Starting phenix.real_space_refine on Fri Jan 17 03:30:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xs0_38612/01_2025/8xs0_38612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xs0_38612/01_2025/8xs0_38612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xs0_38612/01_2025/8xs0_38612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xs0_38612/01_2025/8xs0_38612.map" model { file = "/net/cci-nas-00/data/ceres_data/8xs0_38612/01_2025/8xs0_38612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xs0_38612/01_2025/8xs0_38612.cif" } resolution = 3.89 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= 0.008 sd= 0.057 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 6826 2.51 5 N 1696 2.21 5 O 1801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 10353 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5129 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 30, 'TRANS': 657} Chain breaks: 1 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5224 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 31, 'TRANS': 668} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 230 Time building chain proxies: 6.65, per 1000 atoms: 0.64 Number of scatterers: 10353 At special positions: 0 Unit cell: (88.62, 138.205, 103.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1801 8.00 N 1696 7.00 C 6826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.70 Conformation dependent library (CDL) restraints added in 1.6 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2656 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 2 sheets defined 71.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Processing helix chain 'A' and resid 36 through 42 removed outlier: 3.742A pdb=" N ILE A 42 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 112 removed outlier: 3.781A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 4.099A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 117 through 125 removed outlier: 6.183A pdb=" N ALA A 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 removed outlier: 6.845A pdb=" N MET A 139 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 142 " --> pdb=" O MET A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 184 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 279 through 305 removed outlier: 3.967A pdb=" N THR A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 355 through 377 Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.237A pdb=" N ILE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.586A pdb=" N ILE A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.748A pdb=" N ALA A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 523 removed outlier: 3.723A pdb=" N THR A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.959A pdb=" N PHE A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 540 through 548 removed outlier: 3.764A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 572 removed outlier: 3.540A pdb=" N VAL A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Proline residue: A 560 - end of helix removed outlier: 3.584A pdb=" N TYR A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 4.029A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 removed outlier: 4.314A pdb=" N GLY A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 638 removed outlier: 4.544A pdb=" N HIS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 622 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.608A pdb=" N ILE A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.670A pdb=" N GLU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.865A pdb=" N CYS A 677 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 removed outlier: 3.837A pdb=" N PHE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 27 removed outlier: 4.170A pdb=" N LEU B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 112 removed outlier: 3.618A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 3.808A pdb=" N LEU B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.643A pdb=" N ASN B 121 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA B 122 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 184 removed outlier: 3.610A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.623A pdb=" N GLN B 277 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 278 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 278' Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.617A pdb=" N TYR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.525A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 Processing helix chain 'B' and resid 377 through 387 removed outlier: 4.253A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 396 Processing helix chain 'B' and resid 401 through 408 removed outlier: 4.012A pdb=" N GLU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 408' Processing helix chain 'B' and resid 