tpp) cc_final: 0.8773 (tpt) REVERT: A 289 GLN cc_start: 0.8126 (mm-40) cc_final: 0.7757 (mm-40) REVERT: A 323 MET cc_start: 0.8953 (mmm) cc_final: 0.8455 (mmp) REVERT: A 596 LYS cc_start: 0.8556 (tttt) cc_final: 0.8293 (ttpt) REVERT: B 529 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7079 (mtt90) REVERT: B 536 ARG cc_start: 0.7443 (tpm170) cc_final: 0.6787 (tpp80) REVERT: B 570 VAL cc_start: 0.8492 (t) cc_final: 0.8275 (t) outliers start: 16 outliers final: 4 residues processed: 101 average time/residue: 1.3082 time to fit residues: 139.0743 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 77 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 99 GLN A 159 HIS A 195 ASN A 553 GLN A 711 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.135936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.093808 restraints weight = 7634.818| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.54 r_work: 0.2956 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7377 Z= 0.135 Angle : 0.662 23.766 10084 Z= 0.330 Chirality : 0.045 0.409 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.578 54.595 1422 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.72 % Allowed : 9.22 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % 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: 1.96 (0.28), residues: 891 helix: 2.14 (0.24), residues: 452 sheet: 0.91 (0.52), residues: 84 loop : 0.39 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.015 0.002 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.002 0.000 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00559 ( 11) link_NAG-ASN : angle 3.75604 ( 33) link_BETA1-4 : bond 0.00527 ( 9) link_BETA1-4 : angle 1.79086 ( 27) hydrogen bonds : bond 0.06331 ( 386) hydrogen bonds : angle 4.37506 ( 1092) link_BETA1-6 : bond 0.00379 ( 2) link_BETA1-6 : angle 1.21122 ( 6) metal coordination : bond 0.00104 ( 2) SS BOND : bond 0.01278 ( 6) SS BOND : angle 4.75115 ( 12) covalent geometry : bond 0.00277 ( 7347) covalent geometry : angle 0.59842 (10006) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 90 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8507 (tptp) cc_final: 0.8194 (tptp) REVERT: A 233 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 270 MET cc_start: 0.9087 (tpp) cc_final: 0.8752 (tpt) REVERT: A 289 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7736 (mm-40) REVERT: A 596 LYS cc_start: 0.8538 (tttt) cc_final: 0.8279 (ttpt) REVERT: A 615 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.7600 (mm-40) REVERT: B 529 ARG cc_start: 0.7580 (ttm170) cc_final: 0.7292 (mtt90) REVERT: B 536 ARG cc_start: 0.7423 (tpm170) cc_final: 0.6797 (tpp80) outliers start: 11 outliers final: 4 residues processed: 98 average time/residue: 1.3181 time to fit residues: 136.0164 Evaluate side-chains 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 0.0020 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 51 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 159 HIS A 195 ASN A 553 GLN A 711 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.137382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095864 restraints weight = 7653.266| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 2.67 r_work: 0.2970 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7377 Z= 0.120 Angle : 0.631 18.153 10084 Z= 0.312 Chirality : 0.044 0.373 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.493 54.167 1422 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.72 % Allowed : 10.16 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.28), residues: 891 helix: 2.24 (0.24), residues: 452 sheet: 0.91 (0.52), residues: 84 loop : 0.46 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.014 0.001 PHE A 516 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00541 ( 11) link_NAG-ASN : angle 3.97246 ( 33) link_BETA1-4 : bond 0.00576 ( 9) link_BETA1-4 : angle 1.67111 ( 27) hydrogen bonds : bond 0.05737 ( 386) hydrogen bonds : angle 4.26097 ( 1092) link_BETA1-6 : bond 0.00385 ( 2) link_BETA1-6 : angle 1.17084 ( 6) metal coordination : bond 0.00080 ( 2) SS BOND : bond 0.00988 ( 6) SS BOND : angle 4.51835 ( 12) covalent geometry : bond 0.00235 ( 7347) covalent geometry : angle 0.56248 (10006) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.751 Fit side-chains REVERT: A 115 LYS cc_start: 0.8442 (tptp) cc_final: 0.8127 (tptp) REVERT: A 233 ILE cc_start: 0.8580 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 270 MET cc_start: 0.9129 (tpp) cc_final: 0.8791 (tpt) REVERT: A 289 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7701 (mm-40) REVERT: A 323 MET cc_start: 0.8886 (mmm) cc_final: 0.8415 (mmp) REVERT: A 596 LYS cc_start: 0.8521 (tttt) cc_final: 0.8256 (ttpt) REVERT: A 615 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.7606 (mm110) REVERT: B 529 ARG cc_start: 0.7584 (ttm170) cc_final: 0.7125 (mtt90) REVERT: B 536 ARG cc_start: 0.7425 (tpm170) cc_final: 0.6785 (tpp80) outliers start: 11 outliers final: 4 residues processed: 99 average time/residue: 1.3621 time to fit residues: 141.8632 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 53 optimal weight: 0.0670 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 ASN A 159 HIS A 195 ASN A 553 GLN B 466 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.137038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094943 restraints weight = 7664.208| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.55 r_work: 0.2971 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7377 Z= 0.126 Angle : 0.633 16.026 10084 Z= 0.310 Chirality : 0.045 0.436 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.503 55.867 1420 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.72 % Allowed : 9.53 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 891 helix: 2.26 (0.24), residues: 452 sheet: 0.93 (0.53), residues: 84 loop : 0.47 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.015 0.002 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00533 ( 11) link_NAG-ASN : angle 4.21713 ( 33) link_BETA1-4 : bond 0.00524 ( 9) link_BETA1-4 : angle 1.67693 ( 27) hydrogen bonds : bond 0.05932 ( 386) hydrogen bonds : angle 4.24695 ( 1092) link_BETA1-6 : bond 0.00382 ( 2) link_BETA1-6 : angle 1.21434 ( 6) metal coordination : bond 0.00091 ( 2) SS BOND : bond 0.00879 ( 6) SS BOND : angle 4.08386 ( 12) covalent geometry : bond 0.00254 ( 7347) covalent geometry : angle 0.56271 (10006) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.964 Fit side-chains REVERT: A 115 LYS cc_start: 0.8538 (tptp) cc_final: 0.8219 (tptp) REVERT: A 154 LYS cc_start: 0.8471 (pttp) cc_final: 0.8075 (ptpt) REVERT: A 233 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 270 MET cc_start: 0.9130 (tpp) cc_final: 0.8791 (tpt) REVERT: A 289 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7703 (mm-40) REVERT: A 323 MET cc_start: 0.8758 (mmm) cc_final: 0.8219 (mmp) REVERT: A 455 MET cc_start: 0.9109 (tmt) cc_final: 0.8777 (tmt) REVERT: A 596 LYS cc_start: 0.8531 (tttt) cc_final: 0.8270 (ttpt) REVERT: A 615 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7636 (mm-40) REVERT: B 471 LYS cc_start: 0.7948 (tttp) cc_final: 0.7578 (tttp) REVERT: B 529 ARG cc_start: 0.7608 (ttm170) cc_final: 0.7336 (mtt90) REVERT: B 536 ARG cc_start: 0.7461 (tpm170) cc_final: 0.6808 (tpp80) outliers start: 11 outliers final: 3 residues processed: 97 average time/residue: 1.5801 time to fit residues: 161.0589 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 86 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 458 LYS Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 10.0000 chunk 11 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 195 ASN A 553 GLN B 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.095858 restraints weight = 7709.845| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.50 r_work: 0.2988 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7377 Z= 0.118 Angle : 0.606 16.208 10084 Z= 0.301 Chirality : 0.044 0.401 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.366 56.608 1420 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.09 % Allowed : 11.25 