Starting phenix.real_space_refine on Thu Jul 2 15:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snl_40628/07_2026/8snl_40628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snl_40628/07_2026/8snl_40628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2026/8snl_40628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2026/8snl_40628.map" model { file = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2026/8snl_40628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2026/8snl_40628.cif" } resolution = 2.78 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= 0.071 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Zn 1 6.06 5 S 70 5.16 5 C 5784 2.51 5 N 1550 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9098 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5167 Classifications: {'peptide': 656} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 23, 'TRANS': 632} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 3929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3929 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1286 SG CYS A 184 23.499 30.046 115.151 1.00 61.20 S Time building chain proxies: 1.50, per 1000 atoms: 0.16 Number of scatterers: 9098 At special positions: 0 Unit cell: (70.21, 112.336, 151.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 1 19.99 S 70 16.00 O 1692 8.00 N 1550 7.00 C 5784 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 225 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 423 " - pdb=" SG CYS A 453 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 502 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 521 " - pdb=" SG CYS A 548 " distance=2.03 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 600 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 641 " distance=2.03 Simple disulfide: pdb=" SG CYS B 447 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 470 " - pdb=" SG CYS B 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS B 487 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 564 " distance=2.03 Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 548 " distance=2.03 Simple disulfide: pdb=" SG CYS B 571 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 572 " - pdb=" SG CYS B 606 " distance=2.03 Simple disulfide: pdb=" SG CYS B 579 " - pdb=" SG CYS B 601 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 349.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 415 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 409 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 405 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 184 " Number of angles added : 3 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 37.5% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 32 through 39 removed outlier: 4.071A pdb=" N SER A 37 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 38 " --> pdb=" O LYS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 86 through 90 removed outlier: 3.828A pdb=" N ARG A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.757A pdb=" N VAL A 156 " --> pdb=" O TRP A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 170 through 172 No H-bonds generated for 'chain 'A' and resid 170 through 172' Processing helix chain 'A' and resid 190 through 194 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 243 through 265 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 343 through 347 removed outlier: 3.508A pdb=" N GLY A 346 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 347 " --> pdb=" O ASP A 344 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 347' Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 451 through 465 removed outlier: 3.816A pdb=" N SER A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 647 through 658 removed outlier: 3.596A pdb=" N GLN A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 671 Processing helix chain 'A' and resid 671 through 698 removed outlier: 3.528A pdb=" N SER A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'B' and resid 343 through 349 Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 373 through 395 removed outlier: 3.709A pdb=" N TYR B 377 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 451 through 467 removed outlier: 4.049A pdb=" N ASP B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 537 removed outlier: 3.817A pdb=" N ILE B 537 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 545 Processing helix chain 'B' and resid 559 through 564 removed outlier: 3.770A pdb=" N CYS B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 590 Processing helix chain 'B' and resid 600 through 604 Processing helix chain 'B' and resid 605 through 612 removed outlier: 4.062A pdb=" N LYS B 609 " --> pdb=" O HIS B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.524A pdb=" N SER B 631 " --> pdb=" O ARG B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 660 removed outlier: 4.455A pdb=" N ARG B 653 " --> pdb=" O MET B 649 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP B 654 " --> pdb=" O THR B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 683 Processing helix chain 'B' and resid 691 through 709 Processing helix chain 'B' and resid 715 through 735 removed outlier: 4.211A pdb=" N ALA B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 756 removed outlier: 3.764A pdb=" N HIS B 744 " --> pdb=" O ASP B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 795 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 804 through 809 removed outlier: 3.879A pdb=" N THR B 808 " --> pdb=" O ILE B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 820 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.829A pdb=" N ARG A 126 " --> pdb=" O ASN A 141 