Starting phenix.real_space_refine on Wed Sep 17 08:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dak_46691/09_2025/9dak_46691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dak_46691/09_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_46691/09_2025/9dak_46691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dak_46691/09_2025/9dak_46691.map" model { file = "/net/cci-nas-00/data/ceres_data/9dak_46691/09_2025/9dak_46691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dak_46691/09_2025/9dak_46691.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 16, 'GLN:plan1': 4, 'GLU:plan': 21, 'ASN:plan1': 5, 'ARG:plan': 2} 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: {'PHE:plan': 3, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 6} 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: 2.10, per 1000 atoms: 0.29 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: 0.80 Conformation dependent library (CDL) restraints added in 376.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.31 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: 1.19 Time building geometry restraints manager: 0.99 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: 2.340 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.980 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.350 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (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 ARG 0.008 0.000 ARG A 575 TYR 0.033 0.004 TYR A 497 PHE 0.013 0.003 PHE B 520 TRP 0.025 0.003 TRP A 478 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.01124 ( 7347) covalent geometry : angle 1.22000 (10006) SS BOND : bond 0.11921 ( 6) SS BOND : angle 4.68880 ( 12) hydrogen bonds : bond 0.22415 ( 386) hydrogen bonds : angle 6.73263 ( 1092) metal coordination : bond 0.37953 ( 2) link_BETA1-4 : bond 0.05413 ( 9) link_BETA1-4 : angle 5.30054 ( 27) link_BETA1-6 : bond 0.04819 ( 2) link_BETA1-6 : angle 2.44087 ( 6) link_NAG-ASN : bond 0.05386 ( 11) link_NAG-ASN : angle 5.11715 ( 33) *********************** 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 : 0.290 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: 0.8009 time to fit residues: 105.7991 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 : 0.279 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3613 r_free = 0.3613 target = 0.135638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.095570 restraints weight = 7500.635| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.43 r_work: 0.2937 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1850 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= 0.167 Angle : 0.654 14.066 10084 Z= 0.337 Chirality : 0.045 0.197 1144 Planarity : 0.005 0.035 1258 Dihedral : 9.014 70.236 1422 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 2.19 % Allowed : 5.78 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.28), residues: 891 helix: 1.89 (0.24), residues: 444 sheet: 0.93 (0.50), residues: 90 loop : 0.52 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 482 TYR 0.019 0.002 TYR A 385 PHE 0.011 0.002 PHE A 523 TRP 0.019 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 7347) covalent geometry : angle 0.60668 (10006) SS BOND : bond 0.00913 ( 6) SS BOND : angle 2.38317 ( 12) hydrogen bonds : bond 0.07292 ( 386) hydrogen bonds : angle 4.93285 ( 1092) metal coordination : bond 0.00510 ( 2) link_BETA1-4 : bond 0.00605 ( 9) link_BETA1-4 : angle 2.15033 ( 27) link_BETA1-6 : bond 0.00516 ( 2) link_BETA1-6 : angle 1.40053 ( 6) link_NAG-ASN : bond 0.00908 ( 11) link_NAG-ASN : angle 3.60220 ( 33) *********************** 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 107 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: A 115 LYS cc_start: 0.8495 (tptp) cc_final: 0.8255 (tptp) REVERT: A 233 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8239 (mp) REVERT: A 270 MET cc_start: 0.9114 (tpp) cc_final: 0.8739 (tpt) REVERT: A 289 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7609 (mm-40) REVERT: A 323 MET cc_start: 0.8769 (mmp) cc_final: 0.8559 (mmm) REVERT: A 455 MET cc_start: 0.9130 (tmt) cc_final: 0.8691 (tmt) REVERT: A 596 LYS cc_start: 0.8440 (tttt) cc_final: 0.8157 (ttpt) REVERT: A 696 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7504 (ttt-90) REVERT: B 558 LEU cc_start: 0.8521 (mp) cc_final: 0.8255 (mp) outliers start: 14 outliers final: 3 residues processed: 101 average time/residue: 0.6680 time to fit residues: 70.7226 Evaluate side-chains 83 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.276 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3576 r_free = 0.3576 target = 0.132636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092585 restraints weight = 7394.653| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 2.35 r_work: 0.2898 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7377 Z= 0.177 Angle : 0.643 13.626 10084 Z= 0.330 Chirality : 0.045 0.244 1144 Planarity : 0.005 0.037 1258 Dihedral : 6.562 56.468 1422 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.50 % Allowed : 7.50 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.28), residues: 891 helix: 1.95 (0.24), residues: 454 sheet: 0.85 (0.50), residues: 92 loop : 0.34 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 116 TYR 0.018 0.002 TYR A 385 PHE 0.019 0.002 PHE A 523 TRP 0.019 0.002 TRP A 478 HIS 0.006 0.002 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 7347) covalent geometry : angle 0.59234 (10006) SS BOND : bond 0.01135 ( 6) SS BOND : angle 3.43291 ( 12) hydrogen bonds : bond 0.07530 ( 386) hydrogen bonds : angle 4.62339 ( 1092) metal coordination : bond 0.00197 ( 2) link_BETA1-4 : bond 0.00743 ( 9) link_BETA1-4 : angle 2.07810 ( 27) link_BETA1-6 : bond 0.00379 ( 2) link_BETA1-6 : angle 1.29885 ( 6) link_NAG-ASN : bond 0.00663 ( 11) link_NAG-ASN : angle 3.42555 ( 33) *********************** 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: 16 poor density : 87 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8534 (tptp) cc_final: 0.8286 (tptp) REVERT: A 233 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 270 MET cc_start: 0.9109 (tpp) cc_final: 0.8847 (tpt) REVERT: A 289 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7625 (mm-40) REVERT: A 596 LYS cc_start: 0.8519 (tttt) cc_final: 0.8259 (ttpt) REVERT: A 615 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7528 (mm110) REVERT: B 570 VAL cc_start: 0.8511 (t) cc_final: 0.8309 (t) outliers start: 16 outliers final: 4 residues processed: 98 average time/residue: 0.7107 time to fit residues: 73.0143 Evaluate side-chains 86 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 615 GLN Chi-restraints excluded: chain A residue 690 VAL 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 51 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3663 r_free = 0.3663 target = 0.136178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093866 restraints weight = 7774.499| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.56 r_work: 0.2953 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2408 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= 0.131 Angle : 0.669 28.428 10084 Z= 0.332 Chirality : 0.044 0.427 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.761 59.747 1422 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.88 % Allowed : 8.44 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.28), residues: 891 helix: 2.13 (0.24), residues: 452 sheet: 0.93 (0.52), residues: 84 loop : 0.33 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 116 TYR 0.015 0.001 TYR A 385 PHE 0.014 0.002 PHE A 516 TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7347) covalent geometry : angle 0.60821 (10006) SS BOND : bond 0.01352 ( 6) SS BOND : angle 4.66199 ( 12) hydrogen bonds : bond 0.06248 ( 386) hydrogen bonds : angle 4.43813 ( 1092) metal coordination : bond 0.00098 ( 2) link_BETA1-4 : bond 0.00570 ( 9) link_BETA1-4 : angle 1.85808 ( 27) link_BETA1-6 : bond 0.00417 ( 2) link_BETA1-6 : angle 1.21828 ( 6) link_NAG-ASN : bond 0.00585 ( 11) link_NAG-ASN : angle 3.67130 ( 33) *********************** 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 100 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8424 (tptp) cc_final: 0.8171 (tptp) REVERT: A 233 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8230 (mp) REVERT: A 270 MET cc_start: 0.9095 (tpp) cc_final: 0.8760 (tpt) REVERT: A 289 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7727 (mm-40) REVERT: A 323 MET