Starting phenix.real_space_refine on Sun Jul 27 07:14:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snl_40628/07_2025/8snl_40628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snl_40628/07_2025/8snl_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_2025/8snl_40628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2025/8snl_40628.map" model { file = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2025/8snl_40628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snl_40628/07_2025/8snl_40628.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.071 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 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, 2 Unusual residues: {' CA': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 6.10, per 1000 atoms: 0.67 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: 2.28 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.32 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: 2.79 Time building geometry restraints manager: 2.71 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: 8.230 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: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (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 TRP 0.050 0.002 TRP A 312 HIS 0.009 0.001 HIS A 405 PHE 0.015 0.002 PHE A 323 TYR 0.012 0.001 TYR B 797 ARG 0.008 0.001 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.14255 ( 345) hydrogen bonds : angle 6.45404 ( 987) metal coordination : bond 0.12126 ( 4) metal coordination : angle 11.53569 ( 3) SS BOND : bond 0.00311 ( 23) SS BOND : angle 1.71126 ( 46) covalent geometry : bond 0.00431 ( 9313) covalent geometry : angle 0.72895 (12618) *********************** 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 : 1.150 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: 0.6740 (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: 0.7176 (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: 1.2561 time to fit residues: 300.3814 Evaluate side-chains 132 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 GLN A 646 GLN B 403 GLN B 425 GLN B 427 ASN ** B 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN B 556 HIS B 648 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.160517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.123987 restraints weight = 10731.575| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.69 r_work: 0.3458 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9340 Z= 0.151 Angle : 0.589 9.069 12667 Z= 0.306 Chirality : 0.044 0.147 1381 Planarity : 0.005 0.062 1626 Dihedral : 4.727 24.518 1236 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.38 % Allowed : 9.94 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1141 helix: 1.39 (0.27), residues: 362 sheet: -0.65 (0.44), residues: 128 loop : -1.22 (0.23), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 312 HIS 0.006 0.001 HIS B 595 PHE 0.015 0.001 PHE A 679 TYR 0.014 0.002 TYR B 797 ARG 0.005 0.001 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.04107 ( 345) hydrogen bonds : angle 5.14357 ( 987) metal coordination : bond 0.01499 ( 4) metal coordination : angle 1.99245 ( 3) SS BOND : bond 0.00255 ( 23) SS BOND : angle 1.39481 ( 46) covalent geometry : bond 0.00354 ( 9313) covalent geometry : angle 0.58296 (12618) *********************** 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 181 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7515 (ttt180) cc_final: 0.6827 (ttm170) REVERT: A 290 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6666 (pm20) REVERT: A 302 LYS cc_start: 0.6750 (mmtt) cc_final: 0.5908 (ptpp) REVERT: A 355 SER cc_start: 0.6461 (m) cc_final: 0.6141 (t) REVERT: A 367 LYS cc_start: 0.6776 (tptp) cc_final: 0.6153 (tmtt) REVERT: A 410 ASN cc_start: 0.8275 (m-40) cc_final: 0.8046 (m-40) REVERT: A 422 GLU cc_start: 0.5496 (OUTLIER) cc_final: 0.5013 (mt-10) REVERT: A 459 TYR cc_start: 0.7373 (t80) cc_final: 0.6324 (t80) REVERT: A 513 GLN cc_start: 0.6614 (mt0) cc_final: 0.6405 (mt0) REVERT: A 572 LYS cc_start: 0.5933 (mttm) cc_final: 0.5544 (mtpm) REVERT: A 574 LYS cc_start: 0.5368 (mptt) cc_final: 0.4129 (mttt) REVERT: A 636 ASP cc_start: 0.6070 (t0) cc_final: 0.5606 (t0) REVERT: A 640 LYS cc_start: 0.5836 (mmtt) cc_final: 0.5524 (ttpt) REVERT: A 653 TRP cc_start: 0.7690 (m100) cc_final: 0.7354 (m100) REVERT: A 666 LYS cc_start: 0.7605 (tttp) cc_final: 0.7070 (ttpp) REVERT: B 354 ARG cc_start: 0.4363 (ptp-110) cc_final: 0.3744 (ptt-90) REVERT: B 372 