Starting phenix.real_space_refine on Thu Mar 13 19:09:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snl_40628/03_2025/8snl_40628.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snl_40628/03_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_40628/03_2025/8snl_40628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snl_40628/03_2025/8snl_40628.map" model { file = "/net/cci-nas-00/data/ceres_data/8snl_40628/03_2025/8snl_40628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snl_40628/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 7.47, per 1000 atoms: 0.82 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: 2.41 Conformation dependent library (CDL) restraints added in 1.0 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: 1.04 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: 2.64 Time building geometry restraints manager: 2.83 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: 4.510 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.240 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.390 ------------------------------------------------------------------------------- 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 : 0.004 0.080 9313 Z= 0.279 Angle : 0.729 9.957 12618 Z= 0.430 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 *********************** 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 : 1.033 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: 1.2443 time to fit residues: 297.5574 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 : 1.126 ------------------------------------------------------------------------------- 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: 7.9990 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.0970 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 646 GLN B 403 GLN B 425 GLN B 427 ASN B 512 GLN B 556 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.162013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.125520 restraints weight = 10713.034| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.70 r_work: 0.3474 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9313 Z= 0.204 Angle : 0.570 9.740 12618 Z= 0.297 Chirality : 0.043 0.137 1381 Planarity : 0.005 0.064 1626 Dihedral : 4.661 24.304 1236 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.48 % Allowed : 9.64 % Favored : 86.88 % 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: -0.41 (0.24), residues: 1141 helix: 1.45 (0.27), residues: 362 sheet: -0.65 (0.44), residues: 130 loop : -1.23 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 312 HIS 0.006 0.001 HIS B 595 PHE 0.013 0.001 PHE A 679 TYR 0.014 0.001 TYR B 797 ARG 0.005 0.000 ARG B 372 *********************** 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 180 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7596 (mppt) REVERT: A 237 ARG cc_start: 0.7637 (ttt180) cc_final: 0.6953 (ttm170) REVERT: A 290 GLU cc_start: 0.7196 (mt-10) cc_final: 0.6675 (pm20) REVERT: A 355 SER cc_start: 0.6553 (m) cc_final: 0.6254 (t) REVERT: A 367 LYS cc_start: 0.6806 (tptp) cc_final: 0.6202 (tmtt) REVERT: A 406 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7872 (mm-30) REVERT: A 410 ASN cc_start: 0.8394 (m-40) cc_final: 0.8172 (m-40) REVERT: A 422 GLU cc_start: 0.5520 (OUTLIER) cc_final: 0.5027 (mt-10) REVERT: A 459 TYR cc_start: 0.7426 (t80) cc_final: 0.6358 (t80) REVERT: A 513 GLN cc_start: 0.6716 (mt0) cc_final: 0.6480 (mt0) REVERT: A 554 GLU cc_start: 0.5849 (OUTLIER) cc_final: 0.5647 (pm20) REVERT: A 572 LYS cc_start: 0.6072 (mttm) cc_final: 0.5711 (mtpm) REVERT: A 574 LYS cc_start: 0.5431 (mptt) cc_final: 0.4141 (mttt) REVERT: A 636 ASP cc_start: 0.6159 (t0) cc_final: 0.5674 (t0) REVERT: A 640 LYS cc_start: 0.6016 (mmtt) cc_final: 0.5668 (ttpt) REVERT: A 653 TRP cc_start: 0.7698 (m100) cc_final: 0.7384 (m100) REVERT: A 666 LYS cc_start: 0.7645 (tttp) cc_final: 0.7101 (tttm) REVERT: B 354 ARG cc_start: 0.4485 (ptp-110) cc_final: 0.3907 (ptt90) REVERT: B 372 ARG cc_start: 0.8051 (ttm-80) cc_final: 0.6304 (tmt170) REVERT: B 505 MET cc_start: 0.8418 (ttm) cc_final: 0.8101 (mtp) REVERT: B 566 ILE cc_start: 0.6035 (pt) cc_final: 0.5686 (pt) REVERT: B 620 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6622 (mm-30) REVERT: B 654 ASP cc_start: 0.7074 (OUTLIER) cc_final: 0.6726 (t0) REVERT: B 666 ILE cc_start: 0.7269 (mm) cc_final: 0.7052 (mp) REVERT: B 688 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7217 (mm-30) REVERT: B 715 ARG cc_start: 0.6707 (mpt180) cc_final: 0.5978 (tpp-160) REVERT: B 773 ARG cc_start: 0.6405 (mtt180) cc_final: 0.5375 (mmt180) REVERT: B 777 LEU cc_start: 0.6707 (tp) cc_final: 0.6197 (mm) outliers start: 35 outliers final: 14 residues processed: 172 average time/residue: 1.3113 time to fit residues: 244.4575 Evaluate side-chains 138 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 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 554 GLU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain B residue 467 ASP 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: 0.8980 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 ASN ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.121309 restraints weight = 10951.067| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.65 r_work: 0.3423 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9313 Z= 0.268 Angle : 0.577 9.441 12618 Z= 0.302 Chirality : 0.044 0.163 1381 Planarity : 0.005 0.051 1626 Dihedral : 4.738 25.323 1236 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.98 % Allowed : 13.02 % Favored : 83.00 % 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: -0.41 (0.24), residues: 1141 helix: 1.42 (0.27), residues: 363 sheet: -0.91 (0.43), residues: 134 loop : -1.15 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 312 HIS 0.005 0.001 HIS B 595 PHE 0.013 0.001 PHE A 470 TYR 0.013 0.001 TYR B 761 ARG 0.004 0.000 ARG B 372 *********************** 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 179 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7388 (pp20) REVERT: A 106 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: A 237 ARG cc_start: 0.7664 (ttt180) cc_final: 0.7029 (ttm170) REVERT: A 290 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6737 (pm20) REVERT: A 302 LYS cc_start: 0.6849 (mmtt) cc_final: 0.6009 (ptpp) REVERT: A 355 SER cc_start: 0.6616 (m) cc_final: 0.6296 (t) REVERT: A 367 LYS cc_start: 0.6886 (tptp) cc_final: 0.6234 (tmtt) REVERT: A 410 ASN cc_start: 0.8470 (m-40) cc_final: 0.8186 (m-40) REVERT: A 422 GLU cc_start: 0.5517 (OUTLIER) cc_final: 0.4975 (mt-10) REVERT: A 459 TYR cc_start: 0.7360 (t80) cc_final: 0.7045 (t80) REVERT: A 525 CYS cc_start: 0.6206 (m) cc_final: 0.5874 (m) REVERT: A 640 LYS cc_start: 0.6624 (mmtt) cc_final: 0.5909 (ttpt) REVERT: A 642 GLU cc_start: 0.6381 (pp20) cc_final: 0.5895 (pp20) REVERT: A 653 TRP cc_start: 0.7722 (m100) cc_final: 0.7361 (m100) REVERT: A 666 LYS cc_start: 0.7755 (tttp) cc_final: 0.7180 (ttpp) REVERT: A 682 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6474 (mp) REVERT: B 354 ARG cc_start: 0.4660 (ptp-110) cc_final: 0.3962 (ptt90) REVERT: B 372 ARG cc_start: 0.8256 (ttm-80) cc_final: 0.6469 (tmt170) REVERT: B 450 LYS cc_start: 0.6998 (ttmm) cc_final: 0.6573 (mmtp) REVERT: B 465 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7568 (tt0) REVERT: B 666 ILE cc_start: 0.7415 (mm) cc_final: 0.7184 (mp) REVERT: B 688 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 715 ARG cc_start: 0.6827 (mpt180) cc_final: 0.6067 (tpp-160) REVERT: B 736 LEU cc_start: 0.7339 (tt) cc_final: 0.7058 (pp) REVERT: B 773 ARG cc_start: 0.6443 (mtt180) cc_final: 0.5441 (mmt180) REVERT: B 777 LEU cc_start: 0.6705 (tp) cc_final: 0.6179 (mm) REVERT: B 821 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7174 (tt0) outliers start: 40 outliers final: 17 residues processed: 166 average time/residue: 1.1246 time to fit residues: 200.9976 Evaluate side-chains 147 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 125 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 580 GLU 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: 0.9990 chunk 6 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117656 restraints weight = 10883.094| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.68 r_work: 0.3393 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 9313 Z= 0.308 Angle : 0.598 8.624 12618 Z= 0.313 Chirality : 0.045 0.175 1381 Planarity : 0.004 0.052 1626 Dihedral : 4.841 26.021 1236 