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER A 125 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 119 " --> pdb=" O SER A 125 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 4.355A pdb=" N VAL A 96 " --> pdb=" O TYR A 107 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N CYS A 225 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE A 279 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N LEU A 227 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLN A 281 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N LEU A 334 " --> pdb=" O THR A 224 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N LYS A 226 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS A 336 " --> pdb=" O LYS A 226 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 228 " --> pdb=" O HIS A 336 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N PHE A 338 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL A 230 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 368 through 371 Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'A' and resid 522 through 523 Processing sheet with id=AA6, first strand: chain 'A' and resid 533 through 535 Processing sheet with id=AA7, first strand: chain 'A' and resid 589 through 590 removed outlier: 4.112A pdb=" N GLU A 589 " --> pdb=" O ARG A 605 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 612 " --> pdb=" O CYS A 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 633 through 635 Processing sheet with id=AA9, first strand: chain 'B' and resid 403 through 411 Processing sheet with id=AB1, first strand: chain 'B' and resid 481 through 482 Processing sheet with id=AB2, first strand: chain 'B' and resid 579 through 582 removed outlier: 3.514A pdb=" N TYR B 593 " --> pdb=" O CYS B 572 " (cutoff:3.500A) 345 hydrogen bonds defined for protein. 987 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: 1.17 Time building geometry restraints manager: 0.69 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: 1669 1.32 - 1.45: 2699 1.45 - 1.59: 4861 1.59 - 1.72: 0 1.72 - 1.85: 84 Bond restraints: 9313 Sorted by residual: bond pdb=" CA HIS A 409 " pdb=" C HIS A 409 " ideal model delta sigma weight residual 1.523 1.476 0.047 1.30e-02 5.92e+03 1.32e+01 bond pdb=" C GLY A 408 " pdb=" O GLY A 408 " ideal model delta sigma weight residual 1.234 1.194 0.040 1.20e-02 6.94e+03 1.08e+01 bond pdb=" C TRP A 684 " pdb=" O TRP A 684 " ideal model delta sigma weight residual 1.236 1.200 0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" C HIS A 409 " pdb=" O HIS A 409 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.26e+00 bond pdb=" C LEU A 407 " pdb=" O LEU A 407 " ideal model delta sigma weight residual 1.236 1.201 0.035 1.26e-02 6.30e+03 7.67e+00 ... (remaining 9308 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 12256 1.99 - 3.98: 314 3.98 - 5.97: 40 5.97 - 7.97: 5 7.97 - 9.96: 3 Bond angle restraints: 12618 Sorted by residual: angle pdb=" N GLY B 517 " pdb=" CA GLY B 517 " pdb=" C GLY B 517 " ideal model delta sigma weight residual 111.09 102.48 8.61 1.33e+00 5.65e-01 4.20e+01 angle pdb=" C ALA A 270 " pdb=" CA ALA A 270 " pdb=" CB ALA A 270 " ideal model delta sigma weight residual 116.54 110.59 5.95 1.15e+00 7.56e-01 2.68e+01 angle pdb=" C ASN A 269 " pdb=" CA ASN A 269 " pdb=" CB ASN A 269 " ideal model delta sigma weight residual 115.79 110.56 5.23 1.19e+00 7.06e-01 1.93e+01 angle pdb=" CA CYS B 564 " pdb=" CB CYS B 564 " pdb=" SG CYS B 564 " ideal model delta sigma weight residual 114.40 124.36 -9.96 2.30e+00 1.89e-01 1.87e+01 angle pdb=" N SER B 516 " pdb=" CA SER B 516 " pdb=" C SER B 516 " ideal model delta sigma weight residual 110.97 115.37 -4.40 1.09e+00 8.42e-01 1.63e+01 ... (remaining 12613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5109 17.72 - 35.44: 408 35.44 - 53.16: 63 53.16 - 70.89: 22 70.89 - 88.61: 9 Dihedral angle restraints: 5611 sinusoidal: 2280 harmonic: 3331 Sorted by residual: dihedral pdb=" CB CYS A 582 " pdb=" SG CYS A 582 " pdb=" SG CYS A 604 " pdb=" CB CYS A 604 " ideal model delta sinusoidal sigma weight residual -86.00 -174.61 88.61 1 1.00e+01 1.00e-02 9.37e+01 dihedral pdb=" CB CYS A 423 " pdb=" SG CYS A 423 " pdb=" SG CYS A 453 " pdb=" CB CYS A 453 " ideal model delta sinusoidal sigma weight residual -86.00 -170.83 84.83 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS A 591 " pdb=" SG CYS A 591 " pdb=" SG CYS A 611 " pdb=" CB CYS A 611 " ideal model delta sinusoidal sigma weight residual -86.00 -150.84 64.84 1 1.00e+01 1.00e-02 5.52e+01 ... (remaining 5608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 995 0.044 - 0.088: 285 0.088 - 0.132: 91 0.132 - 0.176: 7 0.176 - 0.219: 3 Chirality restraints: 1381 Sorted by residual: chirality pdb=" CA VAL B 430 " pdb=" N VAL B 430 " pdb=" C VAL B 430 " pdb=" CB VAL B 430 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA SER A 608 " pdb=" N SER A 608 " pdb=" C SER A 608 " pdb=" CB SER A 608 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CG LEU B 491 " pdb=" CB LEU B 491 " pdb=" CD1 LEU B 491 " pdb=" CD2 LEU B 491 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1378 not shown) Planarity restraints: 1626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 612 " -0.089 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO A 613 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO A 613 " -0.070 5.00e-02 4.00e+02 pdb=" CD PRO A 613 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 312 " 0.014 2.00e-02 2.50e+03 1.95e-02 9.53e+00 pdb=" CG TRP A 312 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 312 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 312 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 312 