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.6289 (tmt170) REVERT: B 505 MET cc_start: 0.8455 (ttm) cc_final: 0.8122 (mtp) REVERT: B 566 ILE cc_start: 0.5990 (pt) cc_final: 0.5649 (pt) REVERT: B 654 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6669 (t0) REVERT: B 666 ILE cc_start: 0.7155 (mm) cc_final: 0.6902 (mp) REVERT: B 688 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7110 (mm-30) REVERT: B 715 ARG cc_start: 0.6678 (mpt180) cc_final: 0.5908 (tpp-160) REVERT: B 773 ARG cc_start: 0.6312 (mtt180) cc_final: 0.5286 (mmt180) REVERT: B 777 LEU cc_start: 0.6576 (tp) cc_final: 0.6080 (mm) outliers start: 34 outliers final: 13 residues processed: 173 average time/residue: 1.0400 time to fit residues: 194.1966 Evaluate side-chains 136 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 490 THR 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 70 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 427 ASN B 556 HIS ** 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 = 0.3891 r_free = 0.3891 target = 0.158925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.122460 restraints weight = 10897.255| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.70 r_work: 0.3439 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9340 Z= 0.138 Angle : 0.547 9.335 12667 Z= 0.286 Chirality : 0.043 0.141 1381 Planarity : 0.004 0.052 1626 Dihedral : 4.593 25.285 1236 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.28 % Allowed : 13.42 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.24), residues: 1141 helix: 1.53 (0.27), residues: 363 sheet: -0.79 (0.44), residues: 130 loop : -1.15 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.005 0.001 HIS B 595 PHE 0.012 0.001 PHE B 668 TYR 0.011 0.001 TYR B 761 ARG 0.005 0.000 ARG A 610 Details of bonding type rmsd hydrogen bonds : bond 0.03869 ( 345) hydrogen bonds : angle 4.93845 ( 987) metal coordination : bond 0.01219 ( 4) metal coordination : angle 2.42259 ( 3) SS BOND : bond 0.00311 ( 23) SS BOND : angle 1.14422 ( 46) covalent geometry : bond 0.00327 ( 9313) covalent geometry : angle 0.54271 (12618) *********************** 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 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 138 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: A 162 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7672 (mppt) REVERT: A 237 ARG cc_start: 0.7560 (ttt180) cc_final: 0.6983 (ttm170) REVERT: A 290 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6695 (pm20) REVERT: A 302 LYS cc_start: 0.6857 (mmtt) cc_final: 0.6067 (ptpp) REVERT: A 355 SER cc_start: 0.6645 (m) cc_final: 0.6319 (t) REVERT: A 367 LYS cc_start: 0.6812 (tptp) cc_final: 0.6142 (tmtt) REVERT: A 410 ASN cc_start: 0.8384 (m-40) cc_final: 0.8134 (m-40) REVERT: A 422 GLU cc_start: 0.5578 (OUTLIER) cc_final: 0.5077 (mt-10) REVERT: A 459 TYR cc_start: 0.7307 (t80) cc_final: 0.6927 (t80) REVERT: A 572 LYS cc_start: 0.6163 (mttm) cc_final: 0.5717 (mtpm) REVERT: A 574 LYS cc_start: 0.5405 (mptt) cc_final: 0.4125 (mttt) REVERT: A 640 LYS cc_start: 0.6620 (mmtt) cc_final: 0.5898 (ttpt) REVERT: A 642 GLU cc_start: 0.6325 (pp20) cc_final: 0.5942 (pp20) REVERT: A 653 TRP cc_start: 0.7721 (m100) cc_final: 0.7333 (m100) REVERT: A 666 LYS cc_start: 0.7711 (tttp) cc_final: 0.7145 (ttpp) REVERT: A 682 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6471 (mp) REVERT: B 354 ARG cc_start: 0.4610 (ptp-110) cc_final: 0.3905 (ptt90) REVERT: B 372 ARG cc_start: 0.8199 (ttm-80) cc_final: 0.6426 (tmt170) REVERT: B 485 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7853 (ptmm) REVERT: B 505 MET cc_start: 0.8514 (ttm) cc_final: 0.8309 (mtp) REVERT: B 566 ILE cc_start: 0.6276 (pt) cc_final: 0.5794 (pt) REVERT: B 688 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7333 (mm-30) REVERT: B 715 ARG cc_start: 0.6757 (mpt180) cc_final: 0.5974 (tpp-160) REVERT: B 736 LEU cc_start: 0.7288 (tt) cc_final: 0.7057 (pp) REVERT: B 773 ARG cc_start: 0.6445 (mtt180) cc_final: 0.5413 (mmt180) REVERT: B 777 LEU cc_start: 0.6673 (tp) cc_final: 0.6117 (mm) REVERT: B 821 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7102 (tt0) outliers start: 33 outliers final: 13 residues processed: 164 average time/residue: 1.0446 time to fit residues: 185.3339 Evaluate side-chains 140 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 LYS 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 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 485 LYS 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 