cc_start: 0.8960 (mmm) cc_final: 0.8437 (mmp) REVERT: A 552 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8121 (tptp) REVERT: A 596 LYS cc_start: 0.8522 (tttt) cc_final: 0.8256 (ttpt) REVERT: A 615 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7566 (mm-40) REVERT: B 529 ARG cc_start: 0.7557 (ttm170) cc_final: 0.7077 (mtt90) REVERT: B 570 VAL cc_start: 0.8446 (t) cc_final: 0.8212 (t) outliers start: 12 outliers final: 4 residues processed: 98 average time/residue: 0.6853 time to fit residues: 70.5689 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 : 0.295 ------------------------------------------------------------------------------- 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 458 LYS Chi-restraints excluded: chain A residue 552 LYS 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 65 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.134609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090767 restraints weight = 7715.008| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.16 r_work: 0.2938 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7377 Z= 0.159 Angle : 0.693 25.806 10084 Z= 0.347 Chirality : 0.047 0.416 1144 Planarity : 0.004 0.037 1258 Dihedral : 5.741 57.930 1422 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 1.90 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.28), residues: 891 helix: 2.10 (0.24), residues: 452 sheet: 0.91 (0.52), residues: 84 loop : 0.33 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 116 TYR 0.016 0.002 TYR A 385 PHE 0.018 0.002 PHE A 523 TRP 0.018 0.001 TRP A 163 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 7347) covalent geometry : angle 0.63156 (10006) SS BOND : bond 0.01373 ( 6) SS BOND : angle 4.70404 ( 12) hydrogen bonds : bond 0.07010 ( 386) hydrogen bonds : angle 4.43627 ( 1092) metal coordination : bond 0.00151 ( 2) link_BETA1-4 : bond 0.00563 ( 9) link_BETA1-4 : angle 1.90109 ( 27) link_BETA1-6 : bond 0.00336 ( 2) link_BETA1-6 : angle 1.24136 ( 6) link_NAG-ASN : bond 0.00549 ( 11) link_NAG-ASN : angle 3.82012 ( 33) *********************** 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 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8567 (tptp) cc_final: 0.8314 (tptp) REVERT: A 233 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8284 (mp) REVERT: A 270 MET cc_start: 0.9097 (tpp) cc_final: 0.8851 (tpt) REVERT: A 289 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7753 (mm-40) REVERT: A 323 MET cc_start: 0.9019 (mmm) cc_final: 0.8524 (mmp) REVERT: A 552 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8156 (tptp) REVERT: A 596 LYS cc_start: 0.8535 (tttt) cc_final: 0.8305 (ttpt) REVERT: A 615 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7642 (mm110) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 0.7072 time to fit residues: 71.3178 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 : 0.340 ------------------------------------------------------------------------------- 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 552 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 49 optimal weight: 0.9980 chunk 40 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 9 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 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 = 0.3664 r_free = 0.3664 target = 0.136379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.094312 restraints weight = 7723.399| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.48 r_work: 0.2960 rms_B_bonded: 2.49 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: 0.8255 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7377 Z= 0.129 Angle : 0.648 19.845 10084 Z= 0.322 Chirality : 0.045 0.384 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.664 57.475 1422 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.03 % Allowed : 9.06 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.28), residues: 891 helix: 2.20 (0.24), residues: 452 sheet: 0.91 (0.53), residues: 84 loop : 0.39 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 696 TYR 0.015 0.001 TYR A 385 PHE 0.014 0.002 PHE A 516 TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 7347) covalent geometry : angle 0.57984 (10006) SS BOND : bond 0.01159 ( 6) SS