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 312 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 312 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 312 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 312 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 312 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 685 " -0.049 5.00e-02 4.00e+02 7.33e-02 8.60e+00 pdb=" N PRO A 686 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 686 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 686 " -0.042 5.00e-02 4.00e+02 ... (remaining 1623 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 528 2.73 - 3.27: 9418 3.27 - 3.81: 15144 3.81 - 4.36: 19041 4.36 - 4.90: 31856 Nonbonded interactions: 75987 Sorted by model distance: nonbonded pdb=" OE1 GLN B 624 " pdb=" OH TYR B 626 " model vdw 2.183 3.040 nonbonded pdb=" OG1 THR A 62 " pdb=" OD2 ASP B 475 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR A 340 " pdb=" OG1 THR A 393 " model vdw 2.207 3.040 nonbonded pdb=" NH1 ARG A 89 " pdb=" OG1 THR A 116 " model vdw 2.207 3.120 nonbonded pdb=" OG1 THR B 376 " pdb=" OE1 GLU B 656 " model vdw 2.208 3.040 ... (remaining 75982 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.880 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.175 9340 Z= 0.248 Angle : 0.756 14.596 12667 Z= 0.434 Chirality : 0.045 0.219 1381 Planarity : 0.006 0.132 1626 Dihedral : 13.026 83.473 3396 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: -0.70 (0.24), residues: 1141 helix: 0.89 (0.27), residues: 364 sheet: -0.42 (0.46), residues: 121 loop : -1.31 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 372 TYR 0.012 0.001 TYR B 797 PHE 0.015 0.002 PHE A 323 TRP 0.050 0.002 TRP A 312 HIS 0.009 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.24 ( 9313) covalent geometry : angle 0.72895 / 0.43 (12618) SS BOND : bond 0.00311 / 0.23 ( 23) SS BOND : angle 1.71126 / 1.16 ( 46) hydrogen bonds : bond 0.14255 / 9.55 ( 345) hydrogen bonds : angle 6.45404 / 4.57 ( 987) metal coordination : bond 0.12126 / 7.76 ( 4) metal coordination : angle 11.53569 / 9.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 GLU cc_start: 0.8025 (tt0) cc_final: 0.7571 (tt0) REVERT: A 237 ARG cc_start: 0.7258 (ttt180) cc_final: 0.7037 (ttm170) REVERT: A 355 SER cc_start: 0.6951 (m) cc_final: 0.6739 (t) REVERT: A 367 LYS cc_start: 0.6984 (tptp) cc_final: 0.6610 (tmtt) REVERT: A 459 TYR cc_start: 0.7502 (t80) cc_final: 0.7177 (t80) REVERT: A 572 LYS cc_start: 0.6614 (mttm) cc_final: 0.6107 (mtpm) REVERT: A 574 LYS cc_start: 0.6001 (mptt) cc_final: 0.4488 (mtmt) REVERT: A 640 LYS cc_start: 0.6148 (mmtt) cc_final: 0.5537 (ttpt) REVERT: A 643 LYS cc_start: 0.7208 (ptpt) cc_final: 0.6845 (tptp) REVERT: A 653 TRP cc_start: 0.7990 (m100) cc_final: 0.7577 (m100) REVERT: A 666 LYS cc_start: 0.7819 (tttp) cc_final: 0.7573 (tttm) REVERT: B 354 ARG cc_start: 0.4412 (ptp-110) cc_final: 0.4118 (ptt-90) REVERT: B 372 ARG cc_start: 0.7957 (ttm-80) cc_final: 0.6540 (tmt170) REVERT: B 688 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7189 (mm-30) REVERT: B 715 ARG cc_start: 0.6945 (mpt180) cc_final: 0.6466 (mmm160) REVERT: B 773 ARG cc_start: 0.6681 (mtt180) cc_final: 0.5786 (mmt180) REVERT: B 777 LEU cc_start: 0.7075 (tp) cc_final: 0.6558 (mm) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.4536 time to fit residues: 108.2877 Evaluate side-chains 131 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 ASN A 320 GLN A 646 GLN B 403 GLN B 425 GLN B 427 ASN B 512 GLN B 556 HIS ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.158130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.121846 restraints weight = 10934.197| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.64 r_work: 0.3442 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 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 : 0.005 0.053 9340 Z= 0.191 Angle : 0.625 9.368 12667 Z= 0.324 Chirality : 0.045 0.170 1381 Planarity : 0.005 0.061 1626 Dihedral : 4.855 24.965 1236 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.48 % Allowed : 10.04 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: -0.47 (0.24), residues: 1141 helix: 1.30 (0.27), residues: 362 sheet: -0.78 (0.43), residues: 134 loop : -1.19 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 449 TYR 0.014 0.002 TYR B 820 PHE 0.016 0.002 PHE A 679 TRP 0.025 0.002 TRP A 312 HIS 0.007 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 ( 9313) covalent geometry : angle 0.61847 / 0.32 (12618) SS BOND : bond 0.00306 / 0.23 ( 23) SS BOND : angle 1.37375 / 0.92 ( 46) hydrogen bonds : bond 0.04435 / 3.02 ( 345) hydrogen bonds : angle 5.19614 / 3.59 ( 987) metal coordination : bond 0.01905 / 1.07 ( 4) metal coordination : angle 3.08310 / 2.23 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7283 (pp20) REVERT: A 146 GLU cc_start: 0.8605 (tt0) cc_final: 0.8105 (tt0) REVERT: A 237 ARG cc_start: 0.7710 (ttt180) cc_final: 0.7030 (ttm170) REVERT: A 302 LYS cc_start: 0.6761 (mmtt) cc_final: 0.5848 (ptpp) REVERT: A 355 SER cc_start: 0.6497 (m) cc_final: 0.6135 (t) REVERT: A 367 LYS cc_start: 0.6867 (tptp) cc_final: 0.6245 (tmtt) REVERT: A 410 ASN cc_start: 0.8470 (m-40) cc_final: 0.8226 (m-40) REVERT: A 422 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.4825 (mt-10) REVERT: A 459 TYR cc_start: 0.7392 (t80) cc_final: 0.6442 (t80) REVERT: A 513 GLN cc_start: 0.6841 (mt0) cc_final: 0.6624 (mt0) REVERT: A 572 LYS cc_start: 0.6194 (mttm) cc_final: 0.5745 (mtpm) REVERT: A 574 LYS cc_start: 0.5520 (mptt) cc_final: 0.4153 (mttt) REVERT: A 636 ASP cc_start: 0.6133 (t0) cc_final: 0.5732 (t0) REVERT: A 640 LYS cc_start: 0.5869 (mmtt) cc_final: 0.5533 (ttpt) REVERT: A 650 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 