409 through 440 removed outlier: 3.673A pdb=" N GLU B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER B 415 " --> pdb=" O THR B 411 " (cutoff:3.500A) Proline residue: B 418 - end of helix removed outlier: 3.764A pdb=" N PHE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix removed outlier: 3.505A pdb=" N ALA B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 468 removed outlier: 3.778A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.645A pdb=" N LYS B 479 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 481 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 482 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 523 removed outlier: 4.186A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 572 removed outlier: 3.888A pdb=" N VAL B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Proline residue: B 560 - end of helix removed outlier: 3.648A pdb=" N TYR B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 601 removed outlier: 4.110A pdb=" N ILE B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 611 removed outlier: 4.398A pdb=" N GLY B 610 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 665 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.556A pdb=" N GLU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 670' Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 686 through 694 removed outlier: 4.148A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.655A pdb=" N ILE A 194 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 231 removed outlier: 5.534A pdb=" N ALA B 310 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 313 " --> pdb=" O ILE B 194 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1845 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: 3.23 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3164 1.34 - 1.46: 2275 1.46 - 1.58: 5131 1.58 - 1.70: 0 1.70 - 1.81: 46 Bond restraints: 10616 Sorted by residual: bond pdb=" CA LEU B 348 " pdb=" CB LEU B 348 " ideal model delta sigma weight residual 1.528 1.486 0.042 2.61e-02 1.47e+03 2.63e+00 bond pdb=" CA LEU B 195 " pdb=" CB LEU B 195 " ideal model delta sigma weight residual 1.524 1.503 0.022 1.46e-02 4.69e+03 2.21e+00 bond pdb=" C TYR B 549 " pdb=" N PRO B 550 " ideal model delta sigma weight residual 1.336 1.319 0.017 1.20e-02 6.94e+03 1.94e+00 bond pdb=" CG LEU A 649 " pdb=" CD2 LEU A 649 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CA ILE B 689 " pdb=" CB ILE B 689 " ideal model delta sigma weight residual 1.545 1.534 0.012 1.05e-02 9.07e+03 1.26e+00 ... (remaining 10611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 14145 2.34 - 4.68: 317 4.68 - 7.02: 48 7.02 - 9.36: 6 9.36 - 11.70: 1 Bond angle restraints: 14517 Sorted by residual: angle pdb=" C THR B 223 " pdb=" N PHE B 224 " pdb=" CA PHE B 224 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 angle pdb=" N VAL A 675 " pdb=" CA VAL A 675 " pdb=" C VAL A 675 " ideal model delta sigma weight residual 112.80 107.70 5.10 1.15e+00 7.56e-01 1.97e+01 angle pdb=" N GLU A 679 " pdb=" CA GLU A 679 " pdb=" C GLU A 679 " ideal model delta sigma weight residual 110.06 115.77 -5.71 1.43e+00 4.89e-01 1.60e+01 angle pdb=" N GLU B 241 " pdb=" CA GLU B 241 " pdb=" CB GLU B 241 " ideal model delta sigma weight residual 110.28 115.98 -5.70 1.55e+00 4.16e-01 1.35e+01 angle pdb=" C LYS B 663 " pdb=" N PHE B 664 " pdb=" CA PHE B 664 " ideal model delta sigma weight residual 122.08 116.61 5.47 1.53e+00 4.27e-01 1.28e+01 ... (remaining 14512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 5570 15.83 - 31.66: 504 31.66 - 47.49: 114 47.49 - 63.32: 16 63.32 - 79.15: 4 Dihedral angle restraints: 6208 sinusoidal: 2115 harmonic: 4093 Sorted by residual: dihedral pdb=" CA ALA B 34 " pdb=" C ALA B 34 " pdb=" N PRO B 35 " pdb=" CA PRO B 35 " ideal model delta harmonic sigma weight residual 180.00 -129.23 -50.77 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA ALA A 34 " pdb=" C ALA A 34 " pdb=" N PRO A 35 " pdb=" CA PRO A 35 " ideal model delta harmonic sigma weight residual -180.00 -130.98 -49.02 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA GLY B 441 " pdb=" C GLY B 441 " pdb=" N ILE B 442 " pdb=" CA ILE B 442 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 6205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1579 0.076 - 0.153: 169 0.153 - 0.229: 2 0.229 - 0.306: 1 0.306 - 0.382: 1 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB ILE A 256 " pdb=" CA ILE A 256 " pdb=" CG1 ILE A 256 " pdb=" CG2 ILE A 256 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CG LEU A 564 " pdb=" CB LEU A 564 " pdb=" CD1 LEU A 564 " pdb=" CD2 LEU A 564 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TRP A 613 " pdb=" N TRP A 613 " pdb=" C TRP A 613 " pdb=" CB TRP A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1749 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 341 