564 CYS 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 7 optimal weight: 0.0000 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN A 65 HIS B 427 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.159128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.122777 restraints weight = 10815.663| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.69 r_work: 0.3445 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9340 Z= 0.120 Angle : 0.527 8.382 12667 Z= 0.276 Chirality : 0.042 0.132 1381 Planarity : 0.004 0.051 1626 Dihedral : 4.484 25.236 1236 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.07 % Allowed : 14.02 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1141 helix: 1.62 (0.27), residues: 363 sheet: -0.81 (0.45), residues: 128 loop : -1.14 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.004 0.001 HIS B 595 PHE 0.012 0.001 PHE B 668 TYR 0.020 0.001 TYR B 797 ARG 0.003 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 345) hydrogen bonds : angle 4.75806 ( 987) metal coordination : bond 0.01079 ( 4) metal coordination : angle 1.73375 ( 3) SS BOND : bond 0.00248 ( 23) SS BOND : angle 1.33198 ( 46) covalent geometry : bond 0.00280 ( 9313) covalent geometry : angle 0.52120 (12618) *********************** 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 177 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 126 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7456 (pp20) REVERT: A 106 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7423 (tt0) REVERT: A 162 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7687 (mppt) REVERT: A 190 ASP cc_start: 0.5770 (OUTLIER) cc_final: 0.5496 (t0) REVERT: A 237 ARG cc_start: 0.7711 (ttt180) cc_final: 0.7054 (ttm170) REVERT: A 256 ASP cc_start: 0.7136 (m-30) cc_final: 0.6862 (m-30) REVERT: A 290 GLU cc_start: 0.7244 (mt-10) cc_final: 0.6625 (pm20) REVERT: A 302 LYS cc_start: 0.6869 (mmtt) cc_final: 0.6162 (ptpp) REVERT: A 355 SER cc_start: 0.6649 (m) cc_final: 0.6293 (t) REVERT: A 367 LYS cc_start: 0.6766 (tptp) cc_final: 0.6122 (tmtt) REVERT: A 410 ASN cc_start: 0.8505 (m-40) cc_final: 0.8271 (m-40) REVERT: A 422 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.4942 (mt-10) REVERT: A 640 LYS cc_start: 0.6629 (mmtt) cc_final: 0.6104 (ttpt) REVERT: A 642 GLU cc_start: 0.6621 (pp20) cc_final: 0.6099 (pp20) REVERT: A 644 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6807 (ttp-170) REVERT: A 653 TRP cc_start: 0.7730 (m100) cc_final: 0.7334 (m100) REVERT: A 666 LYS cc_start: 0.7726 (tttp) cc_final: 0.7170 (ttpp) REVERT: A 682 ILE cc_start: 0.7021 (OUTLIER) cc_final: 0.6412 (mp) REVERT: B 354 ARG cc_start: 0.4762 (ptp-110) cc_final: 0.4043 (ptt90) REVERT: B 372 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.6429 (tmt170) REVERT: B 436 ASP cc_start: 0.8048 (m-30) cc_final: 0.7834 (m-30) REVERT: B 566 ILE cc_start: 0.6045 (OUTLIER) cc_final: 0.5515 (pt) REVERT: B 567 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8346 (mmtp) REVERT: B 666 ILE cc_start: 0.7690 (OUTLIER) cc_final: 0.7209 (mp) REVERT: B 688 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7293 (mm-30) REVERT: B 715 ARG cc_start: 0.6721 (mpt180) cc_final: 0.5925 (tpp-160) REVERT: B 736 LEU cc_start: 0.7334 (tt) cc_final: 0.7005 (pp) REVERT: B 773 ARG cc_start: 0.6428 (mtt180) cc_final: 0.5427 (mmt180) REVERT: B 777 LEU cc_start: 0.6681 (tp) cc_final: 0.6210 (mm) outliers start: 51 outliers final: 15 residues processed: 161 average time/residue: 0.9890 time to fit residues: 172.8370 Evaluate side-chains 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 64 THR 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 162 LYS 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 552 SER Chi-restraints excluded: chain A residue 644 ARG Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE 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 566 ILE Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 666 ILE Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 28 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 102 optimal weight: 0.0970 chunk 112 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 427 ASN B 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.158410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.121926 restraints weight = 10755.680| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.67 r_work: 0.3443 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9340 Z= 0.139 Angle : 0.557 7.932 12667 Z= 0.289 Chirality : 0.043 