653 TRP cc_start: 0.7616 (m100) cc_final: 0.7281 (m100) REVERT: A 666 LYS cc_start: 0.7615 (tttp) cc_final: 0.7087 (ttpp) REVERT: B 354 ARG cc_start: 0.4311 (ptp-110) cc_final: 0.3653 (ptt-90) REVERT: B 372 ARG cc_start: 0.8164 (ttm-80) cc_final: 0.6382 (tmt170) REVERT: B 450 LYS cc_start: 0.6927 (ttmm) cc_final: 0.6568 (mmtp) REVERT: B 654 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6936 (t0) REVERT: B 666 ILE cc_start: 0.7314 (mm) cc_final: 0.7070 (mp) REVERT: B 688 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7265 (mm-30) REVERT: B 715 ARG cc_start: 0.6706 (mpt180) cc_final: 0.5892 (tpp-160) REVERT: B 773 ARG cc_start: 0.6326 (mtt180) cc_final: 0.5324 (mmt180) REVERT: B 777 LEU cc_start: 0.6567 (tp) cc_final: 0.6084 (mm) outliers start: 35 outliers final: 13 residues processed: 175 average time/residue: 0.4261 time to fit residues: 80.4792 Evaluate side-chains 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 650 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 ASN A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 551 GLN B 556 HIS ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120525 restraints weight = 10969.652| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.68 r_work: 0.3421 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9340 Z= 0.162 Angle : 0.576 9.603 12667 Z= 0.301 Chirality : 0.044 0.156 1381 Planarity : 0.004 0.054 1626 Dihedral : 4.735 25.592 1236 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.17 % Allowed : 13.02 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: -0.40 (0.24), residues: 1141 helix: 1.41 (0.27), residues: 362 sheet: -0.88 (0.44), residues: 130 loop : -1.14 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.010 0.001 TYR B 761 PHE 0.012 0.001 PHE B 668 TRP 0.014 0.001 TRP B 629 HIS 0.005 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 9313) covalent geometry : angle 0.57040 / 0.30 (12618) SS BOND : bond 0.00319 / 0.25 ( 23) SS BOND : angle 1.31588 / 0.99 ( 46) hydrogen bonds : bond 0.04097 / 2.77 ( 345) hydrogen bonds : angle 5.00474 / 3.45 ( 987) metal coordination : bond 0.01411 / 0.78 ( 4) metal coordination : angle 2.74558 / 1.95 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 140 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: A 106 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: A 237 ARG cc_start: 0.7649 (ttt180) cc_final: 0.6978 (ttm170) REVERT: A 290 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6645 (pm20) REVERT: A 302 LYS cc_start: 0.6758 (mmtt) cc_final: 0.5881 (ptpp) REVERT: A 355 SER cc_start: 0.6541 (m) cc_final: 0.6209 (t) REVERT: A 367 LYS cc_start: 0.6857 (tptp) cc_final: 0.6169 (tmtt) REVERT: A 410 ASN cc_start: 0.8517 (m-40) cc_final: 0.8266 (m-40) REVERT: A 422 GLU cc_start: 0.5453 (OUTLIER) cc_final: 0.4949 (mt-10) REVERT: A 459 TYR cc_start: 0.7310 (t80) cc_final: 0.6989 (t80) REVERT: A 525 CYS cc_start: 0.6448 (m) cc_final: 0.6137 (m) REVERT: A 574 LYS cc_start: 0.5487 (mptt) cc_final: 0.3775 (mttt) REVERT: A 636 ASP cc_start: 0.6143 (t0) cc_final: 0.5921 (t0) REVERT: A 640 LYS cc_start: 0.6563 (mmtt) cc_final: 0.5833 (ttpt) REVERT: A 642 GLU cc_start: 0.6400 (pp20) cc_final: 0.5897 (pp20) REVERT: A 653 TRP cc_start: 0.7695 (m100) cc_final: 0.7312 (m100) REVERT: A 666 LYS cc_start: 0.7728 (tttp) cc_final: 0.7155 (ttpp) REVERT: B 354 ARG cc_start: 0.4658 (ptp-110) cc_final: 0.3912 (ptt-90) REVERT: B 372 ARG cc_start: 0.8262 (ttm-80) cc_final: 0.6458 (tmt170) REVERT: B 450 LYS cc_start: 0.7048 (ttmm) cc_final: 0.6625 (mmtp) REVERT: B 465 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7554 (tt0) REVERT: B 566 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5639 (pt) REVERT: B 666 ILE cc_start: 0.7462 (mm) cc_final: 0.7221 (mp) REVERT: B 688 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 715 ARG cc_start: 0.6759 (mpt180) cc_final: 0.5916 (tpp-160) REVERT: B 736 LEU cc_start: 0.7256 (tt) cc_final: 0.6944 (pp) REVERT: B 773 ARG cc_start: 0.6407 (mtt180) cc_final: 0.5398 (mmt180) REVERT: B 777 LEU cc_start: 0.6666 (tp) cc_final: 0.6200 (mm) REVERT: B 821 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7222 (tt0) outliers start: 42 outliers final: 16 residues processed: 171 average time/residue: 0.4065 time to fit residues: 74.9467 Evaluate side-chains 145 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 489 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 566 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.4980 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 0.0470 chunk 101 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 427 ASN B 551 GLN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.121316 restraints weight = 11054.233| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.71 r_work: 0.3427 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9340 Z= 0.132 Angle : 0.539 8.539 12667 Z= 0.282 Chirality : 0.042 0.164 1381 Planarity : 0.004 0.054 1626 Dihedral : 4.568 25.645 1236 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.07 % Allowed : 14.41 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: -0.32 (0.24), residues: 1141 helix: 1.57 (0.27), residues: 357 sheet: -0.85 (0.44), residues: 132 loop : -1.13 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.018 0.001 TYR B 797 PHE 0.012 0.001 PHE B 668 TRP 0.012 0.001 TRP B 629 HIS 0.004 0.001 HIS B 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 9313) covalent geometry : angle 0.53341 / 0.28 (12618) SS BOND : bond 0.00245 / 0.19 ( 23) SS BOND : angle 1.34295 / 1.05 ( 46) hydrogen bonds : bond 0.03686 / 2.50 ( 345) hydrogen bonds : angle 4.81639 / 3.31 ( 987) metal coordination : bond 0.01207 / 0.67 ( 4) metal coordination : angle 2.08076 / 1.