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO A 342 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 38 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO A 39 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 103 " -0.036 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 104 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.031 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 410 2.71 - 3.26: 11714 3.26 - 3.80: 16624 3.80 - 4.35: 19230 4.35 - 4.90: 31855 Nonbonded interactions: 79833 Sorted by model distance: nonbonded pdb=" OH TYR B 164 " pdb=" OG SER B 653 " model vdw 2.158 3.040 nonbonded pdb=" O ASN A 136 " pdb=" ND2 ASN A 141 " model vdw 2.159 3.120 nonbonded pdb=" O ASN A 114 " pdb=" OG1 THR A 119 " model vdw 2.187 3.040 nonbonded pdb=" ND2 ASN A 351 " pdb=" O LYS A 438 " model vdw 2.195 3.120 nonbonded pdb=" O LYS B 144 " pdb=" OG1 THR B 639 " model vdw 2.210 3.040 ... (remaining 79828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 473 or resid 486 through 702)) } 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 group one per residue 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: 0.760 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.200 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.042 10616 Z= 0.288 Angle : 0.839 11.703 14517 Z= 0.468 Chirality : 0.046 0.382 1752 Planarity : 0.006 0.070 1794 Dihedral : 12.990 79.155 3552 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.60 % Favored : 86.25 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.93 (0.24), residues: 1382 helix: 0.86 (0.19), residues: 799 sheet: -5.70 (0.64), residues: 10 loop : -2.81 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 336 HIS 0.004 0.001 HIS A 447 PHE 0.026 0.002 PHE A 664 TYR 0.017 0.002 TYR B 693 ARG 0.008 0.001 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8067 (ptt180) cc_final: 0.7759 (tmm-80) REVERT: A 248 LYS cc_start: 0.9653 (mmpt) cc_final: 0.9389 (mmmt) REVERT: A 513 PHE cc_start: 0.7369 (m-80) cc_final: 0.6780 (m-80) REVERT: B 237 ASN cc_start: 0.8800 (m110) cc_final: 0.8592 (m110) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2037 time to fit residues: 59.2264 Evaluate side-chains 159 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 125 optimal weight: 0.0010 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 GLN B 353 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.152505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110537 restraints weight = 20033.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.108585 restraints weight = 16696.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108894 restraints weight = 12864.075| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10616 Z= 0.258 Angle : 0.763 9.608 14517 Z= 0.387 Chirality : 0.045 0.343 1752 Planarity : 0.005 0.069 1794 Dihedral : 5.847 47.442 1475 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.30 % Favored : 87.55 % Rotamer: Outliers : 2.86 % Allowed : 10.74 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.89 (0.24), residues: 1382 helix: 0.86 (0.18), residues: 836 sheet: -5.24 (0.77), residues: 10 loop : -2.99 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 336 HIS 0.005 0.001 HIS A 447 PHE 0.025 0.002 PHE B 514 TYR 0.025 0.002 TYR A 171 ARG 0.003 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 1.083 Fit side-chains REVERT: A 56 ARG cc_start: 0.7592 (ptt180) cc_final: 0.7338 (tmm-80) REVERT: A 248 LYS cc_start: 0.9612 (mmpt) cc_final: 0.9394 (mmmt) REVERT: A 377 TYR cc_start: 0.6350 (p90) cc_final: 0.5093 (p90) REVERT: A 378 MET cc_start: 0.7620 (mmp) cc_final: 0.6845 (mmm) REVERT: B 437 SER cc_start: 0.9143 (t) cc_final: 0.8895 (t) REVERT: B 589 LEU cc_start: 0.8349 (mp) cc_final: 0.8100 (mp) outliers start: 29 outliers final: 17 residues processed: 183 average time/residue: 0.1947 time to fit residues: 52.3795 Evaluate side-chains 167 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 125 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 308 GLN B 628 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110396 restraints weight = 21101.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108669 restraints weight = 13267.