BOND : angle 4.56015 ( 12) hydrogen bonds : bond 0.06069 ( 386) hydrogen bonds : angle 4.32418 ( 1092) metal coordination : bond 0.00108 ( 2) link_BETA1-4 : bond 0.00543 ( 9) link_BETA1-4 : angle 1.72251 ( 27) link_BETA1-6 : bond 0.00404 ( 2) link_BETA1-6 : angle 1.17571 ( 6) link_NAG-ASN : bond 0.00532 ( 11) link_NAG-ASN : angle 4.03062 ( 33) *********************** 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 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8549 (tptp) cc_final: 0.8241 (tptp) REVERT: A 233 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8225 (mp) REVERT: A 270 MET cc_start: 0.9081 (tpp) cc_final: 0.8750 (tpt) REVERT: A 289 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7696 (mm-40) REVERT: A 323 MET cc_start: 0.8922 (mmm) cc_final: 0.8434 (mmp) REVERT: A 455 MET cc_start: 0.9160 (tmt) cc_final: 0.8677 (tmt) REVERT: A 596 LYS cc_start: 0.8510 (tttt) cc_final: 0.8277 (ttpt) REVERT: A 615 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.7698 (mm110) REVERT: B 529 ARG cc_start: 0.7623 (ttm170) cc_final: 0.7155 (mtt90) outliers start: 13 outliers final: 5 residues processed: 101 average time/residue: 0.6934 time to fit residues: 73.4967 Evaluate side-chains 96 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 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 38 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.130709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.088484 restraints weight = 7597.119| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.67 r_work: 0.2840 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7377 Z= 0.231 Angle : 0.769 19.341 10084 Z= 0.383 Chirality : 0.051 0.394 1144 Planarity : 0.005 0.039 1258 Dihedral : 6.007 55.394 1422 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.72 % Allowed : 9.84 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.27), residues: 891 helix: 1.94 (0.24), residues: 445 sheet: 0.79 (0.52), residues: 86 loop : 0.24 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.015 0.002 TYR A 202 PHE 0.021 0.002 PHE A 523 TRP 0.018 0.002 TRP A 478 HIS 0.008 0.002 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 7347) covalent geometry : angle 0.69793 (10006) SS BOND : bond 0.01430 ( 6) SS BOND : angle 4.59311 ( 12) hydrogen bonds : bond 0.08437 ( 386) hydrogen bonds : angle 4.53974 ( 1092) metal coordination : bond 0.00291 ( 2) link_BETA1-4 : bond 0.00611 ( 9) link_BETA1-4 : angle 2.09343 ( 27) link_BETA1-6 : bond 0.00358 ( 2) link_BETA1-6 : angle 1.34041 ( 6) link_NAG-ASN : bond 0.00545 ( 11) link_NAG-ASN : angle 4.63099 ( 33) *********************** 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 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8554 (tptp) cc_final: 0.8274 (tptp) REVERT: A 154 LYS cc_start: 0.8312 (pttp) cc_final: 0.7904 (ptpt) REVERT: A 233 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8246 (mp) REVERT: A 270 MET cc_start: 0.9053 (tpp) cc_final: 0.8748 (tpt) REVERT: A 289 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7664 (mm-40) REVERT: A 596 LYS cc_start: 0.8519 (tttt) cc_final: 0.8237 (ttpt) REVERT: A 615 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7702 (mm110) REVERT: B 467 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7473 (mtp85) outliers start: 11 outliers final: 5 residues processed: 95 average time/residue: 0.7302 time to fit residues: 72.5682 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.268 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain B residue 467 ARG 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 23 optimal weight: 0.3980 chunk 64 optimal weight: 0.5980 chunk 79 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 34 optimal weight: 0.0870 chunk 56 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.3372 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.137201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.096277 restraints weight = 7736.652| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.52 r_work: 0.2982 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2793 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= 0.118 Angle : 0.648 16.734 10084 Z= 0.317 Chirality : 0.044 0.334 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.912 