Starting phenix.real_space_refine on Fri Jun 6 05:53:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dak_46691/06_2025/9dak_46691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dak_46691/06_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_46691/06_2025/9dak_46691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dak_46691/06_2025/9dak_46691.map" model { file = "/net/cci-nas-00/data/ceres_data/9dak_46691/06_2025/9dak_46691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dak_46691/06_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-5710/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: 5.44, per 1000 atoms: 0.74 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: 2.49 Conformation dependent library (CDL) restraints added in 902.9 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: 0.89 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: 2.24 Time building geometry restraints manager: 2.79 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: 1.940 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.870 Find NCS groups from input model: 0.120 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- 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 : 0.835 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: 2.3928 time to fit residues: 317.0610 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 : 1.823 ------------------------------------------------------------------------------- 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: 2.29 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 : 0.856 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8446 (tptp) cc_final: 0.8211 (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: 0.7942 (mm-40) cc_final: 0.7559 (mm-40) REVERT: A 323 MET cc_start: 0.8710 (mmp) cc_final: 0.8507 (mmm) REVERT: A 596 LYS cc_start: 0.8360 (tttt) cc_final: 0.8070 (ttpt) REVERT: A 696 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7402 (ttt-90) REVERT: B 558 LEU cc_start: 0.8510 (mp) cc_final: 0.8250 (mp) REVERT: B 570 VAL cc_start: 0.8446 (t) cc_final: 0.8212 (t) outliers start: 14 outliers final: 3 residues processed: 106 average time/residue: 1.6438 time to fit residues: 183.8037 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 : 1.720 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3588 r_free = 0.3588 target = 0.133555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.093515 restraints weight = 7480.373| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.31 r_work: 0.2911 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7377 Z= 0.164 Angle : 0.634 15.041 10084 Z= 0.324 Chirality : 0.045 0.270 1144 Planarity : 0.005 0.037 1258 Dihedral : 6.527 57.638 1422 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.03 % Allowed : 7.66 % Favored : 90.31 % 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: 1.91 (0.28), residues: 891 helix: 2.04 (0.24), residues: 447 sheet: 0.99 (0.49), residues: 90 loop : 0.45 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 PHE 0.018 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 0.00666 ( 11) link_NAG-ASN : angle 3.39628 ( 33) link_BETA1-4 : bond 0.00680 ( 9) link_BETA1-4 : angle 2.01982 ( 27) hydrogen bonds : bond 0.07238 ( 386) hydrogen bonds : angle 4.60916 ( 1092) link_BETA1-6 : bond 0.00394 ( 2) link_BETA1-6 : angle 1.30520 ( 6) metal coordination : bond 0.00176 ( 2) SS BOND : bond 0.01014 ( 6) SS BOND : angle 3.47229 ( 12) covalent geometry : bond 0.00360 ( 7347) covalent geometry : angle 0.58343 (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 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7262 (tt0) REVERT: A 115 LYS cc_start: 0.8491 (tptp) cc_final: 0.8248 (tptp) REVERT: A 233 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8301 (mp) REVERT: A 270 MET cc_start: 0.9131 (tpp) cc_final: 0.8763 (tpt) REVERT: A 289 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7660 (mm-40) REVERT: A 589 LYS cc_start: 0.8868 (tttp) cc_final: 0.8533 (ttmt) REVERT: A 596 LYS cc_start: 0.8525 (tttt) cc_final: 0.8285 (ttpt) REVERT: A 696 ARG cc_start: 0.7925 (ttm-80) cc_final: 0.7708 (ttt-90) REVERT: B 529 ARG cc_start: 0.7520 (ttm170) cc_final: 0.7218 (mtt90) REVERT: B 558 LEU cc_start: 0.8538 (mp) cc_final: 0.8270 (mp) REVERT: B 570 VAL cc_start: 0.8517 (t) cc_final: 0.8308 (t) outliers start: 13 outliers final: 2 residues processed: 99 average time/residue: 1.6680 time to fit residues: 175.5031 Evaluate side-chains 87 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 83 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 4.9990 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 