Starting phenix.real_space_refine on Wed Mar 12 04:39:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dak_46691/03_2025/9dak_46691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dak_46691/03_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_46691/03_2025/9dak_46691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dak_46691/03_2025/9dak_46691.map" model { file = "/net/cci-nas-00/data/ceres_data/9dak_46691/03_2025/9dak_46691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dak_46691/03_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-5624/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: 4.93, per 1000 atoms: 0.68 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: 2.27 Conformation dependent library (CDL) restraints added in 773.0 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: 0.80 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: 2.20 Time building geometry restraints manager: 2.46 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.650 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:15.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- 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 : 0.011 0.084 7347 Z= 0.745 Angle : 1.220 21.895 10006 Z= 0.809 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 *********************** 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 : 0.753 Fit side-chains REVERT: A 270 MET cc_start: 0.8713 (tpp) cc_final: 0.8482 (tpt) REVERT: A 297 MET cc_start: 0.8920 (mtp) cc_final: 0.8720 (mtp) REVERT: A 480 MET cc_start: 0.8842 (mtp) cc_final: 0.8630 (mtp) outliers start: 3 outliers final: 1 residues processed: 127 average time/residue: 1.6047 time to fit residues: 212.8910 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 : 0.819 ------------------------------------------------------------------------------- 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 7347 Z= 0.197 Angle : 0.586 8.947 10006 Z= 0.314 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 *********************** 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 : 0.850 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: 1.3365 time to fit residues: 149.1856 Evaluate side-chains 86 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.133629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.093690 restraints weight = 7478.616| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.21 r_work: 0.2913 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7347 Z= 0.232 Angle : 0.583 15.147 10006 Z= 0.311 Chirality : 0.045 0.270 1144 Planarity : 0.005 0.037 1258 Dihedral : 6.539 57.504 1422 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 1.76 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: 1.93 (0.28), residues: 891 helix: 2.06 (0.25), residues: 447 sheet: 0.98 (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 482 *********************** 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 : 0.834 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8492 (tptp) cc_final: 0.8250 (tptp) REVERT: A 233 ILE cc_start: 0.8665 (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: 0.8042 (mm-40) cc_final: 0.7660 (mm-40) REVERT: A 589 LYS cc_start: 0.8872 (tttp) cc_final: 0.8537 (ttmt) REVERT: A 596 LYS cc_start: 0.8533 (tttt) cc_final: 0.8292 (ttpt) REVERT: A 696 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7713 (ttt-90) REVERT: B 558 LEU cc_start: 0.8549 (mp) cc_final: 0.8282 (mp) REVERT: B 570 VAL cc_start: 0.8528 (t) cc_final: 0.8320 (t) outliers start: 13 outliers final: 2 residues processed: 99 average time/residue: 1.3942 time to fit residues: 145.1782 Evaluate side-chains 86 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 83 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 73 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 87 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 overall best weight: 0.6500 ------------------------------------------------------------------------------- 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 = 0.3665 r_free = 0.3665 target = 0.136392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.094270 restraints weight = 7677.786| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.41 r_work: 0.2959 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7347 Z= 0.177 Angle : 0.608 27.569 10006 Z= 0.316 Chirality : 0.046 0.425 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.653 50.758 1422 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.03 % Allowed : 8.91 % 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: 2.00 (0.28), residues: 891 helix: 2.15 (0.24), residues: 452 