55.413 1422 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.56 % Allowed : 10.62 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.28), residues: 891 helix: 2.18 (0.24), residues: 452 sheet: 0.78 (0.53), residues: 84 loop : 0.41 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 696 TYR 0.014 0.001 TYR A 385 PHE 0.014 0.001 PHE A 516 TRP 0.023 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 7347) covalent geometry : angle 0.57987 (10006) SS BOND : bond 0.01043 ( 6) SS BOND : angle 4.28569 ( 12) hydrogen bonds : bond 0.05537 ( 386) hydrogen bonds : angle 4.30028 ( 1092) metal coordination : bond 0.00051 ( 2) link_BETA1-4 : bond 0.00531 ( 9) link_BETA1-4 : angle 1.62015 ( 27) link_BETA1-6 : bond 0.00373 ( 2) link_BETA1-6 : angle 1.18510 ( 6) link_NAG-ASN : bond 0.00566 ( 11) link_NAG-ASN : angle 4.14979 ( 33) *********************** 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 98 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.305 Fit side-chains REVERT: A 115 LYS cc_start: 0.8422 (tptp) cc_final: 0.8093 (tptp) REVERT: A 154 LYS cc_start: 0.8428 (pttp) cc_final: 0.8012 (ptpt) REVERT: A 233 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8201 (mp) REVERT: A 270 MET cc_start: 0.9107 (tpp) cc_final: 0.8777 (tpt) REVERT: A 289 GLN cc_start: 0.8051 (mm-40) cc_final: 0.7605 (mm-40) REVERT: A 326 GLU cc_start: 0.8331 (mp0) cc_final: 0.8044 (mp0) REVERT: A 455 MET cc_start: 0.9190 (tmt) cc_final: 0.8822 (tmt) REVERT: A 596 LYS cc_start: 0.8454 (tttt) cc_final: 0.8201 (ttpt) REVERT: A 615 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7718 (mm110) REVERT: B 529 ARG cc_start: 0.7568 (ttm170) cc_final: 0.7087 (mtt90) outliers start: 10 outliers final: 2 residues processed: 96 average time/residue: 0.6942 time to fit residues: 69.8869 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 : 0.292 ------------------------------------------------------------------------------- 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 B residue 544 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 2 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.0870 chunk 87 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3605 r_free = 0.3605 target = 0.135052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095508 restraints weight = 7441.957| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.30 r_work: 0.2945 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2827 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 : 0.630 15.665 10084 Z= 0.312 Chirality : 0.045 0.452 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.819 54.729 1420 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.25 % Allowed : 11.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.28), residues: 891 helix: 2.23 (0.24), residues: 452 sheet: 0.77 (0.53), residues: 84 loop : 0.40 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 696 TYR 0.015 0.001 TYR A 385 PHE 0.015 0.002 PHE A 523 TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7347) covalent geometry : angle 0.57195 (10006) SS BOND : bond 0.00915 ( 6) SS BOND : angle 4.13406 ( 12) hydrogen bonds : bond 0.05975 ( 386) hydrogen bonds : angle 4.27866 ( 1092) metal coordination : bond 0.00088 ( 2) link_BETA1-4 : bond 0.00528 ( 9) link_BETA1-4 : angle 1.66878 ( 27) link_BETA1-6 : bond 0.00346 ( 2) link_BETA1-6 : angle 1.22986 ( 6) link_NAG-ASN : bond 0.00568 ( 11) link_NAG-ASN : angle 3.64325 ( 33) *********************** 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 96 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.322 Fit side-chains REVERT: A 115 LYS cc_start: 0.8422 (tptp) cc_final: 0.8089 (tptp) REVERT: A 154 LYS cc_start: 0.8433 (pttp) cc_final: 0.8030 (ptpt) REVERT: A 233 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 270 MET cc_start: 0.9099 (tpp) cc_final: 0.8842 (tpt) REVERT: A 289 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7537 (mm-40) REVERT: A 323 MET cc_start: 0.8778 (mmm) cc_final: 0.8349 (mmp) REVERT: A 596 LYS cc_start: 0.8459 (tttt) cc_final: 0.8213 (ttpt) REVERT: A 615 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7721 (mm110) REVERT: B 471 LYS cc_start: 0.7923 (tttp) cc_final: 0.7668 (tttp) REVERT: B 529 ARG