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.28), residues: 891 helix: 2.31 (0.24), residues: 452 sheet: 0.95 (0.54), residues: 83 loop : 0.52 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.014 0.001 PHE A 516 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 11) link_NAG-ASN : angle 3.56493 ( 33) link_BETA1-4 : bond 0.00494 ( 9) link_BETA1-4 : angle 1.61269 ( 27) hydrogen bonds : bond 0.05628 ( 386) hydrogen bonds : angle 4.20246 ( 1092) link_BETA1-6 : bond 0.00324 ( 2) link_BETA1-6 : angle 1.17049 ( 6) metal coordination : bond 0.00084 ( 2) SS BOND : bond 0.00783 ( 6) SS BOND : angle 4.20099 ( 12) covalent geometry : bond 0.00234 ( 7347) covalent geometry : angle 0.54676 (10006) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.840 Fit side-chains REVERT: A 115 LYS cc_start: 0.8531 (tptp) cc_final: 0.8209 (tptp) REVERT: A 154 LYS cc_start: 0.8471 (pttp) cc_final: 0.8036 (ptpt) REVERT: A 233 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8171 (mp) REVERT: A 270 MET cc_start: 0.9113 (tpp) cc_final: 0.8774 (tpt) REVERT: A 289 GLN cc_start: 0.8096 (mm-40) cc_final: 0.7659 (mm-40) REVERT: A 455 MET cc_start: 0.9103 (tmt) cc_final: 0.8641 (tmt) REVERT: A 596 LYS cc_start: 0.8549 (tttt) cc_final: 0.8290 (ttpt) REVERT: A 615 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7699 (mm110) REVERT: B 471 LYS cc_start: 0.7953 (tttp) cc_final: 0.7617 (tttp) REVERT: B 529 ARG cc_start: 0.7571 (ttm170) cc_final: 0.7302 (mtt90) REVERT: B 536 ARG cc_start: 0.7474 (tpm170) cc_final: 0.6833 (tpp80) outliers start: 7 outliers final: 4 residues processed: 94 average time/residue: 1.3960 time to fit residues: 138.2969 Evaluate side-chains 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 0.9980 chunk 83 optimal weight: 0.0570 chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 159 HIS A 195 ASN A 553 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095416 restraints weight = 7578.298| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.33 r_work: 0.2946 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7377 Z= 0.133 Angle : 0.638 15.256 10084 Z= 0.316 Chirality : 0.046 0.407 1144 Planarity : 0.004 0.036 1258 Dihedral : 6.184 69.556 1420 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.72 % Allowed : 10.62 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.28), residues: 891 helix: 2.27 (0.24), residues: 452 sheet: 0.97 (0.54), residues: 83 loop : 0.45 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.002 PHE A 523 TYR 0.017 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00481 ( 11) link_NAG-ASN : angle 3.51840 ( 33) link_BETA1-4 : bond 0.00517 ( 9) link_BETA1-4 : angle 1.66721 ( 27) hydrogen bonds : bond 0.06072 ( 386) hydrogen bonds : angle 4.23493 ( 1092) link_BETA1-6 : bond 0.00360 ( 2) link_BETA1-6 : angle 1.22820 ( 6) metal coordination : bond 0.00112 ( 2) SS BOND : bond 0.00891 ( 6) SS BOND : angle 4.10007 ( 12) covalent geometry : bond 0.00275 ( 7347) covalent geometry : angle 0.58407 (10006) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.745 Fit side-chains REVERT: A 115 LYS cc_start: 0.8541 (tptp) cc_final: 0.8209 (tptp) REVERT: A 154 LYS cc_start: 0.8441 (pttp) cc_final: 0.8031 (ptpt) REVERT: A 233 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8152 (mp) REVERT: A 270 MET cc_start: 0.9098 (tpp) cc_final: 0.8739 (tpt) REVERT: A 289 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7581 (mm-40) REVERT: A 323 MET cc_start: 0.8765 (mmm) cc_final: 0.8275 (mmp) REVERT: A 326 GLU cc_start: 0.8276 (mp0) cc_final: 0.8006 (mp0) REVERT: A 455 MET cc_start: 0.9085 (tmt) cc_final: 0.8575 (tmt) REVERT: A 596 LYS cc_start: 0.8504 (tttt) cc_final: 0.8263 (ttpt) REVERT: A 615 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.7661 (mm110) REVERT: B 467 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7512 (mtp85) REVERT: B 471 LYS cc_start: 0.7931 (tttp) cc_final: 0.7603 (tttp) REVERT: B 529 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7290 (mtt90) REVERT: B 536 ARG cc_start: 0.7326 (tpm170) cc_final: 0.6713 (tpp80) outliers start: 11 