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.47 % Allowed : 15.01 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.45 (0.24), residues: 1141 helix: 1.35 (0.27), residues: 363 sheet: -1.06 (0.43), residues: 134 loop : -1.13 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 629 HIS 0.005 0.001 HIS B 595 PHE 0.014 0.002 PHE A 470 TYR 0.015 0.002 TYR A 547 ARG 0.004 0.000 ARG B 449 *********************** 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 176 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 131 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: A 237 ARG cc_start: 0.7763 (ttt180) cc_final: 0.7092 (ttm170) REVERT: A 256 ASP cc_start: 0.7241 (m-30) cc_final: 0.6965 (m-30) REVERT: A 355 SER cc_start: 0.6465 (m) cc_final: 0.6106 (t) REVERT: A 410 ASN cc_start: 0.8610 (m-40) cc_final: 0.8302 (m-40) REVERT: A 422 GLU cc_start: 0.5405 (OUTLIER) cc_final: 0.4826 (mt-10) REVERT: A 435 MET cc_start: 0.8180 (mmm) cc_final: 0.7979 (tpp) REVERT: A 574 LYS cc_start: 0.5461 (mptt) cc_final: 0.3677 (mttp) REVERT: A 640 LYS cc_start: 0.6646 (mmtt) cc_final: 0.5907 (ttpt) REVERT: A 642 GLU cc_start: 0.6539 (pp20) cc_final: 0.6006 (pp20) REVERT: A 653 TRP cc_start: 0.7725 (m100) cc_final: 0.7314 (m100) REVERT: A 666 LYS cc_start: 0.7766 (tttp) cc_final: 0.7201 (ttpp) REVERT: A 682 ILE cc_start: 0.7043 (OUTLIER) cc_final: 0.6405 (mp) REVERT: A 683 PHE cc_start: 0.5688 (m-10) cc_final: 0.5379 (t80) REVERT: B 354 ARG cc_start: 0.4894 (ptp-110) cc_final: 0.4075 (ptt90) REVERT: B 372 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.6534 (tmt170) REVERT: B 450 LYS cc_start: 0.7129 (ttmm) cc_final: 0.6853 (tptm) REVERT: B 485 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7811 (ptmm) REVERT: B 654 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7031 (p0) REVERT: B 666 ILE cc_start: 0.7590 (mm) cc_final: 0.7361 (mp) REVERT: B 688 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7368 (mm-30) REVERT: B 715 ARG cc_start: 0.6795 (mpt180) cc_final: 0.6012 (tpp-160) REVERT: B 736 LEU cc_start: 0.7428 (tt) cc_final: 0.6976 (pp) REVERT: B 773 ARG cc_start: 0.6507 (mtt180) cc_final: 0.5500 (mmt180) REVERT: B 777 LEU cc_start: 0.6725 (tp) cc_final: 0.6242 (mm) outliers start: 45 outliers final: 19 residues processed: 161 average time/residue: 1.0181 time to fit residues: 178.0918 Evaluate side-chains 148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 422 GLU Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 435 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 654 ASP Chi-restraints excluded: chain B residue 664 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: 3.9990 chunk 105 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.153223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.116877 restraints weight = 10879.838| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.67 r_work: 0.3390 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3260 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 9313 Z= 0.303 Angle : 0.597 8.009 12618 Z= 0.310 Chirality : 0.045 0.200 1381 Planarity : 0.004 0.052 1626 Dihedral : 4.850 26.349 1236 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.07 % Allowed : 15.31 % Favored : 79.62 % 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: -0.46 (0.24), residues: 1141 helix: 1.34 (0.27), residues: 361 sheet: -1.06 (0.43), residues: 136 loop : -1.11 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.004 0.001 HIS B 595 PHE 0.013 0.002 PHE A 470 TYR 0.026 0.002 TYR B 797 ARG 0.003 0.000 ARG A 139 *********************** 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 183 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 132 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: A 237 ARG cc_start: 0.7638 (ttt180) cc_final: 0.6962 (ttm170) REVERT: A 256 ASP cc_start: 0.7046 (m-30) cc_final: 0.6836 (m-30) REVERT: A 302 LYS cc_start: 0.7150 (mmpt) cc_final: 0.5959 (ptpp) REVERT: A 355 SER cc_start: 0.6405 (m) cc_final: 0.6029 (t) REVERT: A 410 ASN cc_start: 0.8500 (m-40) cc_final: 0.8174 (m-40) REVERT: A 422 GLU cc_start: 0.5379 (OUTLIER) cc_final: 0.4838 (mt-10) REVERT: A 525 CYS cc_start: 0.6529 (m) cc_final: 0.6148 (m) REVERT: A 574 LYS cc_start: 0.5256 (mptt) cc_final: 0.3535 (mttm) REVERT: A 640 