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.109098 restraints weight = 11656.952| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10616 Z= 0.218 Angle : 0.728 10.612 14517 Z= 0.363 Chirality : 0.044 0.316 1752 Planarity : 0.005 0.067 1794 Dihedral : 5.636 48.364 1475 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 2.76 % Allowed : 15.47 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.59 (0.24), residues: 1382 helix: 1.05 (0.18), residues: 829 sheet: None (None), residues: 0 loop : -2.80 (0.26), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.005 0.001 HIS A 447 PHE 0.034 0.002 PHE B 514 TYR 0.027 0.001 TYR A 171 ARG 0.003 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.9665 (mmpt) cc_final: 0.9440 (mmmt) REVERT: A 306 LYS cc_start: 0.8600 (pttp) cc_final: 0.8274 (pttp) REVERT: A 504 PHE cc_start: 0.7767 (t80) cc_final: 0.7552 (t80) REVERT: B 231 THR cc_start: 0.8358 (p) cc_final: 0.7910 (p) REVERT: B 308 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: B 432 LEU cc_start: 0.9138 (tt) cc_final: 0.8919 (tp) REVERT: B 437 SER cc_start: 0.9101 (t) cc_final: 0.8828 (t) outliers start: 28 outliers final: 15 residues processed: 184 average time/residue: 0.1901 time to fit residues: 52.4962 Evaluate side-chains 173 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 4 optimal weight: 9.9990 chunk 115 optimal weight: 0.3980 chunk 131 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 124 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 110 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 127 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.155966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.114073 restraints weight = 19871.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.112711 restraints weight = 15947.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.113620 restraints weight = 12179.645| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10616 Z= 0.193 Angle : 0.709 10.059 14517 Z= 0.353 Chirality : 0.043 0.294 1752 Planarity : 0.005 0.066 1794 Dihedral : 5.495 48.417 1475 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.22 % Favored : 88.64 % Rotamer: Outliers : 3.84 % Allowed : 16.65 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.48 (0.24), residues: 1382 helix: 1.12 (0.19), residues: 831 sheet: -2.00 (2.91), residues: 5 loop : -2.72 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.005 0.001 HIS A 447 PHE 0.032 0.002 PHE B 513 TYR 0.049 0.001 TYR A 171 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 1.295 Fit side-chains REVERT: A 248 LYS cc_start: 0.9571 (mmpt) cc_final: 0.9362 (mmmt) REVERT: A 306 LYS cc_start: 0.8531 (pttp) cc_final: 0.8233 (pttp) REVERT: A 377 TYR cc_start: 0.6347 (p90) cc_final: 0.5142 (p90) REVERT: B 369 PHE cc_start: 0.8759 (t80) cc_final: 0.8484 (t80) REVERT: B 437 SER cc_start: 0.9074 (t) cc_final: 0.8745 (t) outliers start: 39 outliers final: 21 residues processed: 191 average time/residue: 0.1899 time to fit residues: 54.5905 Evaluate side-chains 177 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 624 LEU Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 104 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 67 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 GLN A 329 HIS A 353 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113373 restraints weight = 20240.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108158 restraints weight = 19365.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.109527 restraints weight = 18167.645| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 10616 Z= 0.304 Angle : 0.740 10.828 14517 Z= 0.370 Chirality : 0.044 0.278 1752 Planarity : 0.005 0.067 1794 Dihedral : 5.505 49.071 1475 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 12.23 % Favored : 87.63 % Rotamer: Outliers : 4.53 % Allowed : 18.33 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.58 (0.24), residues: 1382 helix: 1.05 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -2.85 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 336 HIS 0.003 0.001 HIS A 84 PHE 0.042 0.002 PHE B 505 TYR 0.044 0.002 TYR A 171 ARG 0.005 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 151 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8673 (pttp) cc_final: 0.8324 (pttp) REVERT: A 377 TYR cc_start: 0.5966 (p90) cc_final: 0.5564 (p90) REVERT: A 378 MET cc_start: 0.7773 (mmm) cc_final: 0.7259 (mmm) REVERT: B 86 VAL cc_start: 0.9188 (OUTLIER) cc_final: 0.8967 (p) REVERT: B 198 ASP cc_start: 0.7826 (m-30) cc_final: 0.7605 (m-30) REVERT: B 437 SER cc_start: 0.9101 (t) cc_final: 0.8743 (t) outliers start: 46 outliers final: 27 residues processed: 175 average time/residue: 0.1953 time to fit residues: 51.1675 Evaluate side-chains 170 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 132 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 88 optimal weight: 0.0670 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 25 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.155546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114501 restraints weight = 20234.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.112520 restraints weight = 17469.