sheet: 0.88 (0.50), residues: 90 loop : 0.45 (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 *********************** 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: 13 poor density : 90 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8428 (tptp) cc_final: 0.8179 (tptp) REVERT: A 233 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8248 (mp) REVERT: A 270 MET cc_start: 0.9106 (tpp) cc_final: 0.8771 (tpt) REVERT: A 289 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7730 (mm-40) REVERT: A 323 MET cc_start: 0.8955 (mmm) cc_final: 0.8464 (mmp) REVERT: A 589 LYS cc_start: 0.8904 (tttp) cc_final: 0.8576 (ttmt) REVERT: A 596 LYS cc_start: 0.8524 (tttt) cc_final: 0.8277 (ttpt) REVERT: B 529 ARG cc_start: 0.7585 (ttm170) cc_final: 0.7124 (mtt90) REVERT: B 536 ARG cc_start: 0.7434 (tpm170) cc_final: 0.6786 (tpp80) REVERT: B 558 LEU cc_start: 0.8525 (mp) cc_final: 0.8260 (mp) REVERT: B 570 VAL cc_start: 0.8453 (t) cc_final: 0.8232 (t) outliers start: 13 outliers final: 4 residues processed: 100 average time/residue: 1.5848 time to fit residues: 166.9296 Evaluate side-chains 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 615 GLN Chi-restraints excluded: chain B residue 544 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 85 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.135880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.092126 restraints weight = 7644.416| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.15 r_work: 0.2961 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7347 Z= 0.190 Angle : 0.606 23.651 10006 Z= 0.315 Chirality : 0.046 0.408 1144 Planarity : 0.004 0.036 1258 Dihedral : 5.462 51.025 1422 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 1.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.19 % Allowed : 8.91 % 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 (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: 2.18 (0.24), residues: 452 sheet: 0.89 (0.52), residues: 84 loop : 0.42 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.016 0.002 PHE A 523 TYR 0.017 0.001 TYR A 385 ARG 0.003 0.000 ARG A 116 *********************** 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 105 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 1.092 Fit side-chains REVERT: A 115 LYS cc_start: 0.8530 (tptp) cc_final: 0.8277 (tptp) REVERT: A 233 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 270 MET cc_start: 0.9096 (tpp) cc_final: 0.8759 (tpt) REVERT: A 289 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7729 (mm-40) REVERT: A 323 MET cc_start: 0.8921 (mmm) cc_final: 0.8479 (mmp) REVERT: A 589 LYS cc_start: 0.8921 (tttp) cc_final: 0.8589 (ttmt) REVERT: A 596 LYS cc_start: 0.8557 (tttt) cc_final: 0.8295 (ttpt) REVERT: A 615 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.7591 (mm-40) REVERT: B 529 ARG cc_start: 0.7589 (ttm170) cc_final: 0.7299 (mtt90) REVERT: B 536 ARG cc_start: 0.7423 (tpm170) cc_final: 0.6809 (tpp80) outliers start: 14 outliers final: 4 residues processed: 102 average time/residue: 1.7828 time to fit residues: 192.1927 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 1.673 ------------------------------------------------------------------------------- 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: 2.9990 chunk 71 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 = 0.3643 r_free = 0.3643 target = 0.134573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.094067 restraints weight = 7627.613| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.29 r_work: 0.2931 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7347 Z= 0.242 Angle : 0.627 19.719 10006 Z= 0.327 Chirality : 0.048 0.452 1144 Planarity : 0.004 0.037 1258 Dihedral : 5.620 57.466 1420 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.88 % Allowed : 9.69 % 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 (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: 1.89 (0.28), residues: 891 helix: 2.07 (0.24), residues: 452 sheet: 0.90 (0.51), residues: 84 loop : 0.37 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 163 HIS 0.006 0.001 HIS A 159 PHE 0.018 0.002 PHE A 523 TYR 0.016 0.002 TYR A 385 ARG 0.003 0.000 ARG A 116 *********************** 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: 12 poor density : 89 time to evaluate : 0.843 Fit side-chains REVERT: A 115 LYS cc_start: 0.8399 (tptp) cc_final: 0.8105 (tptp) REVERT: A 233 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8128 (mp) REVERT: A 270 MET cc_start: 0.8999 (tpp) cc_final: 0.8752 (tpt) REVERT: A 289 GLN cc_start: 0.8043 (mm-40) cc_final: 0.7646 (mm-40) REVERT: A 589 LYS cc_start: 0.8785 (tttp) cc_final: 0.8386 (ttmt) REVERT: A 596 LYS cc_start: 0.8387 (tttt) cc_final: 0.8095 (ttpt) REVERT: A 615 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7492 (mm110) REVERT: B 467 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7368 (mtp85) REVERT: B 536 ARG cc_start: 0.7196 (tpm170) cc_final: 0.6578 (tpp80) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 1.7634 time to fit residues: 177.8459 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 : 0.765 ------------------------------------------------------------------------------- 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: 0.0070 chunk 3 optimal weight: 0.9990 chunk 70 optimal weight: 0.0470 chunk 30 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.138453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.094972 restraints weight = 7686.713| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.14 r_work: 0.3008 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7347 Z= 0.133 Angle : 0.539 15.050 10006 Z= 0.280 Chirality : 0.045 0.526 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.436 55.568 1420 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.09 % Allowed : 10.31 % 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: 2.15 (0.28), residues: 891 helix: 2.31 (0.24), residues: 448 sheet: 0.88 (0.53), residues: 84 loop : 0.52 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 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 *********************** 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: 7 poor density : 90 time to evaluate : 0.811 Fit side-chains REVERT: A 115 LYS cc_start: 0.8432 (tptp) cc_final: 0.8119 (tptp) REVERT: A 233 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8181 (mp) REVERT: A 270 MET cc_start: 0.9117 (tpp) cc_final: 0.8779 (tpt) REVERT: A 289 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7713 (mm-40) REVERT: A 589 LYS cc_start: 0.8872 (tttp) cc_final: 0.8560 (ttmt) REVERT: A 596 LYS cc_start: 0.8511 (tttt) cc_final: 0.8259 (ttpt) REVERT: A 615 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7634 (mm110) REVERT: B 529 ARG cc_start: 0.7590 (ttm170) cc_final: 0.7160 (mtt90) REVERT: B 536 ARG cc_start: 0.7478 (tpm170) cc_final: 0.6840 (tpp80) outliers start: 7 outliers final: 0 residues processed: 95 average time/residue: 1.3994 time to fit residues: 139.7859 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 89 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE 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: 0.0770 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 48 optimal weight: 0.3980 chunk 30 optimal weight: 0.4980 chunk 88 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 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 B 466 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.096769 restraints weight = 7714.786| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.51 r_work: 0.2988 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7347 Z= 0.153 Angle : 0.543 15.302 10006 Z= 0.283 Chirality : 0.044 0.478 1144 Planarity : 0.004 0.034 1258 Dihedral : 5.308 56.492 1420 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.94 % Allowed : 11.09 % Favored : 87.97 % 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: 2.14 (0.28), residues: 891 helix: 2.30 (0.24), residues: 452 sheet: 0.87 (0.53), residues: 84 loop : 0.50 (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 0.001 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.005 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 1.319 Fit side-chains REVERT: A 115 LYS cc_start: 0.8421 (tptp) cc_final: 0.8093 (tptp) REVERT: A 154 LYS cc_start: 0.8455 (pttp) cc_final: 0.8030 (ptpt) REVERT: A 233 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8165 (mp) REVERT: A 270 MET cc_start: 0.9108 (tpp) cc_final: 0.8754 (tpt) REVERT: A 289 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7687 (mm-40) REVERT: A 589 LYS cc_start: 0.8873 (tttp) cc_final: 0.8534 (ttmt) REVERT: A 596 LYS cc_start: 0.8556 (tttt) cc_final: 0.8280 (ttpt) REVERT: B 471 LYS cc_start: 0.7944 (tttp) cc_final: 0.7600 (tttp) REVERT: B 529 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7027 (mtt90) REVERT: B 536 ARG cc_start: 0.7435 (tpm170) cc_final: 0.6785 (tpp80) outliers start: 6 outliers final: 3 residues processed: 97 average time/residue: 1.4214 time to fit residues: 144.8415 Evaluate side-chains 91 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 532 ILE 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: 0.3980 chunk 83 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 