0.180 1381 Planarity : 0.004 0.050 1626 Dihedral : 4.599 25.783 1236 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.47 % Allowed : 15.31 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1141 helix: 1.63 (0.27), residues: 364 sheet: -0.86 (0.44), residues: 128 loop : -1.16 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.004 0.001 HIS B 595 PHE 0.012 0.001 PHE B 668 TYR 0.010 0.001 TYR A 459 ARG 0.002 0.000 ARG B 372 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 345) hydrogen bonds : angle 4.74777 ( 987) metal coordination : bond 0.01309 ( 4) metal coordination : angle 2.13142 ( 3) SS BOND : bond 0.00356 ( 23) SS BOND : angle 1.53262 ( 46) covalent geometry : bond 0.00330 ( 9313) covalent geometry : angle 0.54938 (12618) *********************** 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 169 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 124 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: A 106 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: A 190 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5533 (t0) REVERT: A 237 ARG cc_start: 0.7643 (ttt180) cc_final: 0.7049 (ttm170) REVERT: A 256 ASP cc_start: 0.6995 (m-30) cc_final: 0.6689 (m-30) REVERT: A 290 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6673 (pm20) REVERT: A 302 LYS cc_start: 0.7051 (mmtt) cc_final: 0.6251 (ptpp) REVERT: A 355 SER cc_start: 0.6681 (m) cc_final: 0.6334 (t) REVERT: A 367 LYS cc_start: 0.6812 (tptp) cc_final: 0.6178 (tmtt) REVERT: A 410 ASN cc_start: 0.8415 (m-40) cc_final: 0.8136 (m-40) REVERT: A 422 GLU cc_start: 0.5470 (OUTLIER) cc_final: 0.4915 (mt-10) REVERT: A 574 LYS cc_start: 0.5467 (mptt) cc_final: 0.3815 (mttt) REVERT: A 601 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.6369 (mptt) REVERT: A 640 LYS cc_start: 0.6526 (mmtt) cc_final: 0.5963 (ttpt) REVERT: A 642 GLU cc_start: 0.6489 (pp20) cc_final: 0.5978 (pp20) REVERT: A 653 TRP cc_start: 0.7731 (m100) cc_final: 0.7337 (m100) REVERT: A 666 LYS cc_start: 0.7719 (tttp) cc_final: 0.7162 (ttpp) REVERT: A 682 ILE cc_start: 0.7046 (OUTLIER) cc_final: 0.6437 (mp) REVERT: A 683 PHE cc_start: 0.5636 (m-10) cc_final: 0.5331 (t80) REVERT: B 354 ARG cc_start: 0.4985 (ptp-110) cc_final: 0.4188 (ptt90) REVERT: B 372 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.6378 (tmt170) REVERT: B 620 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6658 (mm-30) REVERT: B 666 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7373 (mt) REVERT: B 688 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7230 (mm-30) REVERT: B 715 ARG cc_start: 0.6733 (mpt180) cc_final: 0.5920 (tpp-160) REVERT: B 736 LEU cc_start: 0.7412 (tt) cc_final: 0.7012 (pp) REVERT: B 773 ARG cc_start: 0.6480 (mtt180) cc_final: 0.5504 (mmt180) REVERT: B 777 LEU cc_start: 0.6653 (tp) cc_final: 0.6167 (mm) outliers start: 45 outliers final: 19 residues processed: 155 average time/residue: 1.1211 time to fit residues: 189.8609 Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.011 ------------------------------------------------------------------------------- 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 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 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 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 457 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 804 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 16 optimal weight: 0.2980 chunk 59 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 427 ASN B 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.159094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.122555 restraints weight = 10805.703| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.68 r_work: 0.3450 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9340 Z= 0.121 Angle : 0.541 7.368 12667 Z= 0.283 Chirality : 0.043 0.205 1381 Planarity : 0.004 0.049 1626 Dihedral : 4.613 30.769 1236 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.68 % Allowed : 17.50 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.24), residues: 1141 helix: 1.69 (0.27), residues: 359 sheet: -0.59 (0.45), residues: 125 loop : -1.18 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 536 PHE 0.013 0.001 PHE B 668 TYR 0.023 0.001 TYR B 797 ARG 0.002 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 345) hydrogen bonds : angle 4.70535 ( 987) metal coordination : bond 0.00999 ( 4) metal coordination : angle 1.80367 ( 3) SS BOND : bond 0.00226 ( 23) SS BOND : angle 1.25425 ( 46) covalent geometry : bond 0.00284 ( 9313) covalent geometry : angle 0.53583 (12618) *********************** 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 161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 124 time to evaluate : 2.