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113203 restraints weight = 13934.446| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10616 Z= 0.195 Angle : 0.703 10.150 14517 Z= 0.348 Chirality : 0.043 0.259 1752 Planarity : 0.005 0.066 1794 Dihedral : 5.378 48.700 1475 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.85 % Favored : 89.00 % Rotamer: Outliers : 4.04 % Allowed : 19.61 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: 1382 helix: 1.20 (0.19), residues: 832 sheet: -2.64 (1.22), residues: 15 loop : -2.73 (0.27), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 613 HIS 0.005 0.001 HIS A 447 PHE 0.026 0.002 PHE A 513 TYR 0.036 0.001 TYR A 171 ARG 0.007 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 160 time to evaluate : 1.096 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8664 (pttp) cc_final: 0.8290 (pttp) REVERT: A 377 TYR cc_start: 0.5952 (p90) cc_final: 0.5722 (p90) REVERT: A 378 MET cc_start: 0.7895 (mmm) cc_final: 0.7307 (mmm) REVERT: B 437 SER cc_start: 0.9008 (t) cc_final: 0.8683 (t) outliers start: 41 outliers final: 26 residues processed: 184 average time/residue: 0.1830 time to fit residues: 51.6685 Evaluate side-chains 175 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 110 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 132 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 115 optimal weight: 40.0000 chunk 102 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.156946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118149 restraints weight = 20011.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.115699 restraints weight = 17341.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.116427 restraints weight = 14434.390| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10616 Z= 0.198 Angle : 0.695 10.441 14517 Z= 0.344 Chirality : 0.043 0.311 1752 Planarity : 0.005 0.064 1794 Dihedral : 5.291 48.035 1475 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.71 % Favored : 89.15 % Rotamer: Outliers : 3.84 % Allowed : 20.20 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.23 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1382 helix: 1.36 (0.19), residues: 818 sheet: -1.54 (2.92), residues: 5 loop : -2.71 (0.26), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.004 0.001 HIS A 447 PHE 0.026 0.001 PHE A 513 TYR 0.035 0.001 TYR A 171 ARG 0.009 0.001 ARG B 619 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.7074 (m100) cc_final: 0.6832 (m100) REVERT: A 306 LYS cc_start: 0.8569 (pttp) cc_final: 0.8223 (pttp) REVERT: A 351 ASN cc_start: 0.8581 (t0) cc_final: 0.8355 (t0) REVERT: A 378 MET cc_start: 0.7878 (mmm) cc_final: 0.7429 (mmm) REVERT: B 437 SER cc_start: 0.9045 (t) cc_final: 0.8704 (t) outliers start: 39 outliers final: 28 residues processed: 180 average time/residue: 0.1865 time to fit residues: 51.6510 Evaluate side-chains 172 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 99 optimal weight: 0.9990 chunk 5 optimal weight: 0.0050 chunk 108 optimal weight: 5.9990 chunk 90 optimal weight: 0.6980 chunk 40 optimal weight: 8.9990 chunk 38 optimal weight: 0.0470 chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 overall best weight: 0.4692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.157686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.116539 restraints weight = 19849.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.115431 restraints weight = 15802.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116105 restraints weight = 12746.284| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10616 Z= 0.192 Angle : 0.706 15.662 14517 Z= 0.345 Chirality : 0.042 0.231 1752 Planarity : 0.005 0.064 1794 Dihedral : 5.201 47.836 1475 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.49 % Favored : 89.36 % Rotamer: Outliers : 3.55 % Allowed : 21.38 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % 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: -0.25 (0.24), residues: 1382 helix: 1.35 (0.19), residues: 823 sheet: -1.67 (2.73), residues: 5 loop : -2.65 (0.26), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 61 HIS 0.004 0.001 HIS A 447 PHE 0.029 0.001 PHE A 504 TYR 0.040 0.001 TYR A 586 ARG 0.006 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 49 TRP cc_start: 0.7135 (m100) cc_final: 0.6916 (m100) REVERT: A 306 LYS cc_start: 0.8543 (pttp) cc_final: 0.8221 (pttp) REVERT: A 351 ASN cc_start: 0.8592 (t0) cc_final: 0.8381 (t0) REVERT: A 563 MET cc_start: 0.8183 (mtp) cc_final: 0.7977 (mtp) REVERT: B 347 LEU cc_start: 0.8779 (tt) cc_final: 0.8219 (tp) REVERT: B 437 SER cc_start: 0.9042 (t) cc_final: 0.8676 (t) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 0.1732 time to fit residues: 47.3993 Evaluate side-chains 177 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 677 CYS Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 62 optimal weight: 0.0050 chunk 117 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.157290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.116192 restraints weight = 20084.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115075 restraints weight = 13769.