87 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.136469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.094862 restraints weight = 7673.638| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.67 r_work: 0.2959 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7377 Z= 0.134 Angle : 0.668 28.077 10084 Z= 0.332 Chirality : 0.045 0.406 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.697 51.413 1422 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.19 % Allowed : 8.59 % Favored : 89.22 % 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: 1.98 (0.28), residues: 891 helix: 2.13 (0.24), residues: 452 sheet: 0.89 (0.49), residues: 90 loop : 0.44 (0.33), residues: 349 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 0.002 0.000 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00570 ( 11) link_NAG-ASN : angle 3.75205 ( 33) link_BETA1-4 : bond 0.00592 ( 9) link_BETA1-4 : angle 1.86679 ( 27) hydrogen bonds : bond 0.06315 ( 386) hydrogen bonds : angle 4.45004 ( 1092) link_BETA1-6 : bond 0.00406 ( 2) link_BETA1-6 : angle 1.22224 ( 6) metal coordination : bond 0.00096 ( 2) SS BOND : bond 0.01734 ( 6) SS BOND : angle 4.74193 ( 12) covalent geometry : bond 0.00267 ( 7347) covalent geometry : angle 0.60554 (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 103 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8415 (tptp) cc_final: 0.8162 (tptp) REVERT: A 233 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8235 (mp) REVERT: A 270 MET cc_start: 0.9102 (tpp) cc_final: 0.8765 (tpt) REVERT: A 289 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7711 (mm-40) REVERT: A 323 MET cc_start: 0.8946 (mmm) cc_final: 0.8453 (mmp) REVERT: A 589 LYS cc_start: 0.8902 (tttp) cc_final: 0.8559 (ttmt) REVERT: A 596 LYS cc_start: 0.8515 (tttt) cc_final: 0.8262 (ttpt) REVERT: B 529 ARG cc_start: 0.7549 (ttm170) cc_final: 0.7082 (mtt90) REVERT: B 536 ARG cc_start: 0.7410 (tpm170) cc_final: 0.6754 (tpp80) REVERT: B 570 VAL cc_start: 0.8443 (t) cc_final: 0.8220 (t) outliers start: 14 outliers final: 2 residues processed: 100 average time/residue: 1.4241 time to fit residues: 149.7768 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3652 r_free = 0.3652 target = 0.135387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.091556 restraints weight = 7637.642| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.14 r_work: 0.2954 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7377 Z= 0.147 Angle : 0.666 19.348 10084 Z= 0.334 Chirality : 0.046 0.410 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.525 51.605 1422 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.88 % Allowed : 9.06 % 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: 1.94 (0.28), residues: 891 helix: 2.14 (0.24), residues: 452 sheet: 0.88 (0.52), residues: 84 loop : 0.37 (0.33), residues: 355 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 0.017 0.002 PHE A 523 TYR 0.017 0.002 TYR A 385 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00550 ( 11) link_NAG-ASN : angle 3.79754 ( 33) link_BETA1-4 : bond 0.00564 ( 9) link_BETA1-4 : angle 1.85065 ( 27) hydrogen bonds : bond 0.06664 ( 386) hydrogen bonds : angle 4.39699 ( 1092) link_BETA1-6 : bond 0.00378 ( 2) link_BETA1-6 : angle 1.23899 ( 6) metal coordination : bond 0.00143 ( 2) SS BOND : bond 0.01201 ( 6) SS BOND : angle 4.58534 ( 12) covalent geometry : bond 0.00314 ( 7347) covalent geometry : angle 0.60372 (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: 12 poor density : 89 time to evaluate : 1.508 Fit side-chains REVERT: A 115 LYS cc_start: 0.8531 (tptp) cc_final: 0.8279 (tptp) REVERT: A 233 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8286 (mp) REVERT: A 270 MET cc_start: 0.9098 (tpp) cc_final: 0.8762 (tpt) REVERT: A 289 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7752 (mm-40) REVERT: A 323 MET cc_start: 0.8929 (mmm) cc_final: 0.8482 (mmp) REVERT: A 589 LYS cc_start: 0.8914 (tttp) cc_final: 0.8586 (ttmt) REVERT: A 596 LYS cc_start: 0.8559 (tttt) cc_final: 0.8297 (ttpt) REVERT: A 615 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7609 (mm110) REVERT: B 536 ARG cc_start: 0.7432 (tpm170) cc_final: 0.6814 (tpp80) outliers start: 12 outliers final: 4 residues processed: 98 average time/residue: 1.8931 time to fit residues: 195.1548 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 : 0.992 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 40 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.132263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.090511 restraints weight = 7619.019| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.34 