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: A 190 ASP cc_start: 0.5881 (OUTLIER) cc_final: 0.5631 (t0) REVERT: A 237 ARG cc_start: 0.7642 (ttt180) cc_final: 0.7044 (ttm170) REVERT: A 256 ASP cc_start: 0.6999 (m-30) cc_final: 0.6679 (m-30) REVERT: A 290 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6679 (pm20) REVERT: A 302 LYS cc_start: 0.7072 (mmtt) cc_final: 0.6272 (ptpp) REVERT: A 367 LYS cc_start: 0.6819 (tptp) cc_final: 0.6205 (tmtt) REVERT: A 410 ASN cc_start: 0.8415 (m-40) cc_final: 0.8145 (m-40) REVERT: A 524 ASN cc_start: 0.7784 (m-40) cc_final: 0.6665 (p0) REVERT: A 574 LYS cc_start: 0.5365 (mptt) cc_final: 0.3738 (mttt) REVERT: A 642 GLU cc_start: 0.6478 (pp20) cc_final: 0.5957 (pp20) REVERT: A 653 TRP cc_start: 0.7727 (m100) cc_final: 0.7328 (m100) REVERT: A 666 LYS cc_start: 0.7739 (tttp) cc_final: 0.7179 (ttpp) REVERT: A 682 ILE cc_start: 0.7079 (OUTLIER) cc_final: 0.6472 (mp) REVERT: A 683 PHE cc_start: 0.5679 (m-10) cc_final: 0.5424 (t80) REVERT: B 354 ARG cc_start: 0.5010 (ptp-110) cc_final: 0.4205 (ptt90) REVERT: B 372 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.6294 (tmt170) REVERT: B 436 ASP cc_start: 0.7997 (m-30) cc_final: 0.7769 (m-30) REVERT: B 580 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: B 620 GLU cc_start: 0.7212 (mm-30) cc_final: 0.6721 (mm-30) REVERT: B 666 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7135 (mp) REVERT: B 688 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7288 (mm-30) REVERT: B 715 ARG cc_start: 0.6741 (mpt180) cc_final: 0.5932 (tpp-160) REVERT: B 736 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6989 (pp) REVERT: B 773 ARG cc_start: 0.6474 (mtt180) cc_final: 0.5502 (mmt180) REVERT: B 777 LEU cc_start: 0.6655 (tp) cc_final: 0.6185 (mm) outliers start: 37 outliers final: 17 residues processed: 149 average time/residue: 1.3321 time to fit residues: 217.0167 Evaluate side-chains 143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 1.054 ------------------------------------------------------------------------------- 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 497 ASN Chi-restraints excluded: chain A residue 499 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 93 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 110 optimal weight: 0.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.156868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120131 restraints weight = 10847.866| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.69 r_work: 0.3420 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9340 Z= 0.146 Angle : 0.572 7.728 12667 Z= 0.296 Chirality : 0.044 0.169 1381 Planarity : 0.004 0.048 1626 Dihedral : 4.667 33.616 1236 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.78 % Allowed : 18.09 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.24), residues: 1141 helix: 1.59 (0.27), residues: 364 sheet: -0.67 (0.45), residues: 125 loop : -1.14 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 536 PHE 0.012 0.001 PHE B 668 TYR 0.009 0.001 TYR A 436 ARG 0.002 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 345) hydrogen bonds : angle 4.75006 ( 987) metal coordination : bond 0.01378 ( 4) metal coordination : angle 2.29885 ( 3) SS BOND : bond 0.00393 ( 23) SS BOND : angle 1.40168 ( 46) covalent geometry : bond 0.00351 ( 9313) covalent geometry : angle 0.56554 (12618) *********************** 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 162 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 124 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: A 146 GLU cc_start: 0.8457 (tt0) cc_final: 0.8198 (tt0) REVERT: A 190 ASP cc_start: 0.5829 (OUTLIER) cc_final: 0.5581 (t0) REVERT: A 237 ARG cc_start: 0.7755 (ttt180) cc_final: 0.7069 (ttm170) REVERT: A 256 ASP cc_start: 0.7150 (m-30) cc_final: 0.6877 (m-30) REVERT: A 410 ASN cc_start: 0.8588 (m-40) cc_final: 0.8288 (m-40) REVERT: A 435 MET cc_start: 0.8298 (mmm) cc_final: 0.8045 (tpp) REVERT: A 510 GLU cc_start: 0.7359 (mp0) cc_final: 0.7095 (mm-30) REVERT: A 524 ASN cc_start: 0.7672 (m-40) cc_final: 0.7469 (m-40) REVERT: A 531 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.6788 (mm110) REVERT: A 601 LYS cc_start: 0.7022 (OUTLIER) cc_final: 0.6422 (mptt) REVERT: A 642 GLU