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 133 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7328 (tt0) REVERT: A 190 ASP cc_start: 0.5879 (OUTLIER) cc_final: 0.5633 (t0) REVERT: A 237 ARG cc_start: 0.7536 (ttt180) cc_final: 0.6909 (ttm170) REVERT: A 256 ASP cc_start: 0.6917 (m-30) cc_final: 0.6639 (m-30) REVERT: A 290 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6655 (pm20) REVERT: A 302 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6024 (ptpp) REVERT: A 355 SER cc_start: 0.6672 (m) cc_final: 0.6345 (t) REVERT: A 367 LYS cc_start: 0.6903 (tptp) cc_final: 0.6264 (tmtt) REVERT: A 410 ASN cc_start: 0.8414 (m-40) cc_final: 0.8154 (m-40) REVERT: A 422 GLU cc_start: 0.5621 (OUTLIER) cc_final: 0.5054 (mt-10) REVERT: A 574 LYS cc_start: 0.5440 (mptt) cc_final: 0.3763 (mttt) REVERT: A 640 LYS cc_start: 0.6602 (mmtt) cc_final: 0.6079 (ttpt) REVERT: A 642 GLU cc_start: 0.6402 (pp20) cc_final: 0.5923 (pp20) REVERT: A 650 GLU cc_start: 0.7763 (pt0) cc_final: 0.7517 (pm20) REVERT: A 653 TRP cc_start: 0.7760 (m100) cc_final: 0.7359 (m100) REVERT: A 666 LYS cc_start: 0.7726 (tttp) cc_final: 0.7173 (ttpp) REVERT: A 682 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6498 (mp) REVERT: B 354 ARG cc_start: 0.4918 (ptp-110) cc_final: 0.4099 (ptt90) REVERT: B 362 GLN cc_start: 0.5015 (pm20) cc_final: 0.4764 (pm20) REVERT: B 372 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.6348 (tmt170) REVERT: B 567 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8367 (mmtp) REVERT: B 580 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: B 666 ILE cc_start: 0.7394 (mm) cc_final: 0.7165 (mp) REVERT: B 688 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7282 (mm-30) REVERT: B 715 ARG cc_start: 0.6722 (mpt180) cc_final: 0.5933 (tpp-160) REVERT: B 736 LEU cc_start: 0.7354 (tt) cc_final: 0.6957 (pp) REVERT: B 768 ASP cc_start: 0.5959 (OUTLIER) cc_final: 0.5524 (t0) REVERT: B 773 ARG cc_start: 0.6516 (mtt180) cc_final: 0.5532 (mmt180) REVERT: B 777 LEU cc_start: 0.6667 (tp) cc_final: 0.6186 (mm) REVERT: B 821 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7316 (tt0) outliers start: 51 outliers final: 15 residues processed: 169 average time/residue: 0.3485 time to fit residues: 63.8329 Evaluate side-chains 148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.3980 chunk 86 optimal weight: 0.4980 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 40 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 80 optimal weight: 0.0770 chunk 1 optimal weight: 0.3980 chunk 60 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS B 427 ASN B 512 GLN B 551 GLN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.158656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122397 restraints weight = 10933.446| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.69 r_work: 0.3445 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9340 Z= 0.120 Angle : 0.549 10.129 12667 Z= 0.284 Chirality : 0.042 0.190 1381 Planarity : 0.004 0.052 1626 Dihedral : 4.577 25.866 1236 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.98 % Allowed : 15.90 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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 are not related in a simple way. whole: -0.22 (0.24), residues: 1141 helix: 1.66 (0.27), residues: 358 sheet: -0.65 (0.45), residues: 127 loop : -1.10 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 610 TYR 0.011 0.001 TYR A 436 PHE 0.012 0.001 PHE B 668 TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9313) covalent geometry : angle 0.54216 / 0.28 (12618) SS BOND : bond 0.00352 / 0.26 ( 23) SS BOND : angle 1.47975 / 0.96 ( 46) hydrogen bonds : bond 0.03504 / 2.37 ( 345) hydrogen bonds : angle 4.70684 / 3.24 ( 987) metal coordination : bond 0.00969 / 0.53 ( 4) metal coordination : angle 1.85236 / 1.36 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: A 190 ASP cc_start: 0.5811 (OUTLIER) cc_final: 0.5574 (t0) REVERT: A 237 ARG cc_start: 0.7581 (ttt180) cc_final: 0.6980 (ttm170) REVERT: A 256 ASP cc_start: 0.6880 (m-30) cc_final: 0.6584 (m-30) REVERT: A 290 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6667 (pm20) REVERT: A 367 LYS cc_start: 0.6814 (tptp) cc_final: 0.6173 (tmtt) REVERT: A 410 ASN cc_start: 0.8357 (m-40) cc_final: 0.8106 (m-40) REVERT: A 525 CYS cc_start: 0.6130 (m) cc_final: 0.5829 (m) REVERT: A 574 LYS cc_start: 0.5238 (mptt) cc_final: 0.3621 (mttt) REVERT: A 640 LYS cc_start: 0.6401 (mmtt) cc_final: 0.5914 (ttpt) REVERT: A 642 GLU cc_start: 0.6465 (pp20) cc_final: 0.5916 (pp20) REVERT: A 650 GLU cc_start: 0.7764 (pt0) cc_final: 0.7518 (pm20) REVERT: A 653 TRP cc_start: 0.7741 (m100) cc_final: 0.7345 (m100) REVERT: A 666 LYS cc_start: 0.7695 (tttp) cc_final: 0.7141 (ttpp) REVERT: A 682 ILE cc_start: 0.6999 (OUTLIER) cc_final: 0.6427 (mp) REVERT: B 354 ARG cc_start: 0.5034 (ptp-110) cc_final: 0.4208 (ptt90) REVERT: B 372 ARG cc_start: 0.7886 (ttm-80) cc_final: 0.6216 (tmt170) REVERT: B 436 ASP cc_start: 0.7958 (m-30) cc_final: 0.7738 (m-30) REVERT: B 567 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8263 (mmtp) REVERT: B 580 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6563 (tt0) REVERT: B 688 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7220 (mm-30) REVERT: B 715 ARG cc_start: 0.6693 (mpt180) cc_final: 0.5890 (tpp-160) REVERT: B 736 LEU cc_start: 0.7334 (OUTLIER) cc_final: 0.6928 (pp) REVERT: B 773 ARG cc_start: 0.6450 (mtt180) cc_final: 0.5477 (mmt180) REVERT: B 777 LEU cc_start: 0.6587 (tp) cc_final: 0.6078 (mm) outliers start: 40 outliers final: 14 residues processed: 160 average time/residue: 0.3716 time to fit residues: 64.1435 Evaluate side-chains 