18 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 159 HIS A 195 ASN A 553 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.096305 restraints weight = 7578.205| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.64 r_work: 0.2940 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7347 Z= 0.166 Angle : 0.595 22.564 10006 Z= 0.304 Chirality : 0.046 0.469 1144 Planarity : 0.004 0.035 1258 Dihedral : 5.966 60.719 1420 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % 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: 2.14 (0.28), residues: 891 helix: 2.28 (0.24), residues: 452 sheet: 0.89 (0.54), residues: 83 loop : 0.53 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.015 0.002 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.811 Fit side-chains REVERT: A 115 LYS cc_start: 0.8509 (tptp) cc_final: 0.8180 (tptp) REVERT: A 154 LYS cc_start: 0.8438 (pttp) cc_final: 0.8024 (ptpt) REVERT: A 233 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8131 (mp) REVERT: A 270 MET cc_start: 0.9087 (tpp) cc_final: 0.8712 (tpt) REVERT: A 289 GLN cc_start: 0.7995 (mm-40) cc_final: 0.7536 (mm-40) REVERT: A 589 LYS cc_start: 0.8802 (tttp) cc_final: 0.8449 (ttmt) REVERT: A 596 LYS cc_start: 0.8518 (tttt) cc_final: 0.8234 (ttpt) REVERT: B 471 LYS cc_start: 0.7897 (tttp) cc_final: 0.7502 (tttp) REVERT: B 529 ARG cc_start: 0.7542 (ttm170) cc_final: 0.7247 (mtt90) REVERT: B 536 ARG cc_start: 0.7330 (tpm170) cc_final: 0.6708 (tpp80) outliers start: 8 outliers final: 3 residues processed: 98 average time/residue: 1.4593 time to fit residues: 150.1721 Evaluate side-chains 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 532 ILE 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: 4.9990 chunk 80 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 37 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 159 HIS A 195 ASN A 553 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.094974 restraints weight = 7630.494| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.47 r_work: 0.2913 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7347 Z= 0.249 Angle : 0.683 23.623 10006 Z= 0.348 Chirality : 0.048 0.516 1144 Planarity : 0.004 0.037 1258 Dihedral : 6.555 82.172 1420 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.94 % Allowed : 11.09 % Favored : 87.97 % 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: 1.89 (0.28), residues: 891 helix: 2.09 (0.24), residues: 452 sheet: 0.84 (0.53), residues: 84 loop : 0.35 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.020 0.002 PHE A 523 TYR 0.016 0.002 TYR A 385 ARG 0.004 0.000 ARG A 696 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.744 Fit side-chains REVERT: A 115 LYS cc_start: 0.8765 (tptp) cc_final: 0.8540 (tptp) REVERT: A 141 GLN cc_start: 0.8568 (tt0) cc_final: 0.8344 (pt0) REVERT: A 154 LYS cc_start: 0.8533 (pttp) cc_final: 0.8232 (ptpt) REVERT: A 233 ILE cc_start: 0.8766 (OUTLIER) cc_final: 0.8417 (mp) REVERT: A 270 MET cc_start: 0.9195 (tpp) cc_final: 0.8954 (tpt) REVERT: A 289 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7708 (mm-40) REVERT: A 589 LYS cc_start: 0.8967 (tttp) cc_final: 0.8705 (ttmt) REVERT: A 615 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.7776 (mm110) REVERT: B 471 LYS cc_start: 0.8115 (tttp) cc_final: 0.7754 (tttp) REVERT: B 536 ARG cc_start: 0.7625 (tpm170) cc_final: 0.7112 (tpp80) outliers start: 6 outliers final: 3 residues processed: 93 average time/residue: 1.4554 time to fit residues: 142.0230 Evaluate side-chains 92 residues out of total 795 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 0.0270 overall best weight: 0.4776 ------------------------------------------------------------------------------- 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 A 615 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.096614 restraints weight = 7535.162| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.36 r_work: 0.2966 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7347 Z= 0.157 Angle : 0.598 21.099 10006 Z= 0.305 Chirality : 0.044 0.445 1144 Planarity : 0.004 0.035 1258 Dihedral : 6.437 84.010 1420 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 0.94 % Allowed : 11.56 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: 2.22 (0.24), residues: 452 sheet: 0.76 (0.54), residues: 83 loop : 0.41 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 163 HIS 0.005 0.001 HIS A 77 PHE 0.014 0.001 PHE A 516 TYR 0.015 0.001 TYR A 385 ARG 0.004 0.000 ARG A 696 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7604.18 seconds wall clock time: 133 minutes 8.79 seconds (7988.79 seconds total)