cc_start: 0.6574 (pp20) cc_final: 0.6050 (pp20) REVERT: A 650 GLU cc_start: 0.7818 (pt0) cc_final: 0.7574 (pm20) REVERT: A 653 TRP cc_start: 0.7718 (m100) cc_final: 0.7319 (m100) REVERT: A 666 LYS cc_start: 0.7773 (tttp) cc_final: 0.7207 (ttpp) REVERT: A 682 ILE cc_start: 0.7056 (OUTLIER) cc_final: 0.6440 (mp) REVERT: A 683 PHE cc_start: 0.5741 (m-10) cc_final: 0.5433 (t80) REVERT: B 354 ARG cc_start: 0.4996 (ptp-110) cc_final: 0.4173 (ptt90) REVERT: B 372 ARG cc_start: 0.8079 (ttm-80) cc_final: 0.6411 (tmt170) REVERT: B 666 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7257 (mp) REVERT: B 688 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7387 (mm-30) REVERT: B 715 ARG cc_start: 0.6795 (mpt180) cc_final: 0.5939 (tpp-160) REVERT: B 736 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.6979 (pp) REVERT: B 773 ARG cc_start: 0.6465 (mtt180) cc_final: 0.5486 (mmt180) REVERT: B 777 LEU cc_start: 0.6617 (tp) cc_final: 0.6124 (mm) outliers start: 38 outliers final: 20 residues processed: 149 average time/residue: 0.9783 time to fit residues: 158.7378 Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 190 ASP Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 531 GLN Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 566 VAL 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 457 LEU 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 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 796 ILE 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 104 optimal weight: 0.1980 chunk 35 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 551 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.119050 restraints weight = 11038.195| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.69 r_work: 0.3407 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9340 Z= 0.161 Angle : 0.591 8.116 12667 Z= 0.304 Chirality : 0.044 0.172 1381 Planarity : 0.004 0.047 1626 Dihedral : 4.701 32.326 1236 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.68 % Allowed : 18.19 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.24), residues: 1141 helix: 1.55 (0.27), residues: 364 sheet: -0.78 (0.44), residues: 129 loop : -1.16 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 561 PHE 0.012 0.001 PHE B 668 TYR 0.027 0.001 TYR B 797 ARG 0.003 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03855 ( 345) hydrogen bonds : angle 4.78762 ( 987) metal coordination : bond 0.01519 ( 4) metal coordination : angle 2.32247 ( 3) SS BOND : bond 0.00337 ( 23) SS BOND : angle 1.38678 ( 46) covalent geometry : bond 0.00389 ( 9313) covalent geometry : angle 0.58535 (12618) *********************** 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 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 146 GLU cc_start: 0.8451 (tt0) cc_final: 0.8212 (tt0) REVERT: A 190 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5596 (t0) REVERT: A 237 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7034 (ttm170) REVERT: A 256 ASP cc_start: 0.7095 (m-30) cc_final: 0.6849 (m-30) REVERT: A 302 LYS cc_start: 0.7249 (mmpt) cc_final: 0.6145 (ptpp) REVERT: A 367 LYS cc_start: 0.6889 (tptp) cc_final: 0.6253 (tmtt) REVERT: A 410 ASN cc_start: 0.8590 (m-40) cc_final: 0.8269 (m-40) REVERT: A 422 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.4902 (mt-10) REVERT: A 435 MET cc_start: 0.8212 (mmm) cc_final: 0.7990 (tpp) REVERT: A 510 GLU cc_start: 0.7362 (mp0) cc_final: 0.7124 (mm-30) REVERT: A 524 ASN cc_start: 0.7669 (m-40) cc_final: 0.7467 (m-40) REVERT: A 531 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6653 (mm110) REVERT: A 642 GLU cc_start: 0.6697 (pp20) cc_final: 0.6134 (pp20) REVERT: A 650 GLU cc_start: 0.7796 (pt0) cc_final: 0.7556 (pm20) REVERT: A 653 TRP cc_start: 0.7688 (m100) cc_final: 0.7286 (m100) REVERT: A 666 LYS cc_start: 0.7732 (tttp) cc_final: 0.7121 (ttpp) REVERT: A 682 ILE cc_start: 0.7064 (OUTLIER) cc_final: 0.6473 (mp) REVERT: A 683 PHE cc_start: 0.5713 (m-10) cc_final: 0.5400 (t80) REVERT: B 354 ARG cc_start: 0.4950 (ptp-110) cc_final: 0.4129 (ptt90) REVERT: B 372 ARG cc_start: 0.8084 (ttm-80) cc_final: 0.6379 (tmt170) REVERT: B 620 GLU cc_start: 0.7335 (mm-30) cc_final: 0.6815 (mm-30) REVERT: B 666 ILE cc_start: 0.7674 (OUTLIER) cc_final: 0.7410 (mt) REVERT: B 688 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7424 (mm-30) REVERT: B 715 ARG cc_start: 0.6810 (mpt180) cc_final: 0.5899 (tpp-160) REVERT: B 736 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.6953 (pp) REVERT: B 752 