LYS cc_start: 0.6553 (mmtt) cc_final: 0.6006 (ttpt) REVERT: A 642 GLU cc_start: 0.6601 (pp20) cc_final: 0.6058 (pp20) REVERT: A 650 GLU cc_start: 0.7760 (pt0) cc_final: 0.7462 (pm20) REVERT: A 653 TRP cc_start: 0.7697 (m100) cc_final: 0.7277 (m100) REVERT: A 666 LYS cc_start: 0.7698 (tttp) cc_final: 0.7100 (ttpp) REVERT: A 682 ILE cc_start: 0.6946 (OUTLIER) cc_final: 0.6354 (mp) REVERT: A 683 PHE cc_start: 0.5589 (m-10) cc_final: 0.5308 (t80) REVERT: B 354 ARG cc_start: 0.4910 (ptp-110) cc_final: 0.4063 (ptt-90) REVERT: B 372 ARG cc_start: 0.8292 (ttm-80) cc_final: 0.6405 (tmt170) REVERT: B 450 LYS cc_start: 0.7152 (ttmm) cc_final: 0.6791 (tptm) REVERT: B 485 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7710 (ptmm) REVERT: B 654 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6856 (p0) REVERT: B 666 ILE cc_start: 0.7443 (mm) cc_final: 0.7200 (mp) REVERT: B 688 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7376 (mm-30) REVERT: B 715 ARG cc_start: 0.6887 (mpt180) cc_final: 0.6035 (tpp-160) REVERT: B 726 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7095 (mp) REVERT: B 736 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6860 (pp) REVERT: B 768 ASP cc_start: 0.5898 (OUTLIER) cc_final: 0.5392 (t0) REVERT: B 773 ARG cc_start: 0.6433 (mtt180) cc_final: 0.5449 (mmt180) REVERT: B 777 LEU cc_start: 0.6566 (tp) cc_final: 0.6098 (mm) REVERT: B 821 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7286 (tt0) outliers start: 51 outliers final: 19 residues processed: 163 average time/residue: 1.0189 time to fit residues: 179.8156 Evaluate side-chains 148 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 239 MET 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 648 VAL Chi-restraints excluded: chain A residue 659 LEU 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 580 GLU Chi-restraints excluded: chain B residue 654 ASP Chi-restraints excluded: chain B residue 726 ILE Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 752 LEU Chi-restraints excluded: chain B residue 768 ASP Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 105 optimal weight: 0.4980 chunk 48 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 1 optimal weight: 0.6980 chunk 104 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.119460 restraints weight = 10815.163| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.65 r_work: 0.3415 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 9313 Z= 0.204 Angle : 0.555 7.819 12618 Z= 0.290 Chirality : 0.043 0.163 1381 Planarity : 0.004 0.050 1626 Dihedral : 4.729 26.197 1236 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.27 % Allowed : 17.00 % Favored : 78.73 % 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: -0.35 (0.24), residues: 1141 helix: 1.56 (0.27), residues: 356 sheet: -0.91 (0.43), residues: 131 loop : -1.14 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS A 65 PHE 0.013 0.001 PHE B 668 TYR 0.013 0.001 TYR A 436 ARG 0.002 0.000 ARG A 139 *********************** 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 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7475 (tt0) REVERT: A 146 GLU cc_start: 0.8446 (tt0) cc_final: 0.8185 (tt0) REVERT: A 237 ARG cc_start: 0.7795 (ttt180) cc_final: 0.7063 (ttm170) REVERT: A 256 ASP cc_start: 0.7107 (m-30) cc_final: 0.6866 (m-30) REVERT: A 302 LYS cc_start: 0.7118 (mmpt) cc_final: 0.5982 (ptpp) REVERT: A 355 SER cc_start: 0.6419 (m) cc_final: 0.6037 (t) REVERT: A 410 ASN cc_start: 0.8524 (m-40) cc_final: 0.8245 (m-40) REVERT: A 435 MET cc_start: 0.8265 (mmm) cc_final: 0.7951 (tpp) REVERT: A 525 CYS cc_start: 0.6542 (m) cc_final: 0.6155 (m) REVERT: A 531 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6596 (mm110) REVERT: A 574 LYS cc_start: 0.5278 (mptt) cc_final: 0.3606 (mttp) REVERT: A 640 LYS cc_start: 0.6567 (mmtt) cc_final: 0.5944 (ttpt) REVERT: A 642 GLU cc_start: 0.6657 (pp20) cc_final: 0.6104 (pp20) REVERT: A 650 GLU cc_start: 0.7802 (pt0) cc_final: 0.7579 (pm20) REVERT: A 653 TRP cc_start: 0.7724 (m100) cc_final: 0.7313 (m100) REVERT: A 666 LYS cc_start: 0.7713 (tttp) cc_final: 0.7138 (ttpp) REVERT: A 682 ILE cc_start: 0.7027 (OUTLIER) cc_final: 0.6435 (mp) REVERT: A 683 PHE cc_start: 0.5661 (m-10) cc_final: 0.5373 (t80) REVERT: B 354 