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116036 restraints weight = 10792.670| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10616 Z= 0.205 Angle : 0.718 12.310 14517 Z= 0.353 Chirality : 0.043 0.234 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.192 47.664 1475 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.42 % Favored : 89.44 % Rotamer: Outliers : 2.96 % Allowed : 22.36 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % 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: -0.19 (0.24), residues: 1382 helix: 1.39 (0.19), residues: 822 sheet: -1.52 (2.77), residues: 5 loop : -2.62 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 61 HIS 0.004 0.001 HIS A 447 PHE 0.035 0.002 PHE A 416 TYR 0.032 0.001 TYR A 586 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 1.125 Fit side-chains revert: symmetry clash REVERT: A 306 LYS cc_start: 0.8561 (pttp) cc_final: 0.8202 (pttp) REVERT: A 351 ASN cc_start: 0.8617 (t0) cc_final: 0.8377 (t0) REVERT: A 513 PHE cc_start: 0.7093 (m-80) cc_final: 0.6437 (m-80) REVERT: A 517 TYR cc_start: 0.8641 (m-10) cc_final: 0.8281 (m-80) REVERT: B 224 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: B 300 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8220 (tppt) REVERT: B 437 SER cc_start: 0.9058 (t) cc_final: 0.8702 (t) outliers start: 30 outliers final: 26 residues processed: 168 average time/residue: 0.1881 time to fit residues: 48.0757 Evaluate side-chains 175 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 114 optimal weight: 2.9990 chunk 135 optimal weight: 0.3980 chunk 17 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.3980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.158661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.117916 restraints weight = 20076.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116107 restraints weight = 17199.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.117327 restraints weight = 13205.997| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10616 Z= 0.191 Angle : 0.730 19.453 14517 Z= 0.352 Chirality : 0.042 0.225 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.144 47.480 1475 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.20 % Favored : 89.65 % Rotamer: Outliers : 3.05 % Allowed : 22.46 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % 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: -0.13 (0.24), residues: 1382 helix: 1.36 (0.19), residues: 827 sheet: -1.48 (2.67), residues: 5 loop : -2.47 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 61 HIS 0.004 0.001 HIS A 447 PHE 0.030 0.001 PHE A 416 TYR 0.030 0.001 TYR A 171 ARG 0.005 0.000 ARG B 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 171 TYR cc_start: 0.8844 (OUTLIER) cc_final: 0.8492 (t80) REVERT: A 351 ASN cc_start: 0.8524 (t0) cc_final: 0.8305 (t0) REVERT: A 513 PHE cc_start: 0.7028 (m-80) cc_final: 0.6406 (m-80) REVERT: A 517 TYR cc_start: 0.8542 (m-10) cc_final: 0.8162 (m-80) REVERT: B 224 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7300 (m-80) REVERT: B 300 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8324 (ptpp) REVERT: B 437 SER cc_start: 0.9045 (t) cc_final: 0.8697 (t) REVERT: B 514 PHE cc_start: 0.7299 (m-10) cc_final: 0.7003 (m-80) REVERT: B 563 MET cc_start: 0.8485 (tpp) cc_final: 0.7826 (ttt) outliers start: 31 outliers final: 24 residues processed: 173 average time/residue: 0.1821 time to fit residues: 47.6922 Evaluate side-chains 177 residues out of total 1207 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 631 MET Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 35 optimal weight: 0.4980 chunk 38 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 100 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 ASN ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.156571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116757 restraints weight = 19812.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115892 restraints weight = 14900.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115959 restraints weight = 12728.818| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10616 Z= 0.235 Angle : 0.746 17.247 14517 Z= 0.362 Chirality : 0.043 0.224 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.154 47.464 1475 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.64 % Favored : 89.22 % Rotamer: Outliers : 3.25 % Allowed : 22.27 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % 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: -0.12 (0.24), residues: 1382 helix: 1.35 (0.19), residues: 828 sheet: -1.33 (2.77), residues: 5 loop : -2.46 (0.27), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.003 0.001 HIS A 447 PHE 0.028 0.001 PHE A 416 TYR 0.032 0.001 TYR A 171 ARG 0.005 0.000 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2907.17 seconds wall clock time: 53 minutes 53.61 seconds (3233.61 seconds total)