r_work: 0.2895 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7377 Z= 0.232 Angle : 0.737 15.851 10084 Z= 0.372 Chirality : 0.051 0.484 1144 Planarity : 0.005 0.040 1258 Dihedral : 5.842 56.395 1420 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.03 % Allowed : 9.38 % Favored : 88.59 % 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: 1.64 (0.27), residues: 891 helix: 1.93 (0.24), residues: 443 sheet: 0.92 (0.53), residues: 84 loop : 0.17 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 478 HIS 0.008 0.002 HIS A 321 PHE 0.023 0.003 PHE A 523 TYR 0.015 0.002 TYR A 202 ARG 0.005 0.001 ARG A 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00509 ( 11) link_NAG-ASN : angle 4.18424 ( 33) link_BETA1-4 : bond 0.00551 ( 9) link_BETA1-4 : angle 2.13867 ( 27) hydrogen bonds : bond 0.08587 ( 386) hydrogen bonds : angle 4.57501 ( 1092) link_BETA1-6 : bond 0.00294 ( 2) link_BETA1-6 : angle 1.33368 ( 6) metal coordination : bond 0.00288 ( 2) SS BOND : bond 0.01244 ( 6) SS BOND : angle 4.05467 ( 12) covalent geometry : bond 0.00547 ( 7347) covalent geometry : angle 0.67622 (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 101 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.770 Fit side-chains REVERT: A 115 LYS cc_start: 0.8660 (tptp) cc_final: 0.8406 (tptp) REVERT: A 233 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8385 (mp) REVERT: A 270 MET cc_start: 0.9118 (tpp) cc_final: 0.8814 (tpt) REVERT: A 289 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7789 (mm-40) REVERT: A 455 MET cc_start: 0.9152 (tmt) cc_final: 0.8769 (tmt) REVERT: A 596 LYS cc_start: 0.8606 (tttt) cc_final: 0.8367 (ttpt) REVERT: A 615 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.7733 (mm110) REVERT: B 467 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7573 (mtp85) REVERT: B 536 ARG cc_start: 0.7521 (tpm170) cc_final: 0.6867 (tpp80) REVERT: B 558 LEU cc_start: 0.8546 (mp) cc_final: 0.8291 (mp) outliers start: 13 outliers final: 3 residues processed: 97 average time/residue: 1.6339 time to fit residues: 166.6399 Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.976 ------------------------------------------------------------------------------- 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 467 ARG 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: 0.0470 chunk 3 optimal weight: 0.6980 chunk 70 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 overall best weight: 0.3016 ------------------------------------------------------------------------------- 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 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.137816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.096520 restraints weight = 7663.651| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.35 r_work: 0.2995 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7377 Z= 0.114 Angle : 0.628 18.396 10084 Z= 0.309 Chirality : 0.046 0.557 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.612 57.390 1420 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.25 % Allowed : 10.62 % 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: 2.01 (0.28), residues: 891 helix: 2.21 (0.24), residues: 447 sheet: 0.88 (0.53), residues: 84 loop : 0.42 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.014 0.001 PHE A 516 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00622 ( 11) link_NAG-ASN : angle 4.14024 ( 33) link_BETA1-4 : bond 0.00555 ( 9) link_BETA1-4 : angle 1.64675 ( 27) hydrogen bonds : bond 0.05472 ( 386) hydrogen bonds : angle 4.32295 ( 1092) link_BETA1-6 : bond 0.00372 ( 2) link_BETA1-6 : angle 1.15566 ( 6) metal coordination : bond 0.00022 ( 2) SS BOND : bond 0.00920 ( 6) SS BOND : angle 4.16812 ( 12) covalent geometry : bond 0.00207 ( 7347) covalent geometry : angle 0.55815 (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 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.822 Fit side-chains REVERT: A 115 LYS cc_start: 0.8440 (tptp) cc_final: 0.8111 (tptp) REVERT: A 154 LYS cc_start: 0.8347 (pttp) cc_final: 0.7973 (ptpt) REVERT: A 233 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 270 MET cc_start: 0.9063 (tpp) cc_final: 0.8748 (tpt) REVERT: A 289 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7603 (mm-40) REVERT: A 323 MET cc_start: 0.8548 (mmm) cc_final: 0.8139 (mmp) REVERT: A 596 LYS cc_start: 0.8445 (tttt) cc_final: 0.8210 (ttpt) REVERT: A 615 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7697 (mm110) REVERT: B 529 ARG cc_start: 0.7563 (ttm170) cc_final: 0.7099 (mtt90) REVERT: B 536 ARG cc_start: 0.7449 (tpm170) cc_final: 0.6850 (tpp80) outliers start: 8 