143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 605 HIS ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116566 restraints weight = 11015.325| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.68 r_work: 0.3375 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9340 Z= 0.217 Angle : 0.651 9.048 12667 Z= 0.334 Chirality : 0.047 0.220 1381 Planarity : 0.005 0.046 1626 Dihedral : 4.960 34.185 1236 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.98 % Allowed : 17.00 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.41 (0.24), residues: 1141 helix: 1.31 (0.27), residues: 365 sheet: -0.82 (0.44), residues: 131 loop : -1.12 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 449 TYR 0.027 0.002 TYR B 797 PHE 0.014 0.002 PHE A 470 TRP 0.013 0.001 TRP B 629 HIS 0.005 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 ( 9313) covalent geometry : angle 0.64395 / 0.33 (12618) SS BOND : bond 0.00352 / 0.26 ( 23) SS BOND : angle 1.50260 / 1.08 ( 46) hydrogen bonds : bond 0.04382 / 2.93 ( 345) hydrogen bonds : angle 4.94124 / 3.42 ( 987) metal coordination : bond 0.02037 / 1.15 ( 4) metal coordination : angle 3.34979 / 2.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 126 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: A 190 ASP cc_start: 0.5827 (OUTLIER) cc_final: 0.5589 (t0) REVERT: A 237 ARG cc_start: 0.7756 (ttt180) cc_final: 0.7108 (ttm170) REVERT: A 302 LYS cc_start: 0.7199 (mmpt) cc_final: 0.6018 (ptpp) REVERT: A 410 ASN cc_start: 0.8627 (m-40) cc_final: 0.8273 (m-40) REVERT: A 422 GLU cc_start: 0.5581 (OUTLIER) cc_final: 0.4926 (mt-10) REVERT: A 435 MET cc_start: 0.8188 (mmm) cc_final: 0.7981 (tpp) REVERT: A 525 CYS cc_start: 0.6490 (m) cc_final: 0.6179 (m) REVERT: A 601 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6738 (mptt) REVERT: A 642 GLU cc_start: 0.6499 (pp20) cc_final: 0.6000 (pp20) REVERT: A 650 GLU cc_start: 0.7816 (pt0) cc_final: 0.7526 (pm20) REVERT: A 653 TRP cc_start: 0.7725 (m100) cc_final: 0.7314 (m100) REVERT: A 666 LYS cc_start: 0.7762 (tttp) cc_final: 0.7158 (ttpp) REVERT: A 682 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6458 (mp) REVERT: A 683 PHE cc_start: 0.5684 (m-10) cc_final: 0.5397 (t80) REVERT: B 354 ARG cc_start: 0.4976 (ptp-110) cc_final: 0.4133 (ptt90) REVERT: B 372 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.6502 (tmt170) REVERT: B 450 LYS cc_start: 0.7136 (ttmm) cc_final: 0.6775 (mmtp) REVERT: B 666 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7441 (mt) REVERT: B 688 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7478 (mm-30) REVERT: B 715 ARG cc_start: 0.6940 (mpt180) cc_final: 0.6114 (tpp-160) REVERT: B 736 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.6946 (pp) REVERT: B 768 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5514 (t0) REVERT: B 773 ARG cc_start: 0.6483 (mtt180) cc_final: 0.5492 (mmt180) REVERT: B 777 LEU cc_start: 0.6674 (tp) cc_final: 0.6177 (mm) outliers start: 40 outliers final: 22 residues processed: 153 average time/residue: 0.3981 time to fit residues: 65.9947 Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 435 ILE Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 94 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 107 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 53 optimal weight: 0.3980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 551 GLN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119494 restraints weight = 10957.366| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.67 r_work: 0.3416 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9340 Z= 0.137 Angle : 0.580 8.311 12667 Z= 0.300 Chirality : 0.043 0.169 1381 Planarity : 0.004 0.045 1626 Dihedral : 4.763 34.844 1236 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.88 % Allowed : 18.19 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.34 (0.24), residues: 1141 helix: 1.48 (0.27), residues: 364 sheet: -0.89 (0.43), residues: 131 loop : -1.11 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 610 TYR 0.009 0.001 TYR A 436 PHE 0.013 0.001 PHE B 668 TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 536 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 9313) covalent geometry : angle 0.57489 / 0.30 (12618) SS BOND : bond 0.00199 / 0.15 ( 23) SS BOND : angle 1.26921 / 0.89 ( 46) hydrogen bonds : bond 0.03741 / 2.51 ( 345) hydrogen bonds : angle 4.79567 / 3.31 ( 987) metal coordination : bond 0.01287 / 0.73 ( 4) metal coordination : angle 1.98626 / 1.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7563 (tt0) REVERT: A 237 ARG cc_start: 0.7706 (ttt180) cc_final: 0.7039 (ttm170) REVERT: A 256 ASP cc_start: 0.7178 (m-30) cc_final: 0.6877 (m-30) REVERT: A 302 LYS cc_start: 0.7197 (mmpt) cc_final: 0.6048 (ptpp) REVERT: A 355 SER cc_start: 0.6452 (m) cc_final: 0.6060 (t) REVERT: A 410 ASN cc_start: 0.8548 (m-40) cc_final: 0.8253 (m-40) REVERT: A 525 CYS cc_start: 0.6393 (m) cc_final: 0.6076 (m) REVERT: A 531 GLN cc_start: 0.7025 (OUTLIER) cc_final: 0.6682 (mm110) REVERT: A 601 LYS cc_start: 0.7160 (OUTLIER) cc_final: 0.6756 (mptt) REVERT: A 642 GLU cc_start: 0.6480 (pp20) cc_final: 0.5967 (pp20) REVERT: A 650 GLU cc_start: 0.7829 (pt0) cc_final: 0.7596 (pm20) REVERT: A 653 TRP cc_start: 0.7700 (m100) cc_final: 0.7285 (m100) REVERT: A 666 LYS cc_start: 0.7739 (tttp) cc_final: 0.7159 (ttpp) REVERT: A 682 ILE cc_start: 0.7019 (OUTLIER) cc_final: 0.6434 (mp) REVERT: A 683 PHE cc_start: 0.5701 (m-10) cc_final: 0.5422 (t80) REVERT: B 354 ARG cc_start: 0.5043 (ptp-110) cc_final: 0.4195 (ptt90) REVERT: B 372 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.6409 (tmt170) REVERT: B 435 ILE cc_start: 0.7701 (mt) cc_final: 0.7469 (mp) REVERT: B 450 LYS cc_start: 