outliers final: 3 residues processed: 95 average time/residue: 1.3761 time to fit residues: 137.2797 Evaluate side-chains 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 321 HIS Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 467 ARG Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 5.9990 chunk 74 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 65 optimal weight: 0.0040 chunk 37 optimal weight: 0.5980 chunk 61 optimal weight: 6.9990 overall best weight: 0.4802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 195 ASN A 553 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.136834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.097058 restraints weight = 7644.322| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.35 r_work: 0.2968 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7377 Z= 0.118 Angle : 0.617 21.161 10084 Z= 0.308 Chirality : 0.044 0.384 1144 Planarity : 0.004 0.034 1258 Dihedral : 6.482 86.031 1420 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.28), residues: 891 helix: 2.44 (0.24), residues: 446 sheet: 1.00 (0.52), residues: 90 loop : 0.50 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.014 0.001 PHE A 516 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00464 ( 11) link_NAG-ASN : angle 3.00059 ( 33) link_BETA1-4 : bond 0.00508 ( 9) link_BETA1-4 : angle 1.58345 ( 27) hydrogen bonds : bond 0.05486 ( 386) hydrogen bonds : angle 4.20492 ( 1092) link_BETA1-6 : bond 0.00402 ( 2) link_BETA1-6 : angle 1.22360 ( 6) metal coordination : bond 0.00084 ( 2) SS BOND : bond 0.00915 ( 6) SS BOND : angle 4.62884 ( 12) covalent geometry : bond 0.00234 ( 7347) covalent geometry : angle 0.56666 (10006) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.749 Fit side-chains REVERT: A 115 LYS cc_start: 0.8409 (tptp) cc_final: 0.8082 (tptp) REVERT: A 154 LYS cc_start: 0.8449 (pttp) cc_final: 0.8035 (ptpt) REVERT: A 233 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8103 (mp) REVERT: A 270 MET cc_start: 0.9088 (tpp) cc_final: 0.8722 (tpt) REVERT: A 289 GLN cc_start: 0.7990 (mm-40) cc_final: 0.7538 (mm-40) REVERT: A 323 MET cc_start: 0.8761 (mmm) cc_final: 0.8224 (mmp) REVERT: A 596 LYS cc_start: 0.8504 (tttt) cc_final: 0.8221 (ttpt) REVERT: A 615 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.7664 (mm110) REVERT: B 471 LYS cc_start: 0.7887 (tttp) cc_final: 0.7574 (tttp) REVERT: B 529 ARG cc_start: 0.7546 (ttm170) cc_final: 0.7270 (mtt90) REVERT: B 536 ARG cc_start: 0.7315 (tpm170) cc_final: 0.6721 (tpp80) outliers start: 6 outliers final: 2 residues processed: 94 average time/residue: 1.3476 time to fit residues: 133.2265 Evaluate side-chains 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 195 ASN A 553 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.135158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095283 restraints weight = 7501.001| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.30 r_work: 0.2942 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7377 Z= 0.137 Angle : 0.642 22.053 10084 Z= 0.320 Chirality : 0.045 0.403 1144 Planarity : 0.004 0.036 1258 Dihedral : 6.486 88.606 1420 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.09 % Allowed : 11.09 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.28), residues: 891 helix: 2.25 (0.24), residues: 452 sheet: 0.90 (0.53), residues: 83 loop : 0.52 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.016 0.002 PHE A 523 TYR 0.017 0.002 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00451 ( 11) link_NAG-ASN : angle 3.05064 ( 33) link_BETA1-4 : bond 0.00504 ( 9) link_BETA1-4 : angle 1.67157 ( 27) hydrogen bonds : bond 0.06239 ( 386) hydrogen bonds : angle 4.25966 ( 1092) link_BETA1-6 : bond 0.00339 ( 2) link_BETA1-6 : angle 1.25334 ( 6) metal coordination : bond 0.00118 ( 2) SS BOND : bond 0.01060 ( 6) SS BOND : angle 4.59199 ( 12) covalent geometry : bond 0.00288 ( 7347) covalent geometry : angle 0.59252 (10006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.03 seconds wall clock time: 116 minutes 25.13 seconds (6985.13 seconds total)