outliers final: 1 residues processed: 95 average time/residue: 1.6711 time to fit residues: 167.2467 Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 53 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 A 615 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 = 0.3651 r_free = 0.3651 target = 0.135281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.094430 restraints weight = 7706.155| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.31 r_work: 0.2959 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2767 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 : 0.651 17.425 10084 Z= 0.325 Chirality : 0.047 0.518 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.498 55.943 1420 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.41 % Allowed : 10.94 % 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: 1.95 (0.28), residues: 891 helix: 2.16 (0.24), residues: 452 sheet: 0.85 (0.53), residues: 84 loop : 0.35 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.017 0.002 PHE A 523 TYR 0.016 0.002 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00562 ( 11) link_NAG-ASN : angle 3.78078 ( 33) link_BETA1-4 : bond 0.00533 ( 9) link_BETA1-4 : angle 1.74102 ( 27) hydrogen bonds : bond 0.06423 ( 386) hydrogen bonds : angle 4.32190 ( 1092) link_BETA1-6 : bond 0.00351 ( 2) link_BETA1-6 : angle 1.23447 ( 6) metal coordination : bond 0.00138 ( 2) SS BOND : bond 0.01101 ( 6) SS BOND : angle 4.46632 ( 12) covalent geometry : bond 0.00303 ( 7347) covalent geometry : angle 0.58858 (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 95 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.795 Fit side-chains REVERT: A 23 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: A 115 LYS cc_start: 0.8547 (tptp) cc_final: 0.8287 (tptp) REVERT: A 154 LYS cc_start: 0.8373 (pttp) cc_final: 0.7992 (ptpt) REVERT: A 233 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8269 (mp) REVERT: A 270 MET cc_start: 0.9086 (tpp) cc_final: 0.8843 (tpt) REVERT: A 289 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7666 (mm-40) REVERT: A 596 LYS cc_start: 0.8526 (tttt) cc_final: 0.8290 (ttpt) REVERT: A 615 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7651 (mm110) REVERT: B 471 LYS cc_start: 0.7922 (tttp) cc_final: 0.7683 (tttp) REVERT: B 536 ARG cc_start: 0.7454 (tpm170) cc_final: 0.6800 (tpp80) outliers start: 9 outliers final: 3 residues processed: 93 average time/residue: 1.5479 time to fit residues: 150.9700 Evaluate side-chains 90 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.882 ------------------------------------------------------------------------------- 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 416 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 64 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 A 615 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 = 0.3668 r_free = 0.3668 target = 0.136686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.095070 restraints weight = 7743.489| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.73 r_work: 0.2962 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2812 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= 0.129 Angle : 0.662 17.025 10084 Z= 0.325 Chirality : 0.046 0.488 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.823 55.403 1420 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 2.00 (0.28), residues: 891 helix: 2.17 (0.24), residues: 452 sheet: 0.89 (0.53), residues: 84 loop : 0.42 (0.34), residues: 355 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 0.002 PHE A 523 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 11) link_NAG-ASN : angle 4.27330 ( 33) link_BETA1-4 : bond 0.00525 ( 9) link_BETA1-4 : angle 1.68113 ( 27) hydrogen bonds : bond 0.06056 ( 386) hydrogen bonds : angle 4.29088 ( 1092) link_BETA1-6 : bond 0.00366 ( 2) link_BETA1-6 : angle 1.22333 ( 6) metal coordination : bond 0.00096 ( 2) SS BOND : bond 0.01030 ( 6) SS BOND : angle 4.45457 ( 12) covalent geometry : bond 0.00260 ( 7347) covalent geometry : angle 0.59081 (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 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.800 Fit side-chains REVERT: A 23 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.7080 (tt0) REVERT: A 115 LYS cc_start: 0.8549 (tptp) cc_final: 0.8223 (tptp) REVERT: A 154 LYS cc_start: 0.8384 (pttp) cc_final: 0.7991 (ptpt) REVERT: A 233 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8191 (mp) REVERT: A 270 MET cc_start: 0.9075 (tpp) cc_final: 0.8752 (tpt) REVERT: A 289 GLN cc_start: 0.8059 (mm-40) cc_final: 0.7613 (mm-40) REVERT: A 596 LYS cc_start: 0.8503 (tttt) cc_final: 0.8265 (ttpt) REVERT: A 615 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7656 (mm110) REVERT: B 471 LYS cc_start: 0.7941 (tttp) cc_final: 0.7660 (tttp) REVERT: B 529 ARG cc_start: 0.7551 (ttm170) cc_final: 0.7031 (mtt90) REVERT: B 536 ARG cc_start: 0.7465 (tpm170) cc_final: 0.6815 (tpp80) outliers start: 7 outliers final: 2 residues processed: 91 average time/residue: 1.4666 time to fit residues: 140.0714 Evaluate side-chains 89 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 458 LYS Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain A residue 690 VAL 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: 5.