0.7131 (ttmm) cc_final: 0.6743 (mmtp) REVERT: B 620 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6698 (mm-30) REVERT: B 666 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7437 (mt) REVERT: B 688 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7457 (mm-30) REVERT: B 715 ARG cc_start: 0.6795 (mpt180) cc_final: 0.5916 (tpp-160) REVERT: B 736 LEU cc_start: 0.7477 (OUTLIER) cc_final: 0.6977 (pp) REVERT: B 773 ARG cc_start: 0.6479 (mtt180) cc_final: 0.5506 (mmt180) REVERT: B 777 LEU cc_start: 0.6573 (tp) cc_final: 0.6088 (mm) outliers start: 39 outliers final: 19 residues processed: 158 average time/residue: 0.4245 time to fit residues: 72.5679 Evaluate side-chains 150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 505 MET Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.154830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.118292 restraints weight = 10944.156| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.67 r_work: 0.3402 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9340 Z= 0.161 Angle : 0.602 8.287 12667 Z= 0.311 Chirality : 0.044 0.186 1381 Planarity : 0.004 0.049 1626 Dihedral : 4.781 35.482 1236 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.98 % Allowed : 18.29 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.38 (0.24), residues: 1141 helix: 1.45 (0.27), residues: 364 sheet: -0.89 (0.44), residues: 131 loop : -1.14 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.032 0.001 TYR B 797 PHE 0.012 0.001 PHE B 668 TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 ( 9313) covalent geometry : angle 0.59580 / 0.31 (12618) SS BOND : bond 0.00235 / 0.17 ( 23) SS BOND : angle 1.32374 / 0.94 ( 46) hydrogen bonds : bond 0.03946 / 2.65 ( 345) hydrogen bonds : angle 4.82572 / 3.33 ( 987) metal coordination : bond 0.01769 / 0.98 ( 4) metal coordination : angle 2.96145 / 2.01 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 237 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7110 (ttm170) REVERT: A 256 ASP cc_start: 0.7219 (m-30) cc_final: 0.6891 (m-30) REVERT: A 302 LYS cc_start: 0.7242 (mmpt) cc_final: 0.6062 (ptpp) REVERT: A 367 LYS cc_start: 0.6910 (tptp) cc_final: 0.6287 (tmtt) REVERT: A 410 ASN cc_start: 0.8595 (m-40) cc_final: 0.8271 (m-40) REVERT: A 525 CYS cc_start: 0.6390 (m) cc_final: 0.6068 (m) REVERT: A 531 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6668 (mm110) REVERT: A 601 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6649 (mptt) REVERT: A 642 GLU cc_start: 0.6505 (pp20) cc_final: 0.6003 (pp20) REVERT: A 650 GLU cc_start: 0.7820 (pt0) cc_final: 0.7591 (pm20) REVERT: A 653 TRP cc_start: 0.7683 (m100) cc_final: 0.7294 (m100) REVERT: A 666 LYS cc_start: 0.7725 (tttp) cc_final: 0.7103 (ttpp) REVERT: A 682 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6448 (mp) REVERT: A 683 PHE cc_start: 0.5764 (m-10) cc_final: 0.5496 (t80) REVERT: B 354 ARG cc_start: 0.4995 (ptp-110) cc_final: 0.4188 (ptt90) REVERT: B 372 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.6429 (tmt170) REVERT: B 435 ILE cc_start: 0.7798 (mt) cc_final: 0.7569 (mp) REVERT: B 450 LYS cc_start: 0.7154 (ttmm) cc_final: 0.6789 (mmtp) REVERT: B 485 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7635 (ptmm) REVERT: B 666 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7469 (mt) REVERT: B 688 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 715 ARG cc_start: 0.6815 (mpt180) cc_final: 0.5902 (tpp-160) REVERT: B 736 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6987 (pp) REVERT: B 752 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7205 (mt) REVERT: B 768 ASP cc_start: 0.5978 (OUTLIER) cc_final: 0.5562 (t0) REVERT: B 773 ARG cc_start: 0.6476 (mtt180) cc_final: 0.5505 (mmt180) REVERT: B 777 LEU cc_start: 0.6580 (tp) cc_final: 0.6088 (mm) outliers start: 40 outliers final: 20 residues processed: 157 average time/residue: 0.3955 time to fit residues: 67.3537 Evaluate side-chains 155 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 112 optimal weight: 0.0270 chunk 81 optimal weight: 0.2980 chunk 31 optimal weight: 0.1980 chunk 16 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS B 427 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121805 restraints weight = 10891.815| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.66 r_work: 0.3436 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9340 Z= 0.115 Angle : 0.558 7.756 12667 Z= 0.288 Chirality : 0.042 0.187 1381 Planarity : 0.004 0.049 1626 Dihedral : 4.519 32.127 1236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.78 % Allowed : 19.78 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.28 (0.24), residues: 1141 helix: 1.66 (0.27), residues: 359 sheet: -0.73 (0.45), residues: 125 loop : -1.18 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.012 0.001 TYR A 250 PHE 0.013 0.001 PHE B 668 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 9313) covalent geometry : angle 0.55507 / 0.29 (12618) SS BOND : bond 0.00171 / 0.12 ( 23) SS BOND : angle 1.07538 / 0.77 ( 46) hydrogen bonds : bond 0.03426 / 2.32 ( 345) hydrogen bonds : angle 4.67546 / 3.22 ( 987) metal coordination : bond 0.00894 / 0.55 ( 4) metal coordination : angle 1.48953 / 1.02 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: A 237 ARG cc_start: 0.7837 (ttt180) cc_final: 0.7147 (ttm170) REVERT: A 256 ASP cc_start: 0.7213 (m-30) cc_final: 0.6859 (m-30) REVERT: A 302 LYS cc_start: 0.7194 (mmpt) cc_final: 0.6026 (ptpp) REVERT: A 367 LYS cc_start: 0.6865 (tptp) cc_final: 0.6251 (tmtt) REVERT: A 525 CYS cc_start: 0.6358 (m) cc_final: 0.6049 (m) REVERT: A 642 GLU cc_start: 0.6462 (pp20) cc_final: 0.6009 (pp20) REVERT: A 650 GLU cc_start: 0.7803 (pt0) cc_final: 0.7595 (pm20) REVERT: A 653 TRP cc_start: 0.7703 (m100) cc_final: 0.7323 (m100) REVERT: A 666 LYS cc_start: 0.7757 (tttp) cc_final: 0.7134 (ttpp) REVERT: A 683 PHE cc_start: 0.5723 (m-10) cc_final: 0.5428 (t80) REVERT: B 354 ARG cc_start: 0.5153 (ptp-110) cc_final: 0.4332 (ptt90) REVERT: B 372 ARG cc_start: 0.7920 (ttm-80) cc_final: 0.6333 (tmt170) REVERT: B 435 ILE cc_start: 0.7729 (mt) cc_final: 0.7517 (mp) REVERT: B 580 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6816 (tt0) REVERT: B 620 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6647 (mm-30) REVERT: B 666 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7156 (mp) REVERT: B 686 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7927 (ttt180) REVERT: B 688 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 715 ARG cc_start: 0.6795 (mpt180) cc_final: 0.5902 (tpp-160) REVERT: B 736 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6963 (pp) REVERT: B 768 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5806 (t70) REVERT: B 773 ARG cc_start: 0.6464 (mtt180) cc_final: 0.5500 (mmt180) REVERT: B 777 LEU cc_start: 0.6493 (tp) cc_final: 0.5988 (mm) outliers start: 28 outliers final: 17 residues processed: 146 average time/residue: 0.3741 time to fit residues: 59.1976 Evaluate side-chains 141 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.8980 chunk 17 optimal weight: 0.0020 chunk 75 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS B 427 ASN B 456 GLN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.120750 restraints weight = 10901.125| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.67 r_work: 0.3436 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9340 Z= 0.124 Angle : 0.563 9.929 12667 Z= 0.288 Chirality : 0.042 0.184 1381 Planarity : 0.004 0.050 1626 Dihedral : 4.483 33.511 1236 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.78 % Allowed : 19.88 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.31 (0.24), residues: 1141 helix: 1.63 (0.27), residues: 359 sheet: -0.72 (0.44), residues: 129 loop : -1.19 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 610 TYR 0.025 0.001 TYR B 797 PHE 0.013 0.001 PHE B 668 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 9313) covalent geometry : angle 0.55967 / 0.29 (12618) SS BOND : bond 0.00171 / 0.12 ( 23) SS BOND : angle 1.06501 / 0.76 ( 46) hydrogen bonds : bond 0.03497 / 2.36 ( 345) hydrogen bonds : angle 4.65435 / 3.20 ( 987) metal coordination : bond 0.01422 / 0.78 ( 4) metal coordination : angle 2.35113 / 1.64 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: A 194 LEU cc_start: 0.5688 (OUTLIER) cc_final: 0.5465 (mp) REVERT: A 237 ARG cc_start: 0.7668 (ttt180) cc_final: 0.6950 (ttm170) REVERT: A 256 ASP cc_start: 0.7102 (m-30) cc_final: 0.6736 (m-30) REVERT: A 302 LYS cc_start: 0.7114 (mmpt) cc_final: 0.5940 (ptpp) REVERT: A 367 LYS cc_start: 0.6797 (tptp) cc_final: 0.6179 (tmtt) REVERT: A 525 CYS cc_start: 0.6375 (m) cc_final: 0.6062 (m) REVERT: A 601 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6399 (mptt) REVERT: A 640 LYS cc_start: 0.7082 (mmtt) cc_final: 0.6252 (ttpt) REVERT: A 642 GLU cc_start: 0.6512 (pp20) cc_final: 0.6092 (pp20) REVERT: A 653 TRP cc_start: 0.7669 (m100) cc_final: 0.7433 (m100) REVERT: A 666 LYS cc_start: 0.7714 (tttp) cc_final: 0.7088 (ttpp) REVERT: A 683 PHE cc_start: 0.5657 (m-10) cc_final: 0.5387 (t80) REVERT: B 354 ARG cc_start: 0.5096 (ptp-110) cc_final: 0.4308 (ptt90) REVERT: B 372 ARG cc_start: 0.7885 (ttm-80) cc_final: 0.6247 (tmt170) REVERT: B 435 ILE cc_start: 0.7631 (mt) cc_final: 0.7416 (mp) REVERT: B 580 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6689 (tt0) REVERT: B 666 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.7017 (mp) REVERT: B 686 ARG cc_start: 0.8216 (ttt180) cc_final: 0.7847 (ttt180) REVERT: B 688 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7380 (mm-30) REVERT: B 715 ARG cc_start: 0.6742 (mpt180) cc_final: 0.5846 (tpp-160) REVERT: B 736 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.6902 (pp) REVERT: B 773 ARG cc_start: 0.6335 (mtt180) cc_final: 0.5396 (mmt180) REVERT: B 777 LEU cc_start: 0.6368 (tp) cc_final: 0.5866 (mm) outliers start: 28 outliers final: 19 residues processed: 149 average time/residue: 0.3933 time to fit residues: 63.6032 Evaluate side-chains 143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 100 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 427 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.152384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.114853 restraints weight = 10681.321| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 2.72 r_work: 0.3258 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9340 Z= 0.202 Angle : 0.651 9.144 12667 Z= 0.333 Chirality : 0.046 0.194 1381 Planarity : 0.004 0.051 1626 Dihedral : 4.817 35.480 1236 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.48 % Allowed : 19.58 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 are not related in a simple way. whole: -0.46 (0.24), residues: 1141 helix: 1.33 (0.27), residues: 365 sheet: -0.78 (0.44), residues: 129 loop : -1.19 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 610 TYR 0.013 0.002 TYR A 459 PHE 0.012 0.002 PHE A 470 TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.20 ( 9313) covalent geometry : angle 0.64406 / 0.33 (12618) SS BOND : bond 0.00297 / 0.22 ( 23) SS BOND : angle 1.41455 / 1.00 ( 46) hydrogen bonds : bond 0.04239 / 2.84 ( 345) hydrogen bonds : angle 4.85908 / 3.36 ( 987) metal coordination : bond 0.02048 / 1.12 ( 4) metal coordination : angle 3.38082 / 2.41 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2660.93 seconds wall clock time: 46 minutes 2.42 seconds (2762.42 seconds total)