cc_start: 0.7547 (ttm170) cc_final: 0.7004 (mtt90) outliers start: 8 outliers final: 1 residues processed: 95 average time/residue: 0.7319 time to fit residues: 72.8498 Evaluate side-chains 88 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 615 GLN 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 62 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 37 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 74 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3619 r_free = 0.3619 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.096702 restraints weight = 7519.140| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.50 r_work: 0.2955 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7377 Z= 0.119 Angle : 0.615 17.438 10084 Z= 0.305 Chirality : 0.045 0.505 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.765 54.192 1420 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.08 (0.28), residues: 891 helix: 2.29 (0.24), residues: 445 sheet: 0.75 (0.54), residues: 84 loop : 0.47 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 696 TYR 0.015 0.001 TYR A 385 PHE 0.014 0.001 PHE A 516 TRP 0.020 0.001 TRP A 163 HIS 0.005 0.001 HIS A 321 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7347) covalent geometry : angle 0.56307 (10006) SS BOND : bond 0.00730 ( 6) SS BOND : angle 4.19339 ( 12) hydrogen bonds : bond 0.05616 ( 386) hydrogen bonds : angle 4.24328 ( 1092) metal coordination : bond 0.00073 ( 2) link_BETA1-4 : bond 0.00553 ( 9) link_BETA1-4 : angle 1.59894 ( 27) link_BETA1-6 : bond 0.00389 ( 2) link_BETA1-6 : angle 1.23004 ( 6) link_NAG-ASN : bond 0.00511 ( 11) link_NAG-ASN : angle 3.26164 ( 33) ********************** 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: 5 poor density : 90 time to evaluate : 0.296 Fit side-chains REVERT: A 115 LYS cc_start: 0.8417 (tptp) cc_final: 0.8088 (tptp) REVERT: A 154 LYS cc_start: 0.8415 (pttp) cc_final: 0.8009 (ptpt) REVERT: A 233 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8102 (mp) REVERT: A 270 MET cc_start: 0.9087 (tpp) cc_final: 0.8732 (tpt) REVERT: A 289 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7530 (mm-40) REVERT: A 596 LYS cc_start: 0.8442 (tttt) cc_final: 0.8200 (ttpt) REVERT: A 615 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7774 (mm110) REVERT: B 471 LYS cc_start: 0.7869 (tttp) cc_final: 0.7650 (tttp) REVERT: B 529 ARG cc_start: 0.7525 (ttm170) cc_final: 0.6988 (mtt90) outliers start: 5 outliers final: 2 residues processed: 94 average time/residue: 0.7121 time to fit residues: 70.1454 Evaluate side-chains 90 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 46 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8360 ------------------------------------------------------------------------------- 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 B 466 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.135281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096220 restraints weight = 7507.104| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.32 r_work: 0.2946 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2855 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= 0.145 Angle : 0.646 17.822 10084 Z= 0.321 Chirality : 0.047 0.557 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.749 53.133 1420 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.94 % Allowed : 11.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.28), residues: 891 helix: 2.18 (0.24), residues: 452 sheet: 0.74 (0.53), residues: 84 loop : 0.40 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 696 TYR 0.016 0.002 TYR A 385 PHE 0.016 0.002 PHE A 523 TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7347) covalent geometry : angle 0.59374 (10006) SS BOND : bond 0.00963 ( 6) SS BOND : angle 4.22422 ( 12) hydrogen bonds : bond 0.06408 ( 386) hydrogen bonds : angle 4.30246 ( 1092) metal coordination : bond 0.00132 ( 2) link_BETA1-4 : bond 0.00513 ( 9) link_BETA1-4 : angle 1.68927 ( 27) link_BETA1-6 : bond 0.00344 ( 2) link_BETA1-6 : angle 1.26086 ( 6) link_NAG-ASN : bond 0.00551 ( 11) link_NAG-ASN : angle 3.37315 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3640.00 seconds wall clock time: 62 minutes 35.57 seconds (3755.57 seconds total)