ARG cc_start: 0.4982 (ptp-110) cc_final: 0.4139 (ptt90) REVERT: B 372 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.6322 (tmt170) REVERT: B 450 LYS cc_start: 0.7043 (ttmm) cc_final: 0.6678 (mmtp) REVERT: B 485 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7678 (ptmm) REVERT: B 688 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 715 ARG cc_start: 0.6842 (mpt180) cc_final: 0.5922 (tpp-160) REVERT: B 726 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7218 (mp) REVERT: B 736 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6945 (pp) REVERT: B 773 ARG cc_start: 0.6445 (mtt180) cc_final: 0.5477 (mmt180) REVERT: B 777 LEU cc_start: 0.6602 (tp) cc_final: 0.6112 (mm) outliers start: 43 outliers final: 20 residues processed: 157 average time/residue: 0.9766 time to fit residues: 166.6147 Evaluate side-chains 149 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 123 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 175 VAL 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 500 THR 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 485 LYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 548 CYS Chi-restraints excluded: chain B residue 564 CYS Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 726 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: 1.9990 chunk 10 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 427 ASN B 551 GLN B 605 HIS ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.153629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116020 restraints weight = 10720.125| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 2.73 r_work: 0.3278 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9313 Z= 0.252 Angle : 0.582 7.982 12618 Z= 0.304 Chirality : 0.044 0.228 1381 Planarity : 0.004 0.049 1626 Dihedral : 4.804 31.451 1236 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.17 % Allowed : 17.99 % Favored : 77.83 % 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: -0.35 (0.24), residues: 1141 helix: 1.47 (0.27), residues: 364 sheet: -0.97 (0.43), residues: 131 loop : -1.10 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.005 0.001 HIS B 561 PHE 0.012 0.001 PHE B 668 TYR 0.029 0.001 TYR B 797 ARG 0.002 0.000 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 146 GLU cc_start: 0.8266 (tt0) cc_final: 0.8032 (tt0) REVERT: A 237 ARG cc_start: 0.7580 (ttt180) cc_final: 0.6832 (ttm170) REVERT: A 256 ASP cc_start: 0.6768 (m-30) cc_final: 0.6565 (m-30) REVERT: A 302 LYS cc_start: 0.7139 (mmpt) cc_final: 0.5946 (ptpp) REVERT: A 355 SER cc_start: 0.6341 (m) cc_final: 0.5978 (t) REVERT: A 367 LYS cc_start: 0.6869 (tptp) cc_final: 0.6229 (tmtt) REVERT: A 410 ASN cc_start: 0.8305 (m-40) cc_final: 0.7993 (m-40) REVERT: A 525 CYS cc_start: 0.6259 (m) cc_final: 0.5867 (m) REVERT: A 531 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6505 (mm110) REVERT: A 636 ASP cc_start: 0.5937 (t0) cc_final: 0.5684 (t0) REVERT: A 642 GLU cc_start: 0.6369 (pp20) cc_final: 0.5800 (pp20) REVERT: A 650 GLU cc_start: 0.7693 (pt0) cc_final: 0.7472 (pm20) REVERT: A 653 TRP cc_start: 0.7617 (m100) cc_final: 0.7187 (m100) REVERT: A 666 LYS cc_start: 0.7505 (tttp) cc_final: 0.6904 (ttpp) REVERT: A 682 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6350 (mp) REVERT: A 683 PHE cc_start: 0.5555 (m-10) cc_final: 0.5296 (t80) REVERT: B 354 ARG cc_start: 0.4731 (ptp-110) cc_final: 0.3939 (ptt-90) REVERT: B 372 ARG cc_start: 0.7929 (ttm-80) cc_final: 0.6220 (tmt170) REVERT: B 450 LYS cc_start: 0.6970 (ttmm) cc_final: 0.6679 (tptp) REVERT: B 485 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7555 (ptmm) REVERT: B 620 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6938 (mm-30) REVERT: B 650 THR cc_start: 0.7668 (m) cc_final: 0.7458 (m) REVERT: B 666 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.7130 (mt) REVERT: B 688 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7276 (mm-30) REVERT: B 715 ARG cc_start: 0.6876 (mpt180) cc_final: 0.5982 (tpp-160) REVERT: B 736 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6799 (pp) REVERT: B 768 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5323 (t0) REVERT: B 773 ARG cc_start: 0.6322 (mtt180) cc_final: 0.5376 (mmt180) REVERT: B 777 LEU cc_start: 0.6348 (tp) cc_final: 0.5846 (mm) REVERT: B 821 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7346 (tt0) outliers start: 42 outliers final: 25 residues processed: 158 average time/residue: 0.9423 time to fit residues: 162.3558 Evaluate side-chains 156 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 123 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 385 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 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 457 LEU Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 533 SER 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 768 ASP Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 104 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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** A 497 ASN B 413 ASN B 427 ASN B 551 GLN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.152776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114832 restraints weight = 10899.937| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.78 r_work: 0.3253 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9313 Z= 0.281 Angle : 0.601 8.249 12618 Z= 0.313 Chirality : 0.045 0.192 1381 Planarity : 0.004 0.048 1626 Dihedral : 4.849 33.063 1236 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.27 % Allowed : 18.59 % Favored : 77.14 % 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: -0.40 (0.24), residues: 1141 helix: 1.40 (0.27), residues: 364 sheet: -0.98 (0.43), residues: 131 loop : -1.11 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.005 0.001 HIS A 405 PHE 0.012 0.001 PHE B 668 TYR 0.010 0.001 TYR A 436 ARG 0.003 0.000 ARG B 449 *********************** 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 171 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 128 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7558 (tt0) REVERT: A 146 GLU cc_start: 0.8256 (tt0) cc_final: 0.8022 (tt0) REVERT: A 237 ARG cc_start: 0.7572 (ttt180) cc_final: 0.6872 (ttm170) REVERT: A 302 LYS cc_start: 0.7084 (mmpt) cc_final: 0.5907 (ptpp) REVERT: A 367 LYS cc_start: 0.6878 (tptp) cc_final: 0.6225 (tmtt) REVERT: A 410 ASN cc_start: 0.8292 (m-40) cc_final: 0.7941 (m-40) REVERT: A 525 CYS cc_start: 0.6245 (m) cc_final: 0.5836 (m) REVERT: A 636 ASP cc_start: 0.5806 (t0) cc_final: 0.5549 (t0) REVERT: A 638 ASN cc_start: 0.7036 (m-40) cc_final: 0.6767 (m110) REVERT: A 642 GLU cc_start: 0.6398 (pp20) cc_final: 0.5823 (pp20) REVERT: A 653 TRP cc_start: 0.7551 (m100) cc_final: 0.7286 (m100) REVERT: A 666 LYS cc_start: 0.7490 (tttp) cc_final: 0.6886 (ttpp) REVERT: A 682 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6321 (mp) REVERT: A 683 PHE cc_start: 0.5577 (m-10) cc_final: 0.5334 (t80) REVERT: B 354 ARG cc_start: 0.4701 (ptp-110) cc_final: 0.3923 (ptt90) REVERT: B 372 ARG cc_start: 0.7951 (ttm-80) cc_final: 0.6244 (tmt170) REVERT: B 450 LYS cc_start: 0.7012 (ttmm) cc_final: 0.6690 (tptp) REVERT: B 485 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7558 (ptmm) REVERT: B 650 THR cc_start: 0.7645 (m) cc_final: 0.7437 (m) REVERT: B 666 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7127 (mt) REVERT: B 688 GLU cc_start: 0.7792 (mm-30) cc_final: 0.7310 (mm-30) REVERT: B 715 ARG cc_start: 0.6845 (mpt180) cc_final: 0.5983 (tpp-160) REVERT: B 736 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6756 (pp) REVERT: B 768 ASP cc_start: 0.5783 (OUTLIER) cc_final: 0.5342 (t0) REVERT: B 773 ARG cc_start: 0.6288 (mtt180) cc_final: 0.5340 (mmt180) REVERT: B 777 LEU cc_start: 0.6345 (tp) cc_final: 0.5863 (mm) REVERT: B 821 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7385 (tt0) outliers start: 43 outliers final: 23 residues processed: 157 average time/residue: 0.9722 time to fit residues: 166.3029 Evaluate side-chains 152 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.928 ------------------------------------------------------------------------------- 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 175 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 533 SER 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 768 ASP Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 102 optimal weight: 0.9990 chunk 60 optimal weight: 0.1980 chunk 50 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** A 