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7129 (mt) REVERT: B 773 ARG cc_start: 0.6359 (mtt180) cc_final: 0.5408 (mmt180) REVERT: B 777 LEU cc_start: 0.6524 (tp) cc_final: 0.6040 (mm) outliers start: 37 outliers final: 19 residues processed: 145 average time/residue: 0.9589 time to fit residues: 151.7911 Evaluate side-chains 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 112 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 497 ASN Chi-restraints excluded: chain A residue 531 GLN 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 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 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 752 LEU 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 70 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119266 restraints weight = 10832.715| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.66 r_work: 0.3407 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9340 Z= 0.159 Angle : 0.598 8.303 12667 Z= 0.308 Chirality : 0.044 0.183 1381 Planarity : 0.004 0.049 1626 Dihedral : 4.698 33.931 1236 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.08 % Allowed : 19.88 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1141 helix: 1.51 (0.27), residues: 364 sheet: -0.81 (0.44), residues: 129 loop : -1.17 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 561 PHE 0.012 0.001 PHE B 668 TYR 0.009 0.001 TYR A 547 ARG 0.002 0.000 ARG B 449 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 345) hydrogen bonds : angle 4.81827 ( 987) metal coordination : bond 0.01528 ( 4) metal coordination : angle 2.34490 ( 3) SS BOND : bond 0.00333 ( 23) SS BOND : angle 1.32724 ( 46) covalent geometry : bond 0.00385 ( 9313) covalent geometry : angle 0.59305 (12618) *********************** 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 150 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 146 GLU cc_start: 0.8459 (tt0) cc_final: 0.8225 (tt0) REVERT: A 237 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7099 (ttm170) REVERT: A 256 ASP cc_start: 0.7142 (m-30) cc_final: 0.6928 (m-30) REVERT: A 302 LYS cc_start: 0.7201 (mmpt) cc_final: 0.6026 (ptpp) REVERT: A 367 LYS cc_start: 0.6935 (tptp) cc_final: 0.6311 (tmtt) REVERT: A 410 ASN cc_start: 0.8617 (m-40) cc_final: 0.8312 (m-40) REVERT: A 510 GLU cc_start: 0.7356 (mp0) cc_final: 0.7118 (mm-30) REVERT: A 531 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6660 (mm110) REVERT: A 640 LYS cc_start: 0.7129 (mmtt) cc_final: 0.6315 (ttpt) REVERT: A 642 GLU cc_start: 0.6720 (pp20) cc_final: 0.6172 (pp20) REVERT: A 653 TRP cc_start: 0.7704 (m100) cc_final: 0.7446 (m100) REVERT: A 666 LYS cc_start: 0.7730 (tttp) cc_final: 0.7106 (ttpp) REVERT: A 682 ILE cc_start: 0.7059 (OUTLIER) cc_final: 0.6466 (mp) REVERT: A 683 PHE cc_start: 0.5767 (m-10) cc_final: 0.5374 (t80) REVERT: B 354 ARG cc_start: 0.4998 (ptp-110) cc_final: 0.4174 (ptt90) REVERT: B 372 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.6398 (tmt170) REVERT: B 620 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6809 (mm-30) REVERT: B 666 ILE cc_start: 0.7708 (OUTLIER) cc_final: 0.7445 (mt) REVERT: B 688 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7469 (mm-30) REVERT: B 715 ARG cc_start: 0.6866 (mpt180) cc_final: 0.6021 (tpp-160) REVERT: B 736 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.6971 (pp) REVERT: B 752 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7196 (mt) REVERT: B 773 ARG cc_start: 0.6386 (mtt180) cc_final: 0.5426 (mmt180) REVERT: B 777 LEU cc_start: 0.6566 (tp) cc_final: 0.6074 (mm) REVERT: B 821 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7462 (tt0) outliers start: 31 outliers final: 18 residues processed: 142 average time/residue: 0.9495 time to fit residues: 147.0921 Evaluate side-chains 140 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 409 HIS Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 531 GLN 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 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 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 0.0050 chunk 29 optimal weight: 0.1980 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 362 GLN B 427 ASN B 551 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.157145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120650 restraints weight = 10915.760| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.68 r_work: 0.3421 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9340 Z= 0.126 Angle : 0.578 9.089 12667 Z= 0.298 Chirality : 0.043 0.187 1381 Planarity : 0.004 0.049 1626 Dihedral : 4.559 32.403 1236 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.78 % Allowed : 20.