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.0040 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 A 615 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 = 0.3611 r_free = 0.3611 target = 0.135429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.095572 restraints weight = 7624.047| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.26 r_work: 0.2945 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2848 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= 0.128 Angle : 0.640 16.482 10084 Z= 0.317 Chirality : 0.046 0.477 1144 Planarity : 0.004 0.035 1258 Dihedral : 6.005 59.243 1420 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 1.99 (0.28), residues: 891 helix: 2.18 (0.24), residues: 452 sheet: 0.86 (0.53), residues: 84 loop : 0.40 (0.34), 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 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00544 ( 11) link_NAG-ASN : angle 3.58741 ( 33) link_BETA1-4 : bond 0.00545 ( 9) link_BETA1-4 : angle 1.66414 ( 27) hydrogen bonds : bond 0.05994 ( 386) hydrogen bonds : angle 4.27187 ( 1092) link_BETA1-6 : bond 0.00381 ( 2) link_BETA1-6 : angle 1.23587 ( 6) metal coordination : bond 0.00098 ( 2) SS BOND : bond 0.00963 ( 6) SS BOND : angle 4.36173 ( 12) covalent geometry : bond 0.00260 ( 7347) covalent geometry : angle 0.58212 (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 93 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.774 Fit side-chains REVERT: A 115 LYS cc_start: 0.8549 (tptp) cc_final: 0.8227 (tptp) REVERT: A 154 LYS cc_start: 0.8457 (pttp) cc_final: 0.8098 (ptpt) REVERT: A 233 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8198 (mp) REVERT: A 270 MET cc_start: 0.9077 (tpp) cc_final: 0.8729 (tpt) REVERT: A 289 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7564 (mm-40) REVERT: A 596 LYS cc_start: 0.8496 (tttt) cc_final: 0.8274 (ttpt) REVERT: A 615 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.7471 (mm110) REVERT: B 471 LYS cc_start: 0.7961 (tttp) cc_final: 0.7695 (tttp) REVERT: B 529 ARG cc_start: 0.7586 (ttm170) cc_final: 0.7064 (mtt90) REVERT: B 536 ARG cc_start: 0.7400 (tpm170) cc_final: 0.6798 (tpp80) outliers start: 7 outliers final: 2 residues processed: 91 average time/residue: 1.4897 time to fit residues: 142.0042 Evaluate side-chains 88 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 73 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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 A 615 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 = 0.3604 r_free = 0.3604 target = 0.135513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.096712 restraints weight = 7521.072| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.43 r_work: 0.2937 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2859 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= 0.138 Angle : 0.643 16.267 10084 Z= 0.320 Chirality : 0.046 0.479 1144 Planarity : 0.004 0.036 1258 Dihedral : 6.061 62.916 1420 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.78 % Allowed : 11.88 % Favored : 87.34 % 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: 1.95 (0.28), residues: 891 helix: 2.14 (0.24), residues: 452 sheet: 0.84 (0.53), residues: 84 loop : 0.38 (0.34), residues: 355 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 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Details of bonding type rmsd link_NAG-ASN : bond 0.00525 ( 11) link_NAG-ASN : angle 3.39490 ( 33) link_BETA1-4 : bond 0.00517 ( 9) link_BETA1-4 : angle 1.68396 ( 27) hydrogen bonds : bond 0.06280 ( 386) hydrogen bonds : angle 4.29723 ( 1092) link_BETA1-6 : bond 0.00332 ( 2) link_BETA1-6 : angle 1.24592 ( 6) metal coordination : bond 0.00120 ( 2) SS BOND : bond 0.00984 ( 6) SS BOND : angle 4.30949 ( 12) covalent geometry : bond 0.00290 ( 7347) covalent geometry : angle 0.58969 (10006) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8384.44 seconds wall clock time: 148 minutes 50.73 seconds (8930.73 seconds total)