497 ASN B 427 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 695 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.153530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.115949 restraints weight = 10654.739| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.72 r_work: 0.3274 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9313 Z= 0.242 Angle : 0.586 7.955 12618 Z= 0.305 Chirality : 0.044 0.186 1381 Planarity : 0.004 0.048 1626 Dihedral : 4.770 32.132 1236 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.58 % Allowed : 19.38 % 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: -0.36 (0.24), residues: 1141 helix: 1.43 (0.27), residues: 364 sheet: -0.85 (0.44), residues: 129 loop : -1.12 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 561 PHE 0.013 0.001 PHE B 668 TYR 0.031 0.001 TYR B 797 ARG 0.002 0.000 ARG A 139 *********************** 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 160 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 THR cc_start: 0.6157 (OUTLIER) cc_final: 0.5915 (t) REVERT: A 106 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: A 146 GLU cc_start: 0.8251 (tt0) cc_final: 0.8008 (tt0) REVERT: A 237 ARG cc_start: 0.7593 (ttt180) cc_final: 0.6898 (ttm170) REVERT: A 256 ASP cc_start: 0.6865 (m-30) cc_final: 0.6536 (m-30) REVERT: A 302 LYS cc_start: 0.7121 (mmpt) cc_final: 0.5982 (ptpp) REVERT: A 367 LYS cc_start: 0.6872 (tptp) cc_final: 0.6234 (tmtt) REVERT: A 410 ASN cc_start: 0.8321 (m-40) cc_final: 0.8015 (m-40) REVERT: A 525 CYS cc_start: 0.6211 (m) cc_final: 0.5822 (m) REVERT: A 636 ASP cc_start: 0.5664 (t0) cc_final: 0.5447 (t0) REVERT: A 638 ASN cc_start: 0.7038 (m-40) cc_final: 0.6761 (m110) REVERT: A 642 GLU cc_start: 0.6469 (pp20) cc_final: 0.5885 (pp20) REVERT: A 653 TRP cc_start: 0.7534 (m100) cc_final: 0.7268 (m100) REVERT: A 666 LYS cc_start: 0.7494 (tttp) cc_final: 0.6891 (ttpp) REVERT: A 682 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6369 (mp) REVERT: A 683 PHE cc_start: 0.5588 (m-10) cc_final: 0.5358 (t80) REVERT: B 354 ARG cc_start: 0.4748 (ptp-110) cc_final: 0.3976 (ptt90) REVERT: B 372 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.6250 (tmt170) REVERT: B 450 LYS cc_start: 0.7004 (ttmm) cc_final: 0.6624 (tptp) REVERT: B 485 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7475 (ptmm) REVERT: B 666 ILE cc_start: 0.7331 (OUTLIER) cc_final: 0.7117 (mt) REVERT: B 688 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7397 (mm-30) REVERT: B 715 ARG cc_start: 0.6813 (mpt180) cc_final: 0.5854 (tpp-160) REVERT: B 736 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6822 (pp) REVERT: B 773 ARG cc_start: 0.6334 (mtt180) cc_final: 0.5385 (mmt180) REVERT: B 777 LEU cc_start: 0.6361 (tp) cc_final: 0.5873 (mm) REVERT: B 821 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7359 (tt0) outliers start: 36 outliers final: 27 residues processed: 150 average time/residue: 1.2248 time to fit residues: 200.5576 Evaluate side-chains 153 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 119 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 62 THR Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 76 LYS Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 339 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain A residue 648 VAL Chi-restraints excluded: chain A residue 659 LEU Chi-restraints excluded: chain A residue 682 ILE Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 485 LYS Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 527 CYS Chi-restraints excluded: chain B residue 533 SER 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 796 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 821 GLU Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 15 optimal weight: 0.0040 chunk 63 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 6 optimal weight: 0.0670 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 80 optimal weight: 0.4980 chunk 46 optimal weight: 10.0000 overall best weight: 0.3530 ------------------------------------------------------------------------------- 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** A 535 GLN B 362 GLN B 427 ASN ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.156526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118807 