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.24), residues: 1141 helix: 1.59 (0.27), residues: 359 sheet: -0.79 (0.44), residues: 129 loop : -1.20 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.005 0.001 HIS A 65 PHE 0.013 0.001 PHE B 668 TYR 0.029 0.001 TYR B 797 ARG 0.002 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03594 ( 345) hydrogen bonds : angle 4.73453 ( 987) metal coordination : bond 0.01431 ( 4) metal coordination : angle 2.22991 ( 3) SS BOND : bond 0.00271 ( 23) SS BOND : angle 1.11475 ( 46) covalent geometry : bond 0.00300 ( 9313) covalent geometry : angle 0.57434 (12618) ********************** 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 143 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 146 GLU cc_start: 0.8422 (tt0) cc_final: 0.8172 (tt0) REVERT: A 237 ARG cc_start: 0.7735 (ttt180) cc_final: 0.7038 (ttm170) REVERT: A 256 ASP cc_start: 0.7108 (m-30) cc_final: 0.6854 (m-30) REVERT: A 302 LYS cc_start: 0.7148 (mmpt) cc_final: 0.6035 (ptpp) REVERT: A 367 LYS cc_start: 0.6857 (tptp) cc_final: 0.6226 (tmtt) REVERT: A 410 ASN cc_start: 0.8504 (m-40) cc_final: 0.8217 (m-40) REVERT: A 510 GLU cc_start: 0.7356 (mp0) cc_final: 0.7085 (mm-30) REVERT: A 531 GLN cc_start: 0.7051 (OUTLIER) cc_final: 0.6719 (mm110) REVERT: A 640 LYS cc_start: 0.7128 (mmtt) cc_final: 0.6425 (ttpt) REVERT: A 642 GLU cc_start: 0.6793 (pp20) cc_final: 0.6294 (pp20) REVERT: A 653 TRP cc_start: 0.7666 (m100) cc_final: 0.7447 (m100) REVERT: A 666 LYS cc_start: 0.7698 (tttp) cc_final: 0.7084 (ttpp) REVERT: A 683 PHE cc_start: 0.5711 (m-10) cc_final: 0.5346 (t80) REVERT: B 354 ARG cc_start: 0.5008 (ptp-110) cc_final: 0.4175 (ptt90) REVERT: B 372 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.6333 (tmt170) REVERT: B 620 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6811 (mm-30) REVERT: B 666 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7117 (mp) REVERT: B 686 ARG cc_start: 0.8242 (ttt180) cc_final: 0.7891 (ttt180) REVERT: B 688 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7388 (mm-30) REVERT: B 715 ARG cc_start: 0.6785 (mpt180) cc_final: 0.5874 (tpp-160) REVERT: B 736 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.6881 (pp) REVERT: B 773 ARG cc_start: 0.6350 (mtt180) cc_final: 0.5399 (mmt180) REVERT: B 777 LEU cc_start: 0.6522 (tp) cc_final: 0.6029 (mm) REVERT: B 821 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7388 (tt0) outliers start: 28 outliers final: 20 residues processed: 135 average time/residue: 1.0195 time to fit residues: 149.4254 Evaluate side-chains 139 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 409 HIS Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 531 GLN 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 362 GLN 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 666 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.0170 chunk 108 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.0030 chunk 21 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 15 optimal weight: 0.0470 chunk 49 optimal weight: 0.0870 chunk 13 optimal weight: 2.9990 overall best weight: 0.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS B 362 GLN B 427 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.120756 restraints weight = 10855.677| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.67 r_work: 0.3430 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.193 9340 Z= 0.206 Angle : 0.958 59.062 12667 Z= 0.540 Chirality : 0.044 0.450 1381 Planarity : 0.004 0.060 1626 Dihedral : 4.573 32.259 1236 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.88 % Allowed : 20.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.24), residues: 1141 helix: 1.59 (0.27), residues: 359 sheet: -0.80 (0.44), residues: 129 loop : -1.20 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 65 PHE 0.013 0.001 PHE B 668 TYR 0.016 0.001 TYR B 797 ARG 0.001 0.000 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.03570 ( 345) hydrogen bonds : angle 4.74153 ( 987) metal coordination : bond 0.01454 ( 4) metal coordination : angle 2.19557 ( 3) SS BOND : bond 0.00259 ( 23) SS BOND : angle 1.11737 ( 46) covalent geometry : bond 0.00436 ( 9313) covalent geometry : angle 0.95709 (12618) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7706.04 seconds wall clock time: 136 minutes 19.25 seconds (8179.25 seconds total)