restraints weight = 10698.417| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.78 r_work: 0.3310 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9313 Z= 0.173 Angle : 0.553 9.099 12618 Z= 0.287 Chirality : 0.042 0.188 1381 Planarity : 0.004 0.047 1626 Dihedral : 4.517 29.833 1236 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.48 % Allowed : 19.48 % Favored : 77.04 % 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: -0.31 (0.24), residues: 1141 helix: 1.58 (0.27), residues: 359 sheet: -0.82 (0.44), residues: 129 loop : -1.14 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.006 0.001 HIS A 65 PHE 0.013 0.001 PHE B 668 TYR 0.011 0.001 TYR A 436 ARG 0.002 0.000 ARG A 263 ********************** 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 161 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 126 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 LYS cc_start: 0.7964 (tttt) cc_final: 0.7751 (tttp) REVERT: A 106 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 146 GLU cc_start: 0.8215 (tt0) cc_final: 0.7957 (tt0) REVERT: A 237 ARG cc_start: 0.7594 (ttt180) cc_final: 0.6879 (ttm170) REVERT: A 256 ASP cc_start: 0.6840 (m-30) cc_final: 0.6505 (m-30) REVERT: A 302 LYS cc_start: 0.7141 (mmpt) cc_final: 0.5987 (ptpp) REVERT: A 367 LYS cc_start: 0.6795 (tptp) cc_final: 0.6164 (tmtt) REVERT: A 410 ASN cc_start: 0.8211 (m-40) cc_final: 0.7969 (m-40) REVERT: A 472 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.6638 (tm-30) REVERT: A 525 CYS cc_start: 0.6188 (m) cc_final: 0.5824 (m) REVERT: A 642 GLU cc_start: 0.6426 (pp20) cc_final: 0.5902 (pp20) REVERT: A 653 TRP cc_start: 0.7574 (m100) cc_final: 0.7353 (m100) REVERT: A 666 LYS cc_start: 0.7466 (tttp) cc_final: 0.6867 (ttpp) REVERT: A 683 PHE cc_start: 0.5546 (m-10) cc_final: 0.5275 (t80) REVERT: B 354 ARG cc_start: 0.4740 (ptp-110) cc_final: 0.3963 (ptt90) REVERT: B 372 ARG cc_start: 0.7872 (ttm-80) cc_final: 0.6179 (tmt170) REVERT: B 485 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7430 (ptmm) REVERT: B 580 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6544 (tt0) REVERT: B 666 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.7056 (mt) REVERT: B 688 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7442 (mm-30) REVERT: B 715 ARG cc_start: 0.6778 (mpt180) cc_final: 0.5856 (tpp-160) REVERT: B 736 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6767 (pp) REVERT: B 773 ARG cc_start: 0.6284 (mtt180) cc_final: 0.5347 (mmt180) REVERT: B 777 LEU cc_start: 0.6232 (tp) cc_final: 0.5747 (mm) outliers start: 35 outliers final: 19 residues processed: 152 average time/residue: 1.0180 time to fit residues: 169.1038 Evaluate side-chains 144 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 64 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 175 VAL 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 500 THR 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 485 LYS Chi-restraints excluded: chain B residue 493 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 chunk 3 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 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 ** A 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 GLN B 427 ASN ** 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 = 0.3817 r_free = 0.3817 target = 0.156260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118728 restraints weight = 10638.912| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.76 r_work: 0.3302 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.186 9313 Z= 0.297 Angle : 0.935 59.196 12618 Z= 0.531 Chirality : 0.044 0.403 1381 Planarity : 0.004 0.055 1626 Dihedral : 4.533 29.776 1236 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.88 % Allowed : 20.48 % Favored : 76.64 % 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: -0.31 (0.24), residues: 1141 helix: 1.58 (0.27), residues: 359 sheet: -0.81 (0.44), residues: 129 loop : -1.14 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.005 0.001 HIS A 65 PHE 0.013 0.001 PHE B 668 TYR 0.007 0.001 TYR A 236 ARG 0.001 0.000 ARG A 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6848.01